Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003900.1 Hibiscus syriacus cultivar Beakdansim tig00008429_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: 133896
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4445 original size:44 final size:44
Alignment explanation
Indices: 4325--4445 Score: 135
Period size: 44 Copynumber: 2.8 Consensus size: 44
4315 CTTTTGTGCT
* *
4325 CATCGATGCAC--TTCATGCATCGATGCATCCCT-TTGAATGTG
1 CATCGATGCACAGTTCATGCATCGATGCATCCGTCTTGAATATG
* * *
4366 CATCGATTCATCATGTTGATGCACCGATGCA--CGTCTTGAATATG
1 CATCGATGCA-CA-GTTCATGCATCGATGCATCCGTCTTGAATATG
*
4410 CATCGATGCACAGGTCATGCATCGATGCATCCGTCT
1 CATCGATGCACAGTTCATGCATCGATGCATCCGTCT
4446 GGTTTTGGGT
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
41 9 0.14
42 15 0.23
43 4 0.06
44 22 0.34
45 14 0.22
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (44 bp):
CATCGATGCACAGTTCATGCATCGATGCATCCGTCTTGAATATG
Found at i:6593 original size:15 final size:16
Alignment explanation
Indices: 6563--6602 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
6553 AAAAGGGGAG
*
6563 AAGTGTTAAGTGTTAA
1 AAGTTTTAAGTGTTAA
6579 AAGTTTTAA-TGTTAA
1 AAGTTTTAAGTGTTAA
6594 AAGTTTTAA
1 AAGTTTTAA
6603 AGGGGAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (16 bp):
AAGTTTTAAGTGTTAA
Found at i:9328 original size:81 final size:81
Alignment explanation
Indices: 9193--9356 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 81
9183 TTTTATCTTT
9193 AGATCGATATCTTAGCACTGTCTCTACTAAAGGAGTTTATGGAGCTTGGACAAATGAGAGATTTC
1 AGATCGATATCTTAGCACTGTCTCTACTAAAGGAGTTTATGGAGCTTGGACAAATGAGAGATTTC
9258 AAAGAACTGAAATAGA
66 AAAGAACTGAAATAGA
*
9274 AGATCGATATCTTAGCACTGTCTCTGCTAAAGGAGTTTATGGAGCTTGGACAAATGAGAGATTTC
1 AGATCGATATCTTAGCACTGTCTCTACTAAAGGAGTTTATGGAGCTTGGACAAATGAGAGATTTC
9339 AAAGAACTGAAATAGA
66 AAAGAACTGAAATAGA
9355 AG
1 AG
9357 TGTTCTAAAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (81 bp):
AGATCGATATCTTAGCACTGTCTCTACTAAAGGAGTTTATGGAGCTTGGACAAATGAGAGATTTC
AAAGAACTGAAATAGA
Found at i:13371 original size:19 final size:19
Alignment explanation
Indices: 13347--13399 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
13337 AGAGGGCTAA
**
13347 AAAGTATCAGTACTTATAT
1 AAAGTATCAAAACTTATAT
13366 AAAGTATCAAAACTTATAT
1 AAAGTATCAAAACTTATAT
13385 AAAGTATCAAAACTT
1 AAAGTATCAAAACTT
13400 TAGCAGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
AAAGTATCAAAACTTATAT
Found at i:14862 original size:3 final size:3
Alignment explanation
Indices: 14856--14913 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
14846 TCTAGGTTAC
* *
14856 TTA TTA TTA TTA TT- TTA TTA TTTA TATA TTA TTA TTA ATA ATA -TA
1 TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA
14901 TT- TTA TTA TTA TT
1 TTA TTA TTA TTA TT
14914 GTACACGTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
2 6 0.12
3 37 0.76
4 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:14875 original size:14 final size:15
Alignment explanation
Indices: 14856--14912 Score: 71
Period size: 17 Copynumber: 3.7 Consensus size: 15
14846 TCTAGGTTAC
14856 TTATTATTAT-TATT
1 TTATTATTATATATT
14870 TTATTATTTATATATT
1 TTATTA-TTATATATT
*
14886 ATTATTAATAATATATT
1 -TTATT-ATTATATATT
14903 TTATTATTAT
1 TTATTATTAT
14913 TGTACACGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 6 0.16
15 8 0.22
16 9 0.24
17 13 0.35
18 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATTATTATATATT
Found at i:14902 original size:25 final size:25
Alignment explanation
Indices: 14856--14913 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
14846 TCTAGGTTAC
**
14856 TTATTATTATTATTTTATTA-TTTA
1 TTATTATTATTATAATATTATTTTA
14880 TATATTATTATTAATAATA-TATTTTA
1 T-TATTATTATT-ATAATATTATTTTA
14906 TTATTATT
1 TTATTATT
14914 GTACACGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 1 0.03
25 19 0.66
26 9 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TTATTATTATTATAATATTATTTTA
Found at i:20153 original size:90 final size:90
Alignment explanation
Indices: 19995--20175 Score: 317
Period size: 90 Copynumber: 2.0 Consensus size: 90
19985 TTGCTTGATT
* * * *
19995 TGGAATCCCAAGAAAAATGAGAGCTCCCCCATCATGCTCATTTCATATTCGCTTTGCATTAGCTT
1 TGGAATCCCAAGAAAAATGAAAGCTCCCCCATCATGCTCATTTCATAATCGCTTTCCATGAGCTT
20060 AGAAAATTCTTGGCAAAGAACATCA
66 AGAAAATTCTTGGCAAAGAACATCA
*
20085 TGGAGTCCCAAGAAAAATGAAAGCTCCCCCATCATGCTCATTTCATAATCGCTTTCCATGAGCTT
