Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002499.1 Hibiscus syriacus cultivar Beakdansim tig00005094_pilon, 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: 78292
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1736 original size:40 final size:39
Alignment explanation
Indices: 1688--1768 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 39
1678 TTTAAAGAAA
* * * *
1688 TTTTAGTTTTTGTTTTATTTTAGTATCATATCGTT-AAAAT
1 TTTTAGTTTTTATTTCACTTTAATAT--TATCGTTCAAAAT
1728 TTTTAGTTTTTATTTCACTTTAATATTATCGTTCAAAAT
1 TTTTAGTTTTTATTTCACTTTAATATTATCGTTCAAAAT
1767 TT
1 TT
1769 AACATTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 7 0.19
39 7 0.19
40 22 0.61
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (39 bp):
TTTTAGTTTTTATTTCACTTTAATATTATCGTTCAAAAT
Found at i:7956 original size:14 final size:14
Alignment explanation
Indices: 7938--8128 Score: 72
Period size: 14 Copynumber: 13.3 Consensus size: 14
7928 TAAACCCAAC
7938 AAAATAAAAAAAAT
1 AAAATAAAAAAAAT
* * *
7952 GAAATAAAGAAGAT
1 AAAATAAAAAAAAT
*
7966 AAAATAAAATGAGTAAAGA
1 AAAATAAAA--A--AAA-T
* *
7985 AAAATAAAGAAAAG
1 AAAATAAAAAAAAT
*
7999 AATAAT-AATAAAAT
1 AA-AATAAAAAAAAT
*
8013 AAAGATAACAAGTAAAT
1 AAA-ATAA-AA-AAAAT
8030 AAAAT-AAAAAAAT
1 AAAATAAAAAAAAT
* * **
8043 GATAATAAAGAAACG
1 -AAAATAAAAAAAAT
8058 AAAAT--AAAAAAT
1 AAAATAAAAAAAAT
** *
8070 -AAGGAAAATAAAT
1 AAAATAAAAAAAAT
* *
8083 -AAAT-AAATAAAC
1 AAAATAAAAAAAAT
8095 AAAATGAAAAAAAAT
1 AAAAT-AAAAAAAAT
8110 AAAATGAAAAAAAAT
1 AAAAT-AAAAAAAAT
8125 AAAA
1 AAAA
8129 AATAAAGACA
Statistics
Matches: 130, Mismatches: 30, Indels: 33
0.67 0.16 0.17
Matches are distributed among these distances:
11 2 0.02
12 11 0.08
13 17 0.13
14 40 0.31
15 38 0.29
16 4 0.03
17 8 0.06
18 2 0.02
19 8 0.06
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:7997 original size:23 final size:22
Alignment explanation
Indices: 7938--8127 Score: 68
Period size: 23 Copynumber: 8.4 Consensus size: 22
7928 TAAACCCAAC
* *
7938 AAAATAAAAAAAATGAAATAAAG
1 AAAATAAAGAAAATG-AATAAAA
* * *
7961 AAGATAAAATAAAATGAGTAAAGA
1 AAAAT-AAAGAAAATGAATAAA-A
7985 AAAATAAAGAAAA-GAATAATAA
1 AAAATAAAGAAAATGAATAA-AA
* * *
8007 TAAAATAAAGATAA-CAAGTAAAT
1 -AAAATAAAGAAAATGAA-TAAAA
*
8030 AAAATAAA-AAAATG-ATAATA
1 AAAATAAAGAAAATGAATAAAA
* * * *
8050 AAGA-AACGAAAATAAAAAATAA
1 AAAATAAAGAAAATGAATAA-AA
* * *
8072 GGAAAATAAA-TAAATAAATAAAC
1 --AAAATAAAGAAAATGAATAAAA
* *
8095 AAAATGAAAAAAAATAAAATGAAAA
1 AAAAT-AAAGAAAAT-GAAT-AAAA
8120 AAAATAAA
1 AAAATAAA
8128 AAATAAAGAC
Statistics
Matches: 125, Mismatches: 26, Indels: 31
0.69 0.14 0.17
Matches are distributed among these distances:
19 2 0.02
20 11 0.09
21 12 0.10
22 18 0.14
23 37 0.30
24 35 0.28
25 10 0.08
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (22 bp):
AAAATAAAGAAAATGAATAAAA
Found at i:8070 original size:21 final size:20
Alignment explanation
Indices: 8046--8153 Score: 73
Period size: 20 Copynumber: 5.3 Consensus size: 20
8036 AAAAAATGAT
8046 AATAAAGAAACGAAAATAAAA
1 AATAAAGAAA-GAAAATAAAA
*
8067 AATAAGGAAA-ATAAATAAATA
1 AATAAAGAAAGA-AAATAAA-A
*
8088 AATAAACAAAATGAAAA-AAAA
1 AATAAA-GAAA-GAAAATAAAA
* *
8109 TAA-AATGAAAAAAAATAAAA
1 -AATAAAGAAAGAAAATAAAA
*
8129 AATAAAGACAAG-GAA-AAAA
1 AATAAAGA-AAGAAAATAAAA
8148 AATAAA
1 AATAAA
8154 ATATAGGAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 20
0.70 0.09 0.20
Matches are distributed among these distances:
19 17 0.25
20 20 0.29
21 20 0.29
22 8 0.12
23 3 0.04
24 1 0.01
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.12
Consensus pattern (20 bp):
AATAAAGAAAGAAAATAAAA
Found at i:8078 original size:16 final size:17
Alignment explanation
Indices: 8057--8088 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
8047 ATAAAGAAAC
8057 GAAAATAAA-AAATAAG
1 GAAAATAAATAAATAAG
8073 GAAAATAAATAAATAA
1 GAAAATAAATAAATAA
8089 ATAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (17 bp):
GAAAATAAATAAATAAG
Found at i:8099 original size:57 final size:59
Alignment explanation
Indices: 7987--8128 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 59
7977 AGTAAAGAAA
* *
7987 AATAAAGAAAAGAATAATAATAAAATAAAGATAACAAGTAAATAAAATAAAAAAATGAT
1 AATAAAGAAAAGAATAATAATAAAATAAAGAAAACAAATAAATAAAATAAAAAAATGAT
