Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007941.1 Hibiscus syriacus cultivar Beakdansim tig00110357_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: 140088
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:771 original size:91 final size:92
Alignment explanation
Indices: 521--893 Score: 673
Period size: 91 Copynumber: 4.1 Consensus size: 92
511 ATTGCTTAGT
*
521 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGC-GCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
586 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
65 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
614 AATTTGTT-GGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TATTTG
1 AATTTGTTCGGTTGC-GCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
677 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
65 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
705 AATTTGTTCGGTTGC-CCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TATTTGG
1 AATTTGTTCGGTTGCGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTT-G
768 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
65 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
796 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGC-GCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
861 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
65 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
889 AATTT
1 AATTT
894 ATCCATTCAA
Statistics
Matches: 274, Mismatches: 1, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
90 46 0.17
91 86 0.31
92 55 0.20
93 82 0.30
94 5 0.02
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (92 bp):
AATTTGTTCGGTTGCGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGT
CTTTGTTTTGTCTTTTGGTTGAAAGTA
Found at i:977 original size:19 final size:19
Alignment explanation
Indices: 937--1065 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
927 TAGTTTACTT
* *
937 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
957 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
976 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
995 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1009 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1028 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1042 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1061 TCGCA
1 TCGCA
1066 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1016 original size:33 final size:32
Alignment explanation
Indices: 973--1065 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
963 CGCGAAACCA
**
973 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1005 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1038 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1066 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1063 original size:52 final size:52
Alignment explanation
Indices: 937--1065 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
927 TAGTTTACTT
**
937 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
989 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1042 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1066 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1083 original size:19 final size:19
Alignment explanation
Indices: 1061--1194 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1051 GAAACCAAAA
*
1061 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1080 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1096 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1113 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1129 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1146 TCGCGTTGCGA-TTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1164 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1184 TCGTGTTGCGA
1 TCGCGTTGCGA
1195 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
18 16 0.17
19 28 0.30
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1102 original size:14 final size:14
Alignment explanation
Indices: 1083--1139 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1073 TTTCATTTCG
1083 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1097 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1114 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1130 CGTTGCGATT
1 CGTTGCGATT
1140 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1108 original size:33 final size:33
Alignment explanation
Indices: 1066--1194 Score: 168
Period size: 33 Copynumber: 3.8 Consensus size: 33
1056 CAAAATCGCA
1066 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
* *
1099 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
1132 TTGCGATTTTCATTTCGCGTTGCGATTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA-TT-CTTT--CG
* *
1169 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
1195 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 55 0.65
34 2 0.02
35 2 0.02
37 13 0.15
38 12 0.14
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:3093 original size:14 final size:14
Alignment explanation