1 TGGAATCCCAAGAAAAATGAAAGCTCCCCCATCATGCTCATTTCATAATCGCTTTCCATGAGCTT
20150 AGAAAATTCTTGGCAAAGAACATCA
66 AGAAAATTCTTGGCAAAGAACATCA
20175 T
1 T
20176 TAGTAGAACC
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (90 bp):
TGGAATCCCAAGAAAAATGAAAGCTCCCCCATCATGCTCATTTCATAATCGCTTTCCATGAGCTT
AGAAAATTCTTGGCAAAGAACATCA
Found at i:26731 original size:26 final size:25
Alignment explanation
Indices: 26693--26751 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
26683 GAAAGAGAGG
*
26693 GAAA-AAAATGTTAGACACCAAACT
1 GAAACAAAACGTTAGACACCAAACT
*
26717 GAAACGAAAACGTTAGGCACCAAACT
1 GAAAC-AAAACGTTAGACACCAAACT
26743 GAAACAAAA
1 GAAACAAAA
26752 TAAATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 4 0.13
25 4 0.13
26 23 0.74
ACGTcount: A:0.54, C:0.19, G:0.15, T:0.12
Consensus pattern (25 bp):
GAAACAAAACGTTAGACACCAAACT
Found at i:27285 original size:26 final size:23
Alignment explanation
Indices: 27229--27289 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
27219 TATCAAACTC
27229 CGAGTCATCATCATGTCAATCTA
1 CGAGTCATCATCATGTCAATCTA
27252 CGAGTCATCATCATGTCAATCTA
1 CGAGTCATCATCATGTCAATCTA
27275 CGAGTCATCATCATG
1 CGAGTCATCATCATG
27290 ACACTAAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (23 bp):
CGAGTCATCATCATGTCAATCTA
Found at i:27762 original size:2 final size:2
Alignment explanation
Indices: 27757--27829 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
27747 GCAAAAAAAA
27757 AT AT AT AT AT 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
27799 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 A
27830 AAACTCCAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28375 original size:150 final size:150
Alignment explanation
Indices: 28104--28380 Score: 342
Period size: 150 Copynumber: 1.8 Consensus size: 150
28094 CGTGCAGCGG
* * * **
28104 ATTCCCTGTTCTTCATCTTTCTCCTTAACCTCTTCTCAAGTTCATCTTGTGCATCCCTTTTCCGC
1 ATTCCATGTTCTTCACCTTTCTCCTTAACCTCTTCTCAAGTGCATCTTGTGCATCAATTTTCCGC
*** *
28169 CCCGTCATAGGTGGATCAGATAGTGTGCCAATTGACCGTGTAAGTGACAATCCGATCTGATGTGG
66 CCCGTCATAGGTGGATCAGATAACATGCCAATTGACCGTGTAAGTGACAATCCGATCCGATGTGG
28234 TGTGCTTGATCCGACATCGA
131 TGTGCTTGATCCGACATCGA
* * * * *
28254 ATTCCATGTTCTTGACCTTTCTCTTTAACTTCTTCTCAAGTGCATCTTGTGCATCAATTTTTCGT
1 ATTCCATGTTCTTCACCTTTCTCCTTAACCTCTTCTCAAGTGCATCTTGTGCATCAATTTTCCGC
* * * * **
28319 CCCGTCATAGGTCGG-TCCGATAACATGGCGATTGA-CGTTGTAGGTGAGGATCCGATCCGATG
66 CCCGTCATAGGT-GGATCAGATAACATGCCAATTGACCG-TGTAAGTGACAATCCGATCCGATG
28381 CGAAAATCTT
Statistics
Matches: 105, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
149 2 0.02
150 101 0.96
151 2 0.02
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (150 bp):
ATTCCATGTTCTTCACCTTTCTCCTTAACCTCTTCTCAAGTGCATCTTGTGCATCAATTTTCCGC
CCCGTCATAGGTGGATCAGATAACATGCCAATTGACCGTGTAAGTGACAATCCGATCCGATGTGG
TGTGCTTGATCCGACATCGA
Found at i:29963 original size:15 final size:15
Alignment explanation
Indices: 29943--29981 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
29933 CAAAATCAAG
29943 AATAAAAATTAAGAA
1 AATAAAAATTAAGAA
* *
29958 AATAAACATTAAGAT
1 AATAAAAATTAAGAA
*
29973 GATAAAAAT
1 AATAAAAAT
29982 AAATAAAGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.23
Consensus pattern (15 bp):
AATAAAAATTAAGAA
Found at i:32782 original size:39 final size:39
Alignment explanation
Indices: 32734--32817 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
32724 AATAAACATC
* **
32734 AGGTGGTCTTCCCAAGGAGTTTTGACAAGACTAGATATT
1 AGGTTGTCTTCCCAAGGAGTTTCCACAAGACTAGATATT
* *
32773 AGGTTGTCTTCCTAAGGAGTTTCCACAAGACTGGATATT
1 AGGTTGTCTTCCCAAGGAGTTTCCACAAGACTAGATATT
*
32812 GGGTTG
1 AGGTTG
32818 AAATGGTCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32
Consensus pattern (39 bp):
AGGTTGTCTTCCCAAGGAGTTTCCACAAGACTAGATATT
Found at i:41227 original size:21 final size:18
Alignment explanation
Indices: 41203--41241 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
41193 AAAATAATCT
41203 ATTACTTAATAATTTATTTTA
1 ATTAC-TAAT-ATTT-TTTTA
41224 ATTACTAATATTTTTTTA
1 ATTACTAATATTTTTTTA
41242 GTATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 4 0.22
21 5 0.28
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTACTAATATTTTTTTA
Found at i:41247 original size:20 final size:22
Alignment explanation
Indices: 41202--41247 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