* * * *
8046 AATAAAGAAACGAA-AATAA-AAAATAAGGAAAATAAATAAAT-AAATAAACAAAATGAA
1 AATAAAGAAAAGAATAATAATAAAATAAAGAAAACAAATAAATAAAATAAA-AAAATGAT
* * * *
8103 AAAAAATAAAATGAAAAAAAATAAAA
1 AATAAAGAAAA-GAATAATAATAAAA
8129 AATAAAGACA
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
56 7 0.10
57 33 0.48
58 8 0.12
59 17 0.25
60 4 0.06
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (59 bp):
AATAAAGAAAAGAATAATAATAAAATAAAGAAAACAAATAAATAAAATAAAAAAATGAT
Found at i:8115 original size:15 final size:15
Alignment explanation
Indices: 8095--8128 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
8085 ATAAATAAAC
8095 AAAATGAAAAAAAAT
1 AAAATGAAAAAAAAT
8110 AAAATGAAAAAAAAT
1 AAAATGAAAAAAAAT
8125 AAAA
1 AAAA
8129 AATAAAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAATGAAAAAAAAT
Found at i:8123 original size:10 final size:9
Alignment explanation
Indices: 7938--8154 Score: 51
Period size: 9 Copynumber: 23.0 Consensus size: 9
7928 TAAACCCAAC
7938 AAAATAAAA
1 AAAATAAAA
*
7947 AAAATGAAA
1 AAAATAAAA
* * *
7956 TAAAGAAGAT
1 AAAATAA-AA
7966 AAAATAAAA
1 AAAATAAAA
** *
7975 TGAGTAAAGA
1 AAAATAAA-A
*
7985 AAAATAAAG
1 AAAATAAAA
* *
7994 AAAAGAATA
1 AAAATAAAA
*
8003 ATAATAAAA
1 AAAATAAAA
* * *
8012 TAAAGATAA
1 AAAATAAAA
* * *
8021 CAAGTAAAT
1 AAAATAAAA
8030 AAAATAAAA
1 AAAATAAAA
*
8039 AAATGATAATA
1 AAA--ATAAAA
* **
8050 AAGA-AACG
1 AAAATAAAA
8058 AAAATAAAA
1 AAAATAAAA
*
8067 AATAAGGAAAA
1 AA-AA-TAAAA
*
8078 TAAAT-AAA
1 AAAATAAAA
* *
8086 TAAATAAAC
1 AAAATAAAA
8095 AAAATGAAAA
1 AAAAT-AAAA
8105 AAAATAAAATGA
1 AAAAT-AAA--A
*
8117 AAAAAAATAA
1 AAAATAA-AA
8127 AAAATAAAGA
1 AAAATAAA-A
* **
8137 CAAGGAAAA
1 AAAATAAAA
8146 AAAATAAAA
1 AAAATAAAA
8155 TATAGGAAAA
Statistics
Matches: 140, Mismatches: 55, Indels: 26
0.63 0.25 0.12
Matches are distributed among these distances:
8 13 0.09
9 67 0.48
10 40 0.29
11 14 0.10
12 6 0.04
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (9 bp):
AAAATAAAA
Found at i:8167 original size:41 final size:42
Alignment explanation
Indices: 8073--8155 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 42
8063 AAAAAATAAG
* *
8073 GAAAATAAATAAATAAATAAACAAAATGAAAAAAAATAAAAT
1 GAAAAAAAATAAATAAATAAACAAAAGGAAAAAAAATAAAAT
* *
8115 GAAAAAAAATAAA-AAATAAAGACAAGGAAAAAAAATAAAAT
1 GAAAAAAAATAAATAAATAAACAAAAGGAAAAAAAATAAAAT
8156 ATAGGAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 25 0.68
42 12 0.32
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.13
Consensus pattern (42 bp):
GAAAAAAAATAAATAAATAAACAAAAGGAAAAAAAATAAAAT
Found at i:8256 original size:2 final size:2
Alignment explanation
Indices: 8249--8321 Score: 98
Period size: 2 Copynumber: 37.5 Consensus size: 2
8239 AATAAAAATA
* *
8249 AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT A- AT GAT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
8289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8322 ATAGAATAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
1 3 0.05
2 60 0.92
3 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (2 bp):
AT
Found at i:8369 original size:16 final size:17
Alignment explanation
Indices: 8350--8391 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
8340 AAGTAATAAT
8350 AATAATAAATGAAAA-A
1 AATAATAAATGAAAATA
8366 AATAATAAA-GAAAATA
1 AATAATAAATGAAAATA
8382 AATAATAAAT
1 AATAATAAAT
8392 ATATATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AATAATAAATGAAAATA
Found at i:12108 original size:31 final size:32
Alignment explanation
Indices: 12069--12159 Score: 114
Period size: 31 Copynumber: 2.9 Consensus size: 32
12059 AGAGTCGAGG
* *
12069 GTTACCTATGTCTTTCGAGATATATGGACAGT
1 GTTACCTATGTCCTTCGAGACATATGGACAGT
* *
12101 -TTACCTATGCCCTTCGGGACATATGGACAGT
1 GTTACCTATGTCCTTCGAGACATATGGACAGT
*
12132 GTTACCTATGTTCTTCG-GAACATATGGA
1 GTTACCTATGTCCTTCGAG-ACATATGGA
12160 TAGGTTCTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
31 28 0.55
32 23 0.45
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (32 bp):
GTTACCTATGTCCTTCGAGACATATGGACAGT
Found at i:12921 original size:58 final size:59
Alignment explanation
Indices: 12830--12980 Score: 193
Period size: 58 Copynumber: 2.6 Consensus size: 59
12820 CCTCAAATTG
*