Indices: 3074--3109 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3064 ATTGTTTAAT
3074 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3088 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3102 TGATTTGT
1 TGATTTGT
3110 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3284 original size:20 final size:19
Alignment explanation
Indices: 3216--3298 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
3206 AAAAATGACT
3216 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3235 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3249 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3268 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3288 ATCGCAATGCG
1 ATCGCAATGCG
3299 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3351 original size:19 final size:19
Alignment explanation
Indices: 3327--3598 Score: 336
Period size: 19 Copynumber: 15.4 Consensus size: 19
3317 GATTATCTCG
3327 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3346 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3365 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3379 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3398 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3417 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3436 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3454 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3473 -TGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3486 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3505 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3524 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3538 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3558 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
3572 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3591 TTGCGATT
1 TTGCGATT
3599 GTATTTTCCG
Statistics
Matches: 222, Mismatches: 8, Indels: 46
0.80 0.03 0.17
Matches are distributed among these distances:
14 28 0.13
15 4 0.02
16 23 0.10
17 18 0.08
18 25 0.11
19 112 0.50
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3367 original size:52 final size:52
Alignment explanation
Indices: 3305--3570 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
3295 TGCGTTTATA
*
3305 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3357 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3409 ATTTCGCATTGCGATTTCCATTTCGCATTGCGA-TTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
3465 ATTTCGCA-TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
3516 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
3569 AT
1 AT
3571 GTTGGGATTT
Statistics
Matches: 203, Mismatches: 3, Indels: 15
0.92 0.01 0.07
Matches are distributed among these distances:
50 6 0.03
51 31 0.15
52 96 0.47
53 20 0.10
54 3 0.01
55 10 0.05
56 31 0.15
57 6 0.03
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:3561 original size:34 final size:33
Alignment explanation
Indices: 3305--3598 Score: 155
Period size: 33 Copynumber: 8.5 Consensus size: 33
3295 TGCGTTTATA
*
3305 ATTTCGCATTGCGATTATC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCAT-GTTGCGATTTTC
*
3338 ATTTCGCATTGCGATTTTCAT-TT-CGCATTGCGATTC
1 ATTTCGCATTGCGATTCTCATGTTGCG-ATT----TTC
*
3374 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCA--T-G--TTGCGATTTTC
3409 ATTTCGCATTGCGATT-TCCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGATTCT-CA--T-G--TTGCGATTTTC
* *
3446 ATTTCGCATTGCGATTTTCAT-TT-CGCA--TGC
1 ATTTCGCATTGCGATTCTCATGTTGCG-ATTTTC
* * *
3476 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 -ATT-TCGCATTGCGATTCTCA--T-G--TTGCGATTTTC
3516 ATTTCGCATTGCGATTCTC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCAT-GTTGCGATTTTC
* *
3549 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTCATGTTGCGATTTTC
*
3583 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
3599 GTATTTTCCG
Statistics
Matches: 218, Mismatches: 11, Indels: 64
0.74 0.04 0.22
Matches are distributed among these distances:
30 4 0.02
31 8 0.04
32 20 0.09
33 56 0.26
34 31 0.14
35 14 0.06
36 8 0.04
37 23 0.11
38 40 0.18
39 10 0.05
40 4 0.02
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCATGTTGCGATTTTC
Found at i:5891 original size:12 final size:12
Alignment explanation
Indices: 5874--5898 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5864 TCTTCGGGGA
5874 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5886 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5898 C
1 C
5899 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:6106 original size:24 final size:24
Alignment explanation
Indices: 6072--6118 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6062 CTGAAACATC
6072 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
6096 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
6119 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:6822 original size:20 final size:20
Alignment explanation
Indices: 6794--7183 Score: 457
Period size: 20 Copynumber: 19.4 Consensus size: 20
6784 AAATTTCAGT
* * * *
6794 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6814 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