41192 AAAAATAATC
41202 TATTACTTAATAATTTATTTTA
1 TATTACTTAATAATTTATTTTA
41224 -ATTAC-TAAT-ATTT-TTTTA
1 TATTACTTAATAATTTATTTTA
41242 GTATTA
1 -TATTA
41248 TTTTTGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 5 0.23
19 4 0.18
20 8 0.36
21 5 0.23
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTACTTAATAATTTATTTTA
Found at i:45075 original size:29 final size:29
Alignment explanation
Indices: 45041--45099 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
45031 CCTAAATTAA
45041 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
45070 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
45099 T
1 T
45100 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:49758 original size:29 final size:29
Alignment explanation
Indices: 49724--49782 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
49714 CCTAAATTAA
49724 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
49753 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
49782 T
1 T
49783 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:53361 original size:16 final size:16
Alignment explanation
Indices: 53340--53380 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
53330 AAGAATGGGG
53340 CCGCTGCCAACAACCA
1 CCGCTGCCAACAACCA
*
53356 CCGCTGCCAACAACCT
1 CCGCTGCCAACAACCA
53372 CCGCTGCCA
1 CCGCTGCCA
53381 CGGCTACCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.24, C:0.51, G:0.15, T:0.10
Consensus pattern (16 bp):
CCGCTGCCAACAACCA
Found at i:54894 original size:31 final size:31
Alignment explanation
Indices: 54846--54945 Score: 146
Period size: 31 Copynumber: 3.2 Consensus size: 31
54836 AACGTCCAAT
* *
54846 TGACTAAAACTTAATAAAACAATAACATAAG
1 TGACCAAAACTTAATAAAACAATAACACAAG
* *
54877 TGACCAAAATTTAATAAAATAATAACACAAG
1 TGACCAAAACTTAATAAAACAATAACACAAG
* *
54908 TGACTAAAACTTAATAAAACAATAACACAAC
1 TGACCAAAACTTAATAAAACAATAACACAAG
54939 TGACCAA
1 TGACCAA
54946 GATTTATGTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.57, C:0.16, G:0.06, T:0.21
Consensus pattern (31 bp):
TGACCAAAACTTAATAAAACAATAACACAAG
Found at i:55679 original size:18 final size:17
Alignment explanation
Indices: 55646--55678 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55636 CAGATGAGCA
55646 ATATAAAAGACTAAAAT
1 ATATAAAAGACTAAAAT
55663 ATATCAAAAGA-TAAAA
1 ATAT-AAAAGACTAAAA
55679 AAAATGTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (17 bp):
ATATAAAAGACTAAAAT
Found at i:57244 original size:53 final size:53
Alignment explanation
Indices: 57163--57276 Score: 192
Period size: 53 Copynumber: 2.1 Consensus size: 53
57153 TTATGATATG
57163 ATTTATAAGGTTTAGAGTACAATACAAAAATAGAAACAATTATAGGCTAATTTC
1 ATTTA-AAGGTTTAGAGTACAATACAAAAATAGAAACAATTATAGGCTAATTTC
* * *
57217 ATTTAAAGGTTTAGAGTACAATACAAAAATAGAAATAATTATGGGCTAATTTT
1 ATTTAAAGGTTTAGAGTACAATACAAAAATAGAAACAATTATAGGCTAATTTC
57270 ATTTAAA
1 ATTTAAA
57277 AATATACTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 52 0.91
54 5 0.09
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (53 bp):
ATTTAAAGGTTTAGAGTACAATACAAAAATAGAAACAATTATAGGCTAATTTC
Found at i:58175 original size:3 final size:3
Alignment explanation
Indices: 58169--58224 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
58159 ATTACCCATT
* *
58169 TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA TATA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA TTA
58216 TTA TTA TTA
1 TTA TTA TTA
58225 AAAAAATAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 41 0.85
4 7 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:71107 original size:1 final size:1
Alignment explanation
Indices: 71101--71168 Score: 55
Period size: 1 Copynumber: 68.0 Consensus size: 1
71091 ATGCTTGAAG
* * * * * * * * *
71101 AAAAAAAAAGAAAAAAGAAAAAAGAAAGAAAAAAAAAAGAAAAGAAAAAAGAAAAAGAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
71166 AAA
1 AAA
71169 GGGGGTCAAG
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:71116 original size:7 final size:7
Alignment explanation
Indices: 71104--71168 Score: 84
Period size: 7 Copynumber: 9.7 Consensus size: 7
71094 CTTGAAGAAA
71104 AAAAAAG
1 AAAAAAG
71111 AAAAAAG
1 AAAAAAG
71118 AAAAAAG
1 AAAAAAG
71125 AAAGAAA-
1 AAA-AAAG
71132 AAAAAA-
1 AAAAAAG
*
71138 AGAAAAG
1 AAAAAAG
71145 AAAAAAG
1 AAAAAAG
71152 -AAAAAG
1 AAAAAAG
71158 -AAAAAG
1 AAAAAAG
71164 AAAAA
1 AAAAA