12830 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTTTTTGCTTCACCAAATTGG-TT-GTT-
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATC-TTTTGCTTCAACAAATTGGATTAGTTA
* * *
12887 GAATATCCTTCGTCCTGAAGTTGAAATCCAATC-TTTGTTTCAACAATTTGGTATTGAGTTA
1 G-ATATCCTTCGTCGTGAAGTTGAAATCCAATCTTTTGCTTCAACAAATTGG-ATT-AGTTA
*
12948 GATATCCTTCGTTGTGAAGTTGAAATCCAATCT
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATCT
12981 CGAGTAAGTC
Statistics
Matches: 81, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
56 15 0.19
57 1 0.01
58 32 0.40
60 32 0.40
61 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (59 bp):
GATATCCTTCGTCGTGAAGTTGAAATCCAATCTTTTGCTTCAACAAATTGGATTAGTTA
Found at i:12971 original size:60 final size:55
Alignment explanation
Indices: 12830--12980 Score: 185
Period size: 60 Copynumber: 2.6 Consensus size: 55
12820 CCTCAAATTG
*
12830 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTTTTTGCTTCACCAAATTGGTTGTT
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATC--TTTGCTTCAACAAATTGGTTGTT
* * *
12887 GAATATCCTTCGTCCTGAAGTTGAAATCCAATCTTTGTTTCAACAATTTGGTATTGAGTT
1 G-ATATCCTTCGTCGTGAAGTTGAAATCCAATCTTTGCTTCAACAAATTGG--TT--GTT
*
12947 AGATATCCTTCGTTGTGAAGTTGAAATCCAATCT
1 -GATATCCTTCGTCGTGAAGTTGAAATCCAATCT
12981 CGAGTAAGTC
Statistics
Matches: 82, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
56 15 0.18
57 1 0.01
58 32 0.39
60 33 0.40
61 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (55 bp):
GATATCCTTCGTCGTGAAGTTGAAATCCAATCTTTGCTTCAACAAATTGGTTGTT
Found at i:13808 original size:7 final size:7
Alignment explanation
Indices: 13792--13839 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
13782 ACCCACCTTA
13792 TTTT-TT
1 TTTTCTT
13798 TTTTCTT
1 TTTTCTT
13805 TTTTCTT
1 TTTTCTT
*
13812 TTCTCTT
1 TTTTCTT
*
13819 TTGTTATT
1 TT-TTCTT
13827 TTTCTCTT
1 TTT-TCTT
13835 TTTTC
1 TTTTC
13840 AATTCAGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 4 0.11
7 20 0.57
8 11 0.31
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:13903 original size:16 final size:16
Alignment explanation
Indices: 13882--13914 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13872 AAATTTTTTC
13882 TCTTTTTTTGTTCTTT
1 TCTTTTTTTGTTCTTT
*
13898 TCTTTTTTTTTTCTTT
1 TCTTTTTTTGTTCTTT
13914 T
1 T
13915 TCTTCTCCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (16 bp):
TCTTTTTTTGTTCTTT
Found at i:20049 original size:11 final size:10
Alignment explanation
Indices: 20035--20075 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
20025 TTGCAATTCA
20035 TTTATCTTTT
1 TTTATCTTTT
20045 CTTTATCTTTT
1 -TTTATCTTTT
20056 TTTAATCTTATT
1 TTT-ATCTT-TT
20068 TTTATCTT
1 TTTATCTT
20076 GTTTCCAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.11
11 20 0.71
12 5 0.18
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATCTTTT
Found at i:24600 original size:11 final size:11
Alignment explanation
Indices: 24586--24630 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
24576 TTGCAATTCA
24586 TTTATCTT-TT
1 TTTATCTTATT
*
24596 CTTTATCTTGTT
1 -TTTATCTTATT
*
24608 TTAATCTTATT
1 TTTATCTTATT
24619 TTTATCTTATT
1 TTTATCTTATT
24630 T
1 T
24631 CCAGCACCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:26330 original size:13 final size:13
Alignment explanation
Indices: 26312--26359 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
26302 CGATAATAAA
*
26312 GAAATAAAAATAT
1 GAAATAAAAAAAT
26325 GAAATAAGAAAAAT
1 GAAATAA-AAAAAT
26339 -AAATAAATAAAAT
1 GAAATAAA-AAAAT
26352 GAAA-AAAA
1 GAAATAAAA
26360 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 2 0.06
13 21 0.68
14 8 0.26
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (13 bp):
GAAATAAAAAAAT
Found at i:26351 original size:22 final size:22
Alignment explanation
Indices: 26313--26365 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
26303 GATAATAAAG
*
26313 AAATAAAAATATGAAAT-AAGAA
1 AAATAAAAATATAAAATGAA-AA
26335 AAATAAATAA-ATAAAATGAAAA
1 AAATAAA-AATATAAAATGAAAA
*
26357 AAAGAAAAA
1 AAATAAAAA
26366 AAAATAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.07
22 21 0.78
23 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (22 bp):
AAATAAAAATATAAAATGAAAA
Found at i:26383 original size:28 final size:28
Alignment explanation