6834 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6854 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6874 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6894 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6914 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6934 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6954 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6974 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
6994 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
7014 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
7035 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7055 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
7075 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
7095 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
7115 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
7135 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
7155 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
7175 GTTGCGATT
1 GTTGCGATT
7184 ATTGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 295 0.91
21 19 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:8227 original size:14 final size:14
Alignment explanation
Indices: 8208--8234 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8198 AATATAAAAT
8208 TATTTTTTAAATTG
1 TATTTTTTAAATTG
8222 TATTTTTTAAATT
1 TATTTTTTAAATT
8235 TATAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (14 bp):
TATTTTTTAAATTG
Found at i:8248 original size:23 final size:23
Alignment explanation
Indices: 8222--8265 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
8212 TTTTAAATTG
8222 TATTTTTTAAATTTATAATTTAT
1 TATTTTTTAAATTTATAATTTAT
*
8245 TATTTTTTAAATTTGTAATTT
1 TATTTTTTAAATTTATAATTT
8266 TATGACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TATTTTTTAAATTTATAATTTAT
Found at i:8275 original size:23 final size:23
Alignment explanation
Indices: 8226--8276 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
8216 AAATTGTATT
* *
8226 TTTTAAATTTATAATTTATTATT
1 TTTTAAATTTATAATTTATGATC
*
8249 TTTTAAATTTGTAATTTTATGA-C
1 TTTTAAATTTATAA-TTTATGATC
8272 TTTTA
1 TTTTA
8277 TTTATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTAAATTTATAATTTATGATC
Found at i:18154 original size:42 final size:41
Alignment explanation
Indices: 18106--18199 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
18096 GTTGCGATAG
18106 TGGAAAATCGCAACAACAACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAAC-ACAACTGTCA-ACTATCGCAACGCGAAA
* * * *
18148 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACACAACTGTCAACTATCGCAACGCGAAA
18189 TGGAAAATCGC
1 TGGAAAATCGC
18200 TTGAAAATCG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
41 32 0.68
42 15 0.32
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACACAACTGTCAACTATCGCAACGCGAAA
Found at i:18159 original size:20 final size:20
Alignment explanation
Indices: 18134--18199 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
18124 ACTGTAGACT
18134 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
18154 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
18175 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
18195 ATCGC
1 ATCGC
18200 TTGAAAATCG
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:18232 original size:20 final size:20
Alignment explanation
Indices: 18207--18279 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
18197 CGCTTGAAAA
*
18207 TCGCGTTGCGGTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
18227 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
18248 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
18268 TCGCGTTGCGAT
1 TCGCGTTGCGAT
18280 AATTGAAAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:18253 original size:21 final size:21
Alignment explanation
Indices: 18227--18291 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
18217 GTTTTCCATT
*
18227 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
* ** **
18248 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAATTGAAAA
18268 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
18289 TCG
1 TCG
18292 TTTTTCCATT
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:18257 original size:41 final size:40
Alignment explanation
Indices: 18200--18332 Score: 188
Period size: 41 Copynumber: 3.4 Consensus size: 40
18190 GGAAAATCGC
18200 TTGAAAATCGCGTTGCGGTTTTCCATTTCGCGTTGCGATAG
1 TTGAAAATCGCGTTGC-GTTTTCCATTTCGCGTTGCGATAG
*
18241 TTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAA
1 TTGAAAATCGCGTTGCG-TTTTCCATTTCGCGTTGCGATAG
*
18282 TTGAAAAT--CG-T---TTTTCCATTTCACGTTGCGATAG
1 TTGAAAATCGCGTTGCGTTTTCCATTTCGCGTTGCGATAG
18316 TTGAAAATCGCGTTGCG
1 TTGAAAATCGCGTTGCG
18333 ATAGTCTATA
Statistics
Matches: 82, Mismatches: 3, Indels: 15
0.82 0.03 0.15
Matches are distributed among these distances:
34 29 0.35
36 2 0.02
37 1 0.01
38 1 0.01
39 2 0.02
40 1 0.01
41 46 0.56
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (40 bp):
TTGAAAATCGCGTTGCGTTTTCCATTTCGCGTTGCGATAG
Found at i:18302 original size:34 final size:34