71169 GGGGGTCAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
6 20 0.38
7 30 0.57
8 3 0.06
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:71121 original size:6 final size:6
Alignment explanation
Indices: 71101--71169 Score: 83
Period size: 6 Copynumber: 11.8 Consensus size: 6
71091 ATGCTTGAAG
*
71101 AAAA-A AAAAGAA AAAAGA AAAA-A GAAAGA AAAA-A AAAAG- AAAAGAA
1 AAAAGA AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAG-A
71147 AAAAGA AAAAGA AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA AAAAG
71170 GGGGTCAAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
5 18 0.32
6 27 0.48
7 11 0.20
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:71144 original size:34 final size:34
Alignment explanation
Indices: 71101--71168 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
71091 ATGCTTGAAG
*
71101 AAAAAAAAAGAAAAAAGAAAAA-AGAAAGAAAAA
1 AAAAAAAAAGAAAAAAGAAAAAGAAAAAGAAAAA
71134 AAAAAGAAAAGAAAAAAGAAAAAGAAAAAGAAAAA
1 AAAAA-AAAAGAAAAAAGAAAAAGAAAAAGAAAAA
71169 GGGGGTCAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.16
34 17 0.53
35 10 0.31
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAGAAAAAAGAAAAAGAAAAAGAAAAA
Found at i:72296 original size:94 final size:94
Alignment explanation
Indices: 72134--72518 Score: 666
Period size: 94 Copynumber: 4.1 Consensus size: 94
72124 ACAAGTGTCG
*
72134 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCCCGA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
72199 AAAACCAATCATTGAATTTGAAAGATGAA
66 AAAACCAATCATTGAATTTGAAAGATGAA
* * *
72228 GGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGGTATGAACCCCGA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
72293 AAAACCAATCATTGAATTTGAAAGATGAA
66 AAAACCAATCATTGAATTTGAAAGATGAA
*
72322 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCTCGA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
*
72387 AAAACCAATCATTGAATTTGAAAGATAAA
66 AAAACCAATCATTGAATTTGAAAGATGAA
*
72416 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAA-ACC-A
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
*
72479 CAGAACCAATCATTGAATTTGAAAGATGAA
66 -AAAACCAATCATTGAATTTGAAAGATGAA
*
72509 TGTGATCATA
1 TGTGCTCATA
72519 ATAGAAATAA
Statistics
Matches: 276, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
92 1 0.00
93 37 0.13
94 238 0.86
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (94 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
AAAACCAATCATTGAATTTGAAAGATGAA
Found at i:73400 original size:24 final size:23
Alignment explanation
Indices: 73357--73401 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
73347 GTTCATAATG
*
73357 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
73380 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
73402 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:73647 original size:113 final size:112
Alignment explanation
Indices: 73308--73756 Score: 586
Period size: 113 Copynumber: 4.0 Consensus size: 112
73298 TAGCAAAGAT
* * * * *
73308 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAG-TAGAGTTCATAATGAGAAGAACTCAACTGA
*
73373 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * * **
73421 TTAAATTCATCATTTGATGGATTAAC-ATTGAAGGTAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCA-GTAGAGTTCATAATGAGAAGAACTCA--A-C
*
73485 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
62 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
73536 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCAACTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAG-TAGAGTTCATAATGAGAAGAACTCAACTGA
*
73601 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
73649 TCAAATCCATCACTTGATGGATCAGTTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTAG-AGTTCATAATGAGAAGAACTCAACTGA
* ** *
73713 AGAA-G-A-AA-AAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
73757 ATAATTCTAT
Statistics
Matches: 297, Mismatches: 32, Indels: 19
0.85 0.09 0.05
Matches are distributed among these distances:
108 31 0.10
109 2 0.01
110 1 0.00
111 2 0.01
112 55 0.19
113 106 0.36
114 1 0.00
115 72 0.24
116 27 0.09
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (112 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTAGAGTTCATAATGAGAAGAACTCAACTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:73705 original size:228 final size:221
Alignment explanation