Indices: 26330--26386 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
26320 AATATGAAAT
* * *
26330 AAGAAAAATAAATAAATAAAATGAAAAA
1 AAGAAAAAAAAATAAAGAAAAGGAAAAA
*
26358 AAGAAAAAAAAATAAAGACAAGGAAAAA
1 AAGAAAAAAAAATAAAGAAAAGGAAAAA
26386 A
1 A
26387 TAAAATATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.79, C:0.02, G:0.11, T:0.09
Consensus pattern (28 bp):
AAGAAAAAAAAATAAAGAAAAGGAAAAA
Found at i:26484 original size:2 final size:2
Alignment explanation
Indices: 26477--26583 Score: 130
Period size: 2 Copynumber: 54.5 Consensus size: 2
26467 AAATAAAATA
* * * * * *
26477 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AC AC AC A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26518 A- AT GAT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26559 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
26584 ATAGAATAAA
Statistics
Matches: 99, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
1 3 0.03
2 94 0.95
3 2 0.02
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:29230 original size:23 final size:23
Alignment explanation
Indices: 29202--29259 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
29192 AAATTAATAA
29202 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
29225 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
29248 TATA--ATGTAAAA
1 TATATTATGTAAAA
29260 ATTATAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (23 bp):
TATATTATGTAAAATGTTTCGAT
Found at i:32628 original size:126 final size:126
Alignment explanation
Indices: 32405--33007 Score: 1147
Period size: 126 Copynumber: 4.8 Consensus size: 126
32395 CTATAATCGG
32405 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGG-GCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
32468 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
32529 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
32594 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
32655 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
32720 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
32781 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
32846 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGTCACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
*
32907 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
32972 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
33008 ATAACTTAAA
Statistics
Matches: 471, Mismatches: 6, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
124 28 0.06
125 4 0.01
126 439 0.93
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
Found at i:33429 original size:33 final size:32
Alignment explanation
Indices: 33392--33489 Score: 108
Period size: 33 Copynumber: 3.0 Consensus size: 32
33382 AAATTTAATG
33392 TTAAATTTCGAATACTATAATTATATTTTAAAT
1 TTAAATTTCGAATA-TATAATTATATTTTAAAT
* * * *
33425 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAAT-ATA-TAATTATATTTTAAAT
*
33458 TTAAATTTCGAATATATAATTTGTATTTTAAA
1 TTAAATTTCGAATATATAA-TTATATTTTAAA
33490 AACATTTATC
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
32 8 0.15
33 41 0.77
34 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (32 bp):
TTAAATTTCGAATATATAATTATATTTTAAAT
Found at i:34100 original size:21 final size:21
Alignment explanation
Indices: 34015--34094 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
34005 ATAAAACCCT
*
34015 GGGCTAGGCATGTAACCTGGC
1 GGGCTAGGAATGTAACCTGGC
*
34036 GGGCTAGGCATGTAACCTGGC
1 GGGCTAGGAATGTAACCTGGC
34057 GGGCTAGGAATGTAACCCT-GC
1 GGGCTAGGAATGTAA-CCTGGC
*
34078 GGGCTCGGAATGTAACC
1 GGGCTAGGAATGTAACC
34095 CTGCGGAGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.04
21 51 0.91
22 3 0.05
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.19
Consensus pattern (21 bp):
GGGCTAGGAATGTAACCTGGC
Found at i:34130 original size:21 final size:21
Alignment explanation
Indices: 34104--34151 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
34094 CCTGCGGAGA
*
34104 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
34125 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
34146 GGGCAT
1 TGGCAT
34152 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:35910 original size:33 final size:31
Alignment explanation