Alignment explanation
Indices: 18259--18325 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
18249 CGCGTTGCGA
*
18259 TTTTCCATTTCGCGTTGCGATAATTGAAAATCGT
1 TTTTCCATTTCACGTTGCGATAATTGAAAATCGT
*
18293 TTTTCCATTTCACGTTGCGATAGTTGAAAATCG
1 TTTTCCATTTCACGTTGCGATAATTGAAAATCG
18326 CGTTGCGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (34 bp):
TTTTCCATTTCACGTTGCGATAATTGAAAATCGT
Found at i:18372 original size:41 final size:41
Alignment explanation
Indices: 18326--18415 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 41
18316 TTGAAAATCG
* *
18326 CGTTGCGATAGTCTATAGTTGTCGTTGCAATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTCGCAATTTTCCAAATT
* *
18367 CGTTGCGATAGTCTACAGTTGTTGTCGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTCGCAATTTTCCAAATT
18408 CGTTGCGA
1 CGTTGCGA
18416 AAATTCGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTCGCAATTTTCCAAATT
Found at i:19018 original size:6 final size:6
Alignment explanation
Indices: 19009--19058 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
18999 GCCGTCCGTC
19009 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
19057 TC
1 TC
19059 ATACGTGTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.00, C:0.18, G:0.48, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:19201 original size:20 final size:20
Alignment explanation
Indices: 19176--19272 Score: 113
Period size: 20 Copynumber: 4.8 Consensus size: 20
19166 ACTGTAGACT
19176 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
19196 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
19217 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
*
19237 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
*
19257 ATCACAACGCGAAATG
1 ATCGCAACGCGAAATG
19273 CAACGCGAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
20 48 0.76
21 15 0.24
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:19701 original size:25 final size:25
Alignment explanation
Indices: 19664--19716 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
19654 GCAGTAGTTC
*
19664 ATCATTCAGATGGAAAAGAACTGGT
1 ATCATTCAAATGGAAAAGAACTGGT
19689 ATCATTCAAATGGAAAAGAACTGGT
1 ATCATTCAAATGGAAAAGAACTGGT
19714 ATC
1 ATC
19717 CTAATAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.25
Consensus pattern (25 bp):
ATCATTCAAATGGAAAAGAACTGGT
Found at i:20409 original size:21 final size:21
Alignment explanation
Indices: 20379--20431 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
20369 ACTGTGATTG
*
20379 CGACCGTCGCGAGCGCTATTA
1 CGACCGTCGCGAGAGCTATTA
* *
20400 CGACCTTCGCGAGAGCTATTG
1 CGACCGTCGCGAGAGCTATTA
*
20421 CGGCCGTCGCG
1 CGACCGTCGCG
20432 GTAACTAGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.15, C:0.34, G:0.32, T:0.19
Consensus pattern (21 bp):
CGACCGTCGCGAGAGCTATTA
Found at i:23272 original size:21 final size:21
Alignment explanation
Indices: 23248--23308 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
23238 CCAACTTTGA
23248 AAATGGTTTTTAAAGTTTGGT
1 AAATGGTTTTTAAAGTTTGGT
*
23269 AAAT-G-TTTT----TTT-GA
1 AAATGGTTTTTAAAGTTTGGT
*
23283 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTTAAAGTTTGGT
23304 AAATG
1 AAATG
23309 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 3 0.10
19 4 0.13
20 4 0.13
21 10 0.33
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (21 bp):
AAATGGTTTTTAAAGTTTGGT
Found at i:23329 original size:36 final size:36
Alignment explanation
Indices: 23243--23391 Score: 207
Period size: 36 Copynumber: 4.2 Consensus size: 36
23233 GACAACCAAC
23243 TTTG-AAAATGGTTTTT-AAAGTTTGGTAAATGTTTT
1 TTTGAAAAAT-GTTTTTCAAAGTTTGGTAAATGTTTT
* *
23278 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTTT
* *
23313 TTTGAAAAATATTTTTCAAAGTTTGGTAAATATTTT
1 TTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTTT
*
23349 TTTGAAAAATGTTTTTCAAAGTTTGGTAGATG-TTT
1 TTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTTT
*
23384 GTTGAAAA
1 TTTGAAAA
23392 TAGGAATGAG
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
34 5 0.05
35 41 0.40
36 56 0.55
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.48
Consensus pattern (36 bp):
TTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTTT
Found at i:23338 original size:71 final size:70
Alignment explanation
Indices: 23254--23391 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 70
23244 TTGAAAATGG
* *
23254 TTTTTAAAGTTTGGTAAATGTTTTTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 TTTTTAAAGTTTGGTAAATATTTTTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT-GTTGA
23318 AAAATA
65 AAAATA
* *
23324 TTTTTCAAAGTTTGGTAAATATTTTTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTTGTTGA
1 TTTTT-AAAGTTTGGTAAATATTTTTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTGTTGA
23389 AAA
65 AAA
23392 TAGGAATGAG
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 5 0.08
71 29 0.47
72 28 0.45
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (70 bp):
TTTTTAAAGTTTGGTAAATATTTTTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTGTTGAA
AAATA
Found at i:24612 original size:15 final size:15
Alignment explanation