Indices: 73308--73879 Score: 619
Period size: 228 Copynumber: 2.5 Consensus size: 221
73298 TAGCAAAGAT
* * *
73308 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCAACTGA
* * * *
73373 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGA
* *
73438 TGGATTAACATTGAAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAA
131 TGGATCAACATTCAAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA-G-A-AA-AAA
* * *
73503 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
189 TTCACAATGAGAAGAACTTATTCAACCTTTTGC
****
73536 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCAACTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCAACTGA
*
73601 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGA
*** * *
73666 TGGATCAGTTTTTCCA-G-AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCAC
131 TGGATCA-ACATTCAAGGTAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAATTCAC
*
73729 AATGAGAAGAGCTTATTCAACCTTTTGC
194 AATGAGAAGAACTTATTCAACCTTTTGC
* * * * * *
73757 AT-AATTCTATCACAGAAGCAGATAGATTAGCATCAACCTTTCCAGAAAAAGTTCATAATGAGAA
1 -TCAA----ATC-C---ATCA-CTTGA-T-GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAA
* * * ** *
73821 GAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
54 GAACTCAACTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
73880 AATGACTCTA
Statistics
Matches: 290, Mismatches: 40, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
221 33 0.11
222 3 0.01
223 1 0.00
224 1 0.00
225 15 0.05
226 2 0.01
227 2 0.01
228 143 0.49
229 6 0.02
230 3 0.01
231 1 0.00
232 80 0.28
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (221 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCAACTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGA
TGGATCAACATTCAAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAATTCACAA
TGAGAAGAACTTATTCAACCTTTTGC
Found at i:73915 original size:124 final size:121
Alignment explanation
Indices: 73676--73961 Score: 368
Period size: 124 Copynumber: 2.4 Consensus size: 121
73666 TGGATCAGTT
*
73676 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTG-A-AGAAGAAAAAGTTCACAATGAGAAGA
1 TTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAAAAGTTCACAATGAGAAGA
* * * * *
73739 GCTTATTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGCATCAACC
66 GCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACC
* *
73795 TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGA
1 TTTCCAG-AAAAGTTCATAATGAGAAGAACTCATCTGAA-GAG-AAGAAAAAGTTCACAATGAGA
* * * * *
73860 AGAGCTTATTCAACCTTTTGAATGACTCTATCATAGAAGGAAATAGGTCAACATCATCC
63 AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACC
73919 ---CCAGCGAAAAGTTCATAATGAGAAGAACTCATCTGAAGA-AAGA
1 TTTCCA--GAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGA
73962 GAAGAATTTA
Statistics
Matches: 147, Mismatches: 13, Indels: 14
0.84 0.07 0.08
Matches are distributed among these distances:
119 11 0.07
120 28 0.19
121 6 0.04
122 31 0.21
123 3 0.02
124 68 0.46
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (121 bp):
TTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAAAAGTTCACAATGAGAAGA
GCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACC
Found at i:74115 original size:3 final size:3
Alignment explanation
Indices: 74109--74177 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
74099 ATTACCCATT
* * * *
74109 TTA TTA TTA TTA TAA TTA TTA TTA TAA TAA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
74157 -TA TATA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA
74178 AAAAAATAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.03
3 53 0.91
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:74127 original size:15 final size:15
Alignment explanation
Indices: 74109--74200 Score: 89
Period size: 15 Copynumber: 6.2 Consensus size: 15
74099 ATTACCCATT
*
74109 TTATTATTATTATAA
1 TTATTATTATAATAA
74124 TTATTATTATAATAA
1 TTATTATTATAATAA
*
74139 TTATTATTATAATTA
1 TTATTATTATAATAA
* *
74154 TTA-TATATATTATTA
1 TTATTAT-TATAATAA
* *
74169 TTATTATTAAAAAAA
1 TTATTATTATAATAA
* *
74184 TAATAATTA-AATAA
1 TTATTATTATAATAA
74198 TTA
1 TTA
74201 CAAACATGCC
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
14 9 0.14
15 52 0.81
16 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATTATTATAATAA
Found at i:79830 original size:10 final size:10
Alignment explanation