Indices: 35873--35954 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
35863 AATTCTAAAT
35873 AAATAATAATTATATAAATATTATTTAATA-ATA
1 AAATAATAATTATATAAATA-TA-TTAATATA-A
* *
35906 AAATAATATTTACATAAATATATTAATATAA
1 AAATAATAATTATATAAATATATTAATATAA
* *
35937 AAATAATAACTATTTAAA
1 AAATAATAATTATATAAA
35955 AAAATACTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
31 21 0.50
32 3 0.07
33 18 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
AAATAATAATTATATAAATATATTAATATAA
Found at i:35975 original size:33 final size:34
Alignment explanation
Indices: 35907--35975 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
35897 TTAATAATAA
* * *
35907 AATAATATTTACATAAATATATTAATATAAAAAT
1 AATAATATTTACATAAAAATACTAACATAAAAAT
35941 AATAACTATTTA-A-AAAAATACTAACATAAAAAT
1 AATAA-TATTTACATAAAAATACTAACATAAAAAT
35974 AA
1 AA
35976 ATTTCTTACC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 19 0.61
34 6 0.19
35 6 0.19
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (34 bp):
AATAATATTTACATAAAAATACTAACATAAAAAT
Found at i:37713 original size:2 final size:2
Alignment explanation
Indices: 37701--37738 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
37691 AGTCATATTA
* *
37701 AT AT AT GT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37739 TATTTAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:37716 original size:10 final size:9
Alignment explanation
Indices: 37695--37738 Score: 51
Period size: 8 Copynumber: 5.2 Consensus size: 9
37685 TATTTTAGTC
37695 ATATTA-AT
1 ATATTATAT
37703 ATATGTATAT
1 ATAT-TATAT
37713 ATA-TATAT
1 ATATTATAT
37721 ATATT-TAT
1 ATATTATAT
37729 ATA-TATAT
1 ATATTATAT
37737 AT
1 AT
37739 TATTTAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 1 0.03
8 23 0.72
9 3 0.09
10 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (9 bp):
ATATTATAT
Found at i:38547 original size:25 final size:24
Alignment explanation
Indices: 38518--38574 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
38508 ATATATTTAA
* *
38518 TTTATAATTCTTTCTTTTCAAAATT
1 TTTATAATAC-TTATTTTCAAAATT
*
38543 TTTATATATACTTATTTTCATAATT
1 TTTATA-ATACTTATTTTCAAAATT
38568 TTT-TAAT
1 TTTATAAT
38575 GTTTTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 2 0.07
24 2 0.07
25 21 0.75
26 3 0.11
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTATAATACTTATTTTCAAAATT
Found at i:39690 original size:30 final size:30
Alignment explanation
Indices: 39424--39673 Score: 446
Period size: 30 Copynumber: 8.3 Consensus size: 30
39414 GAAGGACCTA
*
39424 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
39454 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
39484 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
* *
39514 TCCAGAGATCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
39544 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
39574 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
39604 TCCATAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
39634 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
39664 TCCATAGGTC
1 TCCAGAGGTC
39674 CCGAAGAACC
Statistics
Matches: 210, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 210 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:40580 original size:21 final size:21
Alignment explanation
Indices: 40550--40594 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40540 ATTCTGTCGT
* *
40550 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
40571 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
40592 TTG
1 TTG
40595 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:43883 original size:89 final size:90
Alignment explanation
Indices: 43722--43943 Score: 383
Period size: 89 Copynumber: 2.5 Consensus size: 90
43712 CCCGAAGGAC
* *
43722 CTATCCAGAGGTCACAAAGATCCTTGGTAACTGTCCAGAGGTCACAAAGATCCTCGGTAACTGTC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCACAAAGATCCTCGGTAACTGTC
43787 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
*
43812 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCC-GAGGTCATAAAGATCCTCGGTAACTGTC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCACAAAGATCCTCGGTAACTGTC
*
43876 CATAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* *