Indices: 24588--24619 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
24578 AGGCAGATCG
*
24588 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
24603 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
24618 AA
1 AA
24620 GAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:27593 original size:21 final size:21
Alignment explanation
Indices: 27569--27629 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
27559 CCATCTTTGA
27569 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
27590 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
27604 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
27625 AAATG
1 AAATG
27630 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:27650 original size:36 final size:35
Alignment explanation
Indices: 27562--27667 Score: 187
Period size: 35 Copynumber: 3.0 Consensus size: 35
27552 TTGGCAACCA
27562 TCTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTT
1 TCTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTT
27597 TCTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTT
1 TCTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTT
*
27632 TCTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTT
1 TCTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTT
27667 T
1 T
27668 GGTAGATGTT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
35 45 0.65
36 24 0.35
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (35 bp):
TCTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTT
Found at i:29031 original size:16 final size:16
Alignment explanation
Indices: 29006--29036 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28996 CTTCTAATTT
*
29006 TTTTTTGAGTTCAAGC
1 TTTTTCGAGTTCAAGC
29022 TTTTTCGAGTTCAAG
1 TTTTTCGAGTTCAAG
29037 TTTCAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCAAGC
Found at i:30006 original size:31 final size:31
Alignment explanation
Indices: 29968--30061 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
29958 CCCGAAGGAC
* * *
29968 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
29999 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
30030 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
30061 C
1 C
30062 CCTCGACCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:38690 original size:6 final size:6
Alignment explanation
Indices: 38680--38712 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
38670 ACTGCTATCA
*
38680 TCACTA TCACTC TCACTC TCACTC TCACTC TCA
1 TCACTC TCACTC TCACTC TCACTC TCACTC TCA
38713 TCCACTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.33
Consensus pattern (6 bp):
TCACTC
Found at i:40433 original size:21 final size:20
Alignment explanation
Indices: 40403--40442 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40393 TTCCTAGATT
* *
40403 AATTATTTTTTTTATAAAAAC
1 AATTAATTTTATTA-AAAAAC
40424 AATTAATTTTATTAAAAAA
1 AATTAATTTTATTAAAAAA
40443 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTAATTTTATTAAAAAAC
Found at i:40446 original size:17 final size:18
Alignment explanation
Indices: 40412--40446 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40402 TAATTATTTT
40412 TTTTATAAAAACAATTAA
1 TTTTATAAAAACAATTAA
*
40430 TTTTATTAAAA-AATTAA
1 TTTTATAAAAACAATTAA
40447 AAAATATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTTATAAAAACAATTAA
Found at i:49131 original size:2 final size:2
Alignment explanation
Indices: 49124--49155 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49114 GAACGATTTA
49124 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
49156 GTGGAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50557 original size:184 final size:181
Alignment explanation
Indices: 50238--50602 Score: 696
Period size: 184 Copynumber: 2.0 Consensus size: 181
50228 TTTTTTTCGG
50238 TCATAATTGGTAGTCAATTGTCACTTATCACTAATCTTCATTTGCATCAAGATTAACACTAAAAT
1 TCATAATTGGTAGTCAATTGTCACTTATCACTAATCTTCATTTGCATCAAGATTAACACTAAAAT
50303 TTTTACATTTTACTCTTATTTTTTTCACGTGATTGAATTTTTATGAGACTAACTCAAAATCAACA
66 TTTTACATTTTACTCTTATTTTTTTCACGTGATTGAATTTTTATGAGACTAACTCAAAATCAAC-
50368 AAAAATTAATCTAAAGGTTCAACATGTCAATAATTTGGTCTCCTCCAATGATTT
130 AAAAA--AATCTAAAGGTTCAACATGTCAATAATTTGGTCTCCTCCAATGATTT
50422 TCATAATTGGTAGTCAATTGTCACTTATCACTAATCTTCATTTGCATCAAGATTAACACTAAAAT
1 TCATAATTGGTAGTCAATTGTCACTTATCACTAATCTTCATTTGCATCAAGATTAACACTAAAAT
50487 TTTTACATTTTACTCTTA-TTTTTTCACGTGATTGAATTTTTATGAGACTAACTCAAAATCAACA
66 TTTTACATTTTACTCTTATTTTTTTCACGTGATTGAATTTTTATGAGACTAACTCAAAATCAACA
50551 AAAAAATCTAAAGGTTCAACATGTCAATAATTTGGTCTCCTCCAATGATTT
131 AAAAAATCTAAAGGTTCAACATGTCAATAATTTGGTCTCCTCCAATGATTT
50602 T
1 T
50603 GACGATGCTA
Statistics
Matches: 181, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
180 48 0.27
182 5 0.03
183 45 0.25
184 83 0.46
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.39
Consensus pattern (181 bp):
TCATAATTGGTAGTCAATTGTCACTTATCACTAATCTTCATTTGCATCAAGATTAACACTAAAAT
TTTTACATTTTACTCTTATTTTTTTCACGTGATTGAATTTTTATGAGACTAACTCAAAATCAACA
AAAAAATCTAAAGGTTCAACATGTCAATAATTTGGTCTCCTCCAATGATTT
Found at i:51269 original size:51 final size:50
Alignment explanation