Indices: 79815--79848 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
79805 TTCATTTACC
79815 ATTTATTTTT
1 ATTTATTTTT
79825 ATTTATTTTT
1 ATTTATTTTT
* *
79835 ATCTATTTCT
1 ATTTATTTTT
79845 ATTT
1 ATTT
79849 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:82252 original size:39 final size:39
Alignment explanation
Indices: 82181--82258 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
82171 CCCGGAATAT
*
82181 TACCCGGGGACGCATATGCTACTAAAGGGAAAGTAGCAC
1 TACCCGGGGACGCATATGCTACCAAAGGGAAAGTAGCAC
* * * *
82220 TACCCGGGGACTCAT-TCGTTACCAAAGTGAAAGTTGCAC
1 TACCCGGGGACGCATAT-GCTACCAAAGGGAAAGTAGCAC
82259 CTGCTGCGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (39 bp):
TACCCGGGGACGCATATGCTACCAAAGGGAAAGTAGCAC
Found at i:88988 original size:51 final size:52
Alignment explanation
Indices: 88908--89006 Score: 146
Period size: 51 Copynumber: 1.9 Consensus size: 52
88898 AATACTTCGC
* ** *
88908 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAA-AAAAAAGAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAGAAAAAAGAACGT
*
88959 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAGAAAAAAGA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAGAAAAAAGA
89007 GAAGAAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 34 0.81
52 8 0.19
ACGTcount: A:0.47, C:0.14, G:0.24, T:0.14
Consensus pattern (52 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAGAAAAAAGAACGT
Found at i:89953 original size:105 final size:105
Alignment explanation
Indices: 89771--90880 Score: 1850
Period size: 105 Copynumber: 10.7 Consensus size: 105
89761 AGGTTTTACC
*
89771 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
89836 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
89876 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
89941 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
89981 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
90046 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
90086 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
90151 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCGAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
90191 CCGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
90256 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
90296 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
90361 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
90401 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
90466 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
90506 CCGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
90571 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* *
90612 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
90677 GCGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* * * * *
90718 CAGAGTCAATTTCAAATTCACAGCGAAGAATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
90783 ACGAAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
90816 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTAC-C-AGTTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA--ACGCAAGTTCAACTTCA
90875 CGACGA
64 CGACGA
90881 GGATGTCATT
Statistics
Matches: 959, Mismatches: 43, Indels: 17
0.94 0.04 0.02
Matches are distributed among these distances:
94 54 0.06
95 1 0.00
96 2 0.00
98 7 0.01
103 1 0.00
105 704 0.73
106 190 0.20
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:92325 original size:19 final size:17
Alignment explanation
Indices: 92287--92330 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
92277 TTGCTTACAA
*
92287 ATTATTATATATATATT
1 ATTATTATATATATACT
*
92304 ATTTTTATATATAATAACT
1 ATTATTATATAT-AT-ACT
92323 ATTATTAT
1 ATTATTAT
92331 TATTATCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 11 0.50
18 2 0.09
19 9 0.41
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATTATATATATACT
Found at i:96835 original size:13 final size:14
Alignment explanation
Indices: 96817--96846 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
96807 AGTTGGACAA
96817 TCTTCATATGCA-G
1 TCTTCATATGCACG
96830 TCTTCATATGCACG
1 TCTTCATATGCACG
96844 TCT
1 TCT
96847 GTAATGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (14 bp):
TCTTCATATGCACG
Found at i:101558 original size:14 final size:14
Alignment explanation
Indices: 101514--101563 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
101504 AAAATCAAAC