43901 CTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTC
43944 CCGAAGAACC
Statistics
Matches: 125, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
89 86 0.69
90 39 0.31
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (90 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCACAAAGATCCTCGGTAACTGTC
CAGAGGTCATAAAGATCCTCGGTAA
Found at i:43943 original size:119 final size:119
Alignment explanation
Indices: 43729--43943 Score: 376
Period size: 119 Copynumber: 1.8 Consensus size: 119
43719 GACCTATCCA
*
43729 GAGGTCACAAAGATCCTTGGTAACTGTCCAGAGGTCACAAAGATCCTCGGTAACTGTCCAGAGGT
1 GAGGTCACAAAGATCCTCGGTAACTGTCCAGAGGTCACAAAGATCCTCGGTAACTGTCCAGAGGT
43794 CATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCC
66 CATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCC
* * *
43848 GAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGT
1 GAGGTCACAAAGATCCTCGGTAACTGTCCAGAGGTCACAAAGATCCTCGGTAACTGTCCAGAGGT
* *
43913 CATAAAGATCCTCGGTAACTGTCCATAGGTC
66 CATAAAGATCCTCGGTAACTATCCAGAGGTC
43944 CCGAAGAACC
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 90 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (119 bp):
GAGGTCACAAAGATCCTCGGTAACTGTCCAGAGGTCACAAAGATCCTCGGTAACTGTCCAGAGGT
CATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCC
Found at i:43960 original size:30 final size:30
Alignment explanation
Indices: 43725--43943 Score: 377
Period size: 30 Copynumber: 7.3 Consensus size: 30
43715 GAAGGACCTA
* *
43725 TCCAGAGGTCACAAAGATCCTTGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
43755 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
43785 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
43815 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
43845 TCC-GAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
43874 TCCATAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
43904 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
43934 TCCATAGGTC
1 TCCAGAGGTC
43944 CCGAAGAACC
Statistics
Matches: 181, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
29 29 0.16
30 152 0.84
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:44846 original size:21 final size:21
Alignment explanation
Indices: 44816--44860 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
44806 ATTCTGTCGT
* *
44816 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
44837 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
44858 TTG
1 TTG
44861 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:49460 original size:15 final size:15
Alignment explanation
Indices: 49433--49478 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
49423 CTCATTCATC
49433 AGAAAAGAAAAGAAAA
1 AGAAAA-AAAAGAAAA
*
49449 AGAAAAAAAAGAATA
1 AGAAAAAAAAGAAAA
*
49464 AG-GAAAAAAGAAAA
1 AGAAAAAAAAGAAAA
49478 A
1 A
49479 ATTGAATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 11 0.41
15 10 0.37
16 6 0.22
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (15 bp):
AGAAAAAAAAGAAAA
Found at i:51895 original size:41 final size:40
Alignment explanation
Indices: 51838--51929 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
51828 CATATGGGGT
** *
51838 ATTTTGAAAGCTCACATCAGTATGAAAAAAAATGTTGAGGC
1 ATTTTGAAAGCTCACATCAACAAG-AAAAAAATGTTGAGGC
**
51879 ATTTTGAAAGCTCACATCAACAAGAAGCAAATGTTGAGGC
1 ATTTTGAAAGCTCACATCAACAAGAAAAAAATGTTGAGGC
*
51919 ATGTTGAAAGC
1 ATTTTGAAAGC
51930 CCATTTCAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 24 0.53
41 21 0.47
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (40 bp):
ATTTTGAAAGCTCACATCAACAAGAAAAAAATGTTGAGGC
Found at i:52029 original size:74 final size:75
Alignment explanation
Indices: 51907--52075 Score: 189
Period size: 74 Copynumber: 2.3 Consensus size: 75
51897 AACAAGAAGC
* * *
51907 AAATGTTGAGGCATGTTGAAAGCCCATTTCAATCAGAAATTGAAATATTAACGCATTTTGAACGT
1 AAATGTTGAGGCATGCTGAAAGCCCATTTCAATCAGAAATAGAAATATTAACGCATTTTAAACGT
51972 TTATATCAGA
66 TTATATCAGA
* * * * * * * *
51982 AAATGCTGAGGCATACTGAAAG-TCATTTCAATCAG-AATCAGGAATATTGATGTATTTTAAATG
1 AAATGTTGAGGCATGCTGAAAGCCCATTTCAATCAGAAAT-AGAAATATTAACGCATTTTAAACG
* *
52045 TTTGTATCAGT
65 TTTATATCAGA
*
52056 AAATGTTGGGGCATGCTGAA
1 AAATGTTGAGGCATGCTGAA
52076 GGTCCATATC
Statistics