*
101514 TTATTTAAGGAGTA
1 TTATTTAAGGAATA
**
101528 TT-TTTTTGGAA-A
1 TTATTTAAGGAATA
101540 CTTATTTAAGGAATA
1 -TTATTTAAGGAATA
101555 TTATTTAAG
1 TTATTTAAG
101564 TAATTGCACG
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
12 1 0.04
13 8 0.29
14 18 0.64
15 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (14 bp):
TTATTTAAGGAATA
Found at i:107400 original size:39 final size:38
Alignment explanation
Indices: 107357--107434 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 38
107347 GTATTTACAT
*
107357 TTTATT-TTAATAATTTAATATTAATATCCTTAAAAATAA
1 TTTATTCTTAATAATTT-ATATTAAT-TACTTAAAAATAA
*
107396 TTTATTGCTTAATAATTTATTTTAATTACTTAAAAATAA
1 TTTATT-CTTAATAATTTATATTAATTACTTAAAAATAA
107435 ATAAAATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 18 0.51
40 7 0.20
41 10 0.29
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (38 bp):
TTTATTCTTAATAATTTATATTAATTACTTAAAAATAA
Found at i:107470 original size:16 final size:14
Alignment explanation
Indices: 107436--107464 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
107426 TAAAAATAAA
107436 TAAAATTCATATAT
1 TAAAATTCATATAT
107450 TAAAATTCATATAT
1 TAAAATTCATATAT
107464 T
1 T
107465 TTAAAAATAA
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:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAAATTCATATAT
Found at i:107498 original size:21 final size:21
Alignment explanation
Indices: 107444--107515 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
107434 AATAAAATTC
*
107444 ATATATTAAAATTCATATATTT
1 ATATATTAAAATTCA-ACATTT
*
107466 -TA-A-AAATAATTC-ACAATTT
1 ATATATTAA-AATTCAAC-ATTT
*
107485 ATATATTAAAATTCAACGTTT
1 ATATATTAAAATTCAACATTT
107506 ATATATTAAA
1 ATATATTAAA
107516 GTTAACTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
18 1 0.03
19 6 0.15
20 8 0.20
21 21 0.52
22 4 0.10
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (21 bp):
ATATATTAAAATTCAACATTT
Found at i:109123 original size:19 final size:21
Alignment explanation
Indices: 109079--109119 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
109069 ATAACTCATA
109079 ATTTATATATTAAAATTCACC
1 ATTTATATATTAAAATTCACC
*
109100 ATTTATATATTAAAGTTCAC
1 ATTTATATATTAAAATTCAC
109120 TTTAATTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTTATATATTAAAATTCACC
Found at i:113074 original size:16 final size:16
Alignment explanation
Indices: 113053--113097 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
113043 ATATTTTTTC
113053 TTATAAAATATTTCAT
1 TTATAAAATATTTCAT
113069 TTATAAAAATATTTCAT
1 TTAT-AAAATATTTCAT
*
113086 CT-TAAAATATTT
1 TTATAAAATATTT
113098 TTTATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.33
16 5 0.19
17 13 0.48
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATAAAATATTTCAT
Found at i:117037 original size:59 final size:59
Alignment explanation
Indices: 116974--117364 Score: 332
Period size: 59 Copynumber: 6.6 Consensus size: 59
116964 TTACCAAATG
* *
116974 GCACTATATGTGCTAAAATGGTAGGGGAATCATACTGAGTGTATGAATTCCCATATGGA
1 GCACTATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
* * *
117033 GCACTGA-GTGTGCTAAAATGGTAAGGGAATCACACTGAGTGTATGAATTTCCATATGAA
1 GCACT-ATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
*
117092 GCACTGA-GTGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
1 GCACT-ATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
* ** * * * * * * *
117151 GCA-T-TGAGTGTGATAAAATAATAAGGAAATCATATTGAATATATGGATTTACAGATAGG-
1 GCACTAT-A-TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATAT-GGA
* * * * * ***
117210 GCATTATATGTACTAAAATGGTAAGGGAATCATACTGAGTGTTTGGATTTCCAGAAAAA
1 GCACTATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
* * ** * * *
117269 GCACTA-AGGGTGCTACAA-GGATAAGAAAATCATACT-AATAGTATGGATTTTCATATAGG-
1 GCACTATA-TGTGCTAAAATGG-TAAGGGAATCATACTGAGT-GTATGAATTTCCATAT-GGA
* *
117328 GCACTTTATGTGCTAAAAATGGTAAAGGAATCATACT
1 GCACTATATGTGCT-AAAATGGTAAGGGAATCATACT
117365 AATGGTATGG
Statistics
Matches: 267, Mismatches: 50, Indels: 29
0.77 0.14 0.08
Matches are distributed among these distances:
58 6 0.02
59 237 0.89
60 21 0.08
61 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (59 bp):
GCACTATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
Found at i:117072 original size:31 final size:31
Alignment explanation
Indices: 117034--117133 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 31
117024 CCATATGGAG
117034 CACTGAGTGTGCTAAAATGGTAAGGGAATCA
1 CACTGAGTGTGCTAAAATGGTAAGGGAATCA
* * * *** * *
117065 CACTGAGTGT-ATGAATTTCCATA-TGAA--G
1 CACTGAGTGTGCTAAAATGGTA-AGGGAATCA
117093 CACTGAGTGTGCTAAAATGGTAAGGGAATCA
1 CACTGAGTGTGCTAAAATGGTAAGGGAATCA
*
117124 TACTGAGTGT
1 CACTGAGTGT
117134 ATGAATTTCC
Statistics
Matches: 47, Mismatches: 17, Indels: 10
0.64 0.23 0.14
Matches are distributed among these distances:
28 11 0.23
29 8 0.17
30 8 0.17
31 20 0.43
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (31 bp):
CACTGAGTGTGCTAAAATGGTAAGGGAATCA
Found at i:117260 original size:118 final size:119
Alignment explanation
Indices: 116973--117421 Score: 448
Period size: 118 Copynumber: 3.8 Consensus size: 119
116963 ATTACCAAAT
* *
116973 GGCAC-TATATGTGCTAAAATGGTAGGGGAATCATACTGAGTGTATGAATTCCCATATGGAGCAC
1 GGCACTTATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCAC
* * * * * * *
117037 TGAGTGTGCTAAAATGGTAAGGGAATCACACTGAGTGTATGAATTTCCATAT-G
66 TGAGTGTGCTAAAATGATAAGGAAATCATACTGAATATATGGATTTACATATAG
* * *
117090 AAGCACTGA-GTGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCA
1 -GGCACTTATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCA
* * * * *
117154 TTGAGTGTGATAAAATAATAAGGAAATCATATTGAATATATGGATTTACAGATAG
65 CTGAGTGTGCTAAAATGATAAGGAAATCATACTGAATATATGGATTTACATATAG
* * * * ***
117209 GGCA-TTATATGTACTAAAATGGTAAGGGAATCATACTGAGTGTTTGGATTTCCAGAAAAAGCAC
1 GGCACTTATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCAC
* * * * * *
117273 TAAGGGTGCTACAAGGATAAGAAAATCATACT-AATAGTATGGATTTTCATATAG
66 TGAGTGTGCTAAAATGATAAGGAAATCATACTGAATA-TATGGATTTACATATAG
* * *
117327 GGCACTT-TATGTGCTAAAAATGGTAAAGGAATCATACT-AATGGTATGGATTCTCGCATA-GG-
1 GGCACTTATATGTGCT-AAAATGGTAAGGGAATCATACTGAGT-GTATGAATT-TC-CATATGGA
** **
117388 GCACTTCGTGTGCTAAAATGAGGAGGAAATCATA
62 GCACTGAGTGTGCTAAAATGATAAGGAAATCATA
117422 TTAAGTATAT
Statistics
Matches: 269, Mismatches: 53, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
117 6 0.02
118 199 0.74
119 59 0.22
120 2 0.01
121 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (119 bp):
GGCACTTATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCAC
TGAGTGTGCTAAAATGATAAGGAAATCATACTGAATATATGGATTTACATATAG
Found at i:117546 original size:44 final size:44
Alignment explanation
Indices: 117497--117742 Score: 368
Period size: 44 Copynumber: 5.6 Consensus size: 44
117487 GTACAAATTT
* * * * * *
117497 CTTATGAAATTATAGTAAGTAGATTGATAAAATAAGCTTACAAG
1 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
* *
117541 CTTATGGAATAAAT-GTAAGTATATTGGTAAAATAAGCTTACAAA
1 CTTATGGAAT-AATGGTAAGTATATTGGTAAAATAAGCTTACGAG
117585 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
1 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
* *
117629 CTTATTGAATAATGGTAAGTATATTGGTAAAATAAGCTTATGAG
1 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
117673 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
1 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
* *
117717 CTTATGGATTAATGGTATGTATATTG
1 CTTATGGAATAATGGTAAGTATATTG
117743 ATAAGAAATC
Statistics
Matches: 187, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
43 3 0.02
44 182 0.97
45 2 0.01
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (44 bp):
CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
Found at i:120523 original size:24 final size:24
Alignment explanation
Indices: 120491--120543 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
120481 TTTAACAAAG
120491 TGGAAGACAAACAAGAATCTTTAC
1 TGGAAGACAAACAAGAATCTTTAC
120515 TGGAAGACAAACAAGAATCTTTAC
1 TGGAAGACAAACAAGAATCTTTAC
*
120539 AGGAA
1 TGGAA
120544 ACAGAATGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (24 bp):
TGGAAGACAAACAAGAATCTTTAC
Found at i:132986 original size:20 final size:23
Alignment explanation
Indices: 132937--133006 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 23
132927 AATGTAAAAA
*
132937 ATATAATTCATTAA-ATTTTAT-T
1 ATATAATT-ATTAATATTATATAT
*
132959 GT-TAATTA-TAAT-TTA-ATAT
1 ATATAATTATTAATATTATATAT
132978 ATATAATTATTAATAATTATATAT
1 ATATAATTATTAAT-ATTATATAT
133002 ATATA
1 ATATA
133007 TAATAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
18 2 0.05
19 7 0.18
20 7 0.18
21 9 0.24
22 1 0.03
23 3 0.08
24 9 0.24
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
ATATAATTATTAATATTATATAT
Done.