Matches: 77, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
73 3 0.04
74 55 0.71
75 19 0.25
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (75 bp):
AAATGTTGAGGCATGCTGAAAGCCCATTTCAATCAGAAATAGAAATATTAACGCATTTTAAACGT
TTATATCAGA
Found at i:53445 original size:22 final size:22
Alignment explanation
Indices: 53420--53496 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
53410 ATCTACATTC
*
53420 TTCAAAGATGATATATTCTCTT
1 TTCAAAGATGATAAATTCTCTT
*
53442 TTCAAAGATGATAAATTCTCTC
1 TTCAAAGATGATAAATTCTCTT
*
53464 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAAATTCTCTT
53486 TTCAAAGATGA
1 TTCAAAGATGA
53497 AAACTTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAAATTCTCTT
Found at i:54277 original size:36 final size:35
Alignment explanation
Indices: 54217--54495 Score: 191
Period size: 36 Copynumber: 7.7 Consensus size: 35
54207 TTCAAATAGT
* **
54217 AATTTATCTCACTTGAGATTGTTTTACTTAAAACA
1 AATTTGTCTCACTTGAGACAGTTTTACTTAAAACA
* * * *
54252 AATTGCGTCTCTCTTGAGACAGTTTTACTCGAAACAGA
1 AATT-TGTCTCACTTGAGACAGTTTTACT-TAAA-ACA
* * *
54290 AATTTATCTCACTTGAGATTA-TTTTTCTTAAAACAA
1 AATTTGTCTCACTTGAGA-CAGTTTTACTTAAAAC-A
** * * * *
54326 AATGCGTTTCTCTTGAGACATTTTTACTTGAAACAGA
1 AATTTGTCTCACTTGAGACAGTTTTACTT-AAA-ACA
* ** *
54363 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTGTCTCACTTGAGACAGTTTTACTTAAAAC-A
* * *
54399 AATTTGTCTCGCTTGAGACAGTTTCACTTGAAACAA
1 AATTTGTCTCACTTGAGACAGTTTTACTTAAAAC-A
* ** *
54435 TAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 -AATTTGTCTCACTTGAGACAGTTTTACTTAAAACA
* *
54471 AGATTCGTCTCGCTTGAGACAGTTT
1 A-ATTTGTCTCACTTGAGACAGTTT
54496 CACTAGAAAC
Statistics
Matches: 182, Mismatches: 51, Indels: 21
0.72 0.20 0.08
Matches are distributed among these distances:
35 8 0.04
36 95 0.52
37 71 0.39
38 8 0.04
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (35 bp):
AATTTGTCTCACTTGAGACAGTTTTACTTAAAACA
Found at i:54521 original size:73 final size:73
Alignment explanation
Indices: 54217--54513 Score: 445
Period size: 73 Copynumber: 4.1 Consensus size: 73
54207 TTCAAATAGT
* * *
54217 AATTTATCTCACTTGAGATTGTTTTACTTAAAAC-AAATTGCGTCTCTCTTGAGACAGTTTTACT
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATT-CGTCTCGCTTGAGACAGTTTCACT
*
54281 CGAAACAGA
65 TGAAACAGA
* * * * * *
54290 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAAATGCGTTTCTCTTGAGACATTTTTACTT
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACTT
54355 GAAACAGA
66 GAAACAGA
*
54363 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTT
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACTT
54428 GAAACA-A
66 GAAACAGA
*
54435 TAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCGTCTCGCTTGAGACAGTTTCACT
1 -AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACT
*
54500 AGAAACAGA
65 TGAAACAGA
54509 AATTT
1 AATTT
54514 CCATCACTCG
Statistics
Matches: 205, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
72 1 0.00
73 199 0.97
74 5 0.02
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACTT
GAAACAGA
Found at i:54749 original size:123 final size:123
Alignment explanation
Indices: 54530--54981 Score: 753
Period size: 123 Copynumber: 3.7 Consensus size: 123
54520 CTCGATGGAT
*
54530 CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAATTCATAAT
* *
54595 GAGAAGAACTTGGTCAACCTTTTGCTCGATTCTATCCCAGAATGAGATAAATCAACAC
66 GAGAAGAACTTGTTCAACCTTTTGCTCGATTCTAACCCAGAATGAGATAAATCAACAC
* * * * *
54653 CAACATTTTCAGAGGAAGATCATAATGAGAATAACTCATCTGAAAAGGAATAAGAAATTCACAAT
1 CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAATTCATAAT
54718 GAGAAGAACTTGTTCAACCTTTTGCTCGATTCTAACCCAGAATGAGATAAATCAACAC
66 GAGAAGAACTTGTTCAACCTTTTGCTCGATTCTAACCCAGAATGAGATAAATCAACAC
* * *
54776 CAACATTTCCAGTGGAAGTTCATAATGAGAATAACTCATCTGAAAAGGAAGAAAAAATTCATAAT
1 CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAATTCATAAT
*
54841 GAGAAGAACTTGTTCAACCTTTTGCTCGATTCTAACCCAGAAGGAGATAAATCAACAC
66 GAGAAGAACTTGTTCAACCTTTTGCTCGATTCTAACCCAGAATGAGATAAATCAACAC
54899 CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAATAAGTTCA
1 CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAA-AAGGAAGAAG-A-AA-TTCA
54963 TAATGAGAAGAACTTGTTC
62 TAATGAGAAGAACTTGTTC
54982 GACTTTAGTT
Statistics
Matches: 307, Mismatches: 18, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
123 279 0.91
124 3 0.01
125 2 0.01
126 23 0.07
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (123 bp):
CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAATTCATAAT
GAGAAGAACTTGTTCAACCTTTTGCTCGATTCTAACCCAGAATGAGATAAATCAACAC
Found at i:55234 original size:140 final size:140
Alignment explanation
Indices: 54899--55257 Score: 412
Period size: 140 Copynumber: 2.6 Consensus size: 140
54889 AAATCAACAC
*
54899 CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAATAAGTTCAT
1 CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-AA-AAGAAGAAGTTCAT
* * ** * *
54964 AATGAGAAGAACTTGTTCGACTTTAGTTTGATTCATCATCTATGAAGTTGAATGAAAGAAGAACC
64 AATGATAAGAACTTGTTCAACCCTAGCTTAATTCATCATCTATGAAGTTGAATGAAAGAAGAACC
55029 TCACTTGAGGAT
129 TCACTTGAGGAT
* * * *
55041 TAATATTTTCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAA-AAATGAAGAAGAAGTTCATA
1 CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAA-AAAGAAGAAGTTCATA
* * * *
55105 ATGATAAGAACTTGTTCAACCCT-GCCTTAATTCATTA-CATATGAAGTTGAAT-CAATAA-CAC
65 ATGATAAGAACTTGTTCAACCCTAG-CTTAATTCATCATC-TATGAAGTTGAATGAAAGAAGAAC
55166 C-C-CTTTCGAGGAT
128 CTCAC-TT-GAGGAT
* * * *
55179 CAGCATTTCCAGATGG-AGTTCATAATGAGAAGAACTCATCTGATGAGAAAA-AAGAAGTTTATA
1 CAACATTTCCAGA-GGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATA
55242 ATGATAAGAACTTGTT
65 ATGATAAGAACTTGTT
55258 TAACTTTTTA
Statistics
Matches: 187, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
136 1 0.01
137 30 0.16
138 47 0.25
139 10 0.05
140 56 0.30
141 2 0.01
142 41 0.22
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (140 bp):
CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAA
TGATAAGAACTTGTTCAACCCTAGCTTAATTCATCATCTATGAAGTTGAATGAAAGAAGAACCTC
ACTTGAGGAT
Found at i:70211 original size:14 final size:14
Alignment explanation
Indices: 70192--70220 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
70182 CTTGTTCCCT
70192 ATAAATTTATCACA
1 ATAAATTTATCACA
70206 ATAAATTTATCACA
1 ATAAATTTATCACA
70220 A
1 A
70221 AAGGTTGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAATTTATCACA
Found at i:72850 original size:35 final size:34
Alignment explanation
Indices: 72811--72888 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
72801 AACACAATCC
72811 TCAATTTCATTCTAAACTCC-AAATTCCAAAATAAT
1 TCAATTT-ATTCTAAAC-CCTAAATTCCAAAATAAT
* ** *
72846 TCAATTATATTTTAAACCCTAAATTTTAAAATACT
1 TCAATT-TATTCTAAACCCTAAATTCCAAAATAAT
72881 TCAATTTA
1 TCAATTTA
72889 GGGTTTTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 4 0.11
35 32 0.86
36 1 0.03
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (34 bp):
TCAATTTATTCTAAACCCTAAATTCCAAAATAAT
Found at i:72922 original size:35 final size:35
Alignment explanation
Indices: 72883--72957 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
72873 AAAATACTTC
*
72883 AATTTAGGGTTTTGAATATAATTAAAGTATTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
* * * *
72918 AATTTGGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
72953 AATTT
1 AATTT
72958 TGAACATGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
Found at i:75484 original size:18 final size:18
Alignment explanation
Indices: 75456--75497 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
75446 ATATAAGAAT
*
75456 TATTAAATTATTAAATAAA
1 TATTTAATTATTAAA-AAA
75475 -ATTTAATTATTAAAAAA
1 TATTTAATTATTAAAAAA
75492 TATTTA
1 TATTTA
75498 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTTAATTATTAAAAAA
Found at i:77721 original size:3 final size:3
Alignment explanation
Indices: 77715--77834 Score: 165
Period size: 3 Copynumber: 39.7 Consensus size: 3
77705 CTCCATTTTC
77715 TAT TAT TAT TATT TAT TAT TAT TAT T-T TAT ATAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
77761 TAT TAT TAT TAT TAT T-T TAT ATAT TAT TAT TAT TAT TAT T-T TATT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA-T
* *
77806 TAT TAT TAT TAT TAA AAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
77835 CAAACAGGCC
Statistics
Matches: 106, Mismatches: 4, Indels: 14
0.85 0.03 0.11
Matches are distributed among these distances:
2 6 0.06
3 88 0.83
4 12 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Done.