Indices: 51154--51272 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 50
51144 ATGTATATAT
* * * *
51154 TTACATCGGTGTAAGTATTTATTAAGTAATACATTATTTATTTTATTTAC
1 TTACACCGGTGTAAGTATTTATTAAGTAATACATTATTTATTTTACTAAA
* * * * *
51204 TTACACTGGCGTAAGTATTTATTAAGTGATACGTTTTTTTATTTTACTAAA
1 TTACACCGGTGTAAGTATTTATTAAGTAATAC-ATTATTTATTTTACTAAA
*
51255 TTACACCGATGTAAGTAT
1 TTACACCGGTGTAAGTAT
51273 ATGTTTTGTG
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
50 28 0.50
51 28 0.50
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (50 bp):
TTACACCGGTGTAAGTATTTATTAAGTAATACATTATTTATTTTACTAAA
Found at i:51948 original size:15 final size:17
Alignment explanation
Indices: 51928--51967 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
51918 TTATATATGA
51928 ATTATA-ATAAATCA-T
1 ATTATATATAAATCACT
*
51943 ATTATATATAACTCACT
1 ATTATATATAAATCACT
51960 ATTA-ATAT
1 ATTATATAT
51968 TTTAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTATATATAAATCACT
Found at i:62610 original size:21 final size:21
Alignment explanation
Indices: 62584--62623 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
62574 CAGAACCCCA
*
62584 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
62605 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
62624 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:66500 original size:22 final size:21
Alignment explanation
Indices: 66457--66496 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
66447 GAGTTTGTTT
*
66457 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
66478 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
66497 ACATTTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:72953 original size:77 final size:78
Alignment explanation
Indices: 72816--72962 Score: 208
Period size: 77 Copynumber: 1.9 Consensus size: 78
72806 CTTTAGTAAC
* * *
72816 ATTTTAGGGGTAATCCATTTTATTAATAAAAAATATTAACATTCCAGATCGCAACCTATTTCTTA
1 ATTTTAGGGATAACCCATTTTATTAATAAAAAATATTAACATTCAAGATCGCAACCTATTTCTTA
72881 ATGAATCATGATA
66 ATGAATCATGATA
* * *
72894 ATTTTAGGTATAACCCATTTTATTAAT-AAAAATATTAACATTCTAAGA-CGTAACTTATTTCTT
1 ATTTTAGGGATAACCCATTTTATTAATAAAAAATATTAACATTC-AAGATCGCAACCTATTTCTT
*
72957 AGTGAA
65 AATGAA
72963 CTATGACATT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
77 34 0.56
78 27 0.44
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (78 bp):
ATTTTAGGGATAACCCATTTTATTAATAAAAAATATTAACATTCAAGATCGCAACCTATTTCTTA
ATGAATCATGATA
Found at i:77530 original size:22 final size:21
Alignment explanation
Indices: 77505--77567 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
77495 ACAAATCACA
*
77505 ATTTGATAATTTTAAAAAATTT
1 ATTT-ATAATTTTAAAAAAATT
*
77527 ATTTAAAATTTTAAAAAAAATT
1 ATTTATAATTTT-AAAAAAATT
77549 ATTTAT-ATTTTAAAAAAAT
1 ATTTATAATTTTAAAAAAAT
77568 ATAAAATTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 8 0.22
21 12 0.32
22 17 0.46
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTTATAATTTTAAAAAAATT
Found at i:77537 original size:21 final size:20
Alignment explanation
Indices: 77512--77567 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
77502 ACAATTTGAT
*
77512 AATTTTAAAAAATTTATTTAA
1 AATTTTAAAAAAATTATTT-A
77533 AATTTTAAAAAAAATTATTTA
1 AATTTT-AAAAAAATTATTTA
*
77554 TATTTTAAAAAAAT
1 AATTTTAAAAAAAT
77568 ATAAAATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 8 0.25
21 12 0.38
22 12 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTTAAAAAAATTATTTA
Found at i:81736 original size:10 final size:10
Alignment explanation
Indices: 81721--81752 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
81711 AATTTAATTC
81721 AATAAATATA
1 AATAAATATA
81731 AATAAATATA
1 AATAAATATA
81741 AATAAATATA
1 AATAAATATA
81751 AA
1 AA
81753 ATTTAGTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAAATATA
Found at i:83766 original size:22 final size:20
Alignment explanation
Indices: 83722--83766 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
83712 ATTATTTGAG
83722 TAAA-TTATTGAATGCTGAA
1 TAAATTTATTGAATGCTGAA
83741 -AAATTTATTAGAATGCTGAA
1 TAAATTTATT-GAATGCTGAA
83761 TTAAAT
1 -TAAAT
83767 ATTGAGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.14
19 5 0.23
20 10 0.45
22 4 0.18
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.38
Consensus pattern (20 bp):
TAAATTTATTGAATGCTGAA
Found at i:84606 original size:36 final size:36
Alignment explanation
Indices: 84560--84662 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
84550 AGTTGAGTAT
* *
84560 TATCAACTTTGATACATTCATGTATCAATGTTATCA
1 TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
* * *
84596 TATTAGCTTTGGTACATTCGTATATCAATGTTATCA
1 TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
84632 TATCAACTTTGGTACATTCGTGTATCAATGT
1 TATCAACTTTGGTACATTCGTGTATCAATGT
84663 CTAGCACTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (36 bp):
TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:92370 original size:18 final size:18
Alignment explanation
Indices: 92349--92390 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
92339 ATATTCATTA
92349 AGATTAAGCCATTCTATT
1 AGATTAAGCCATTCTATT
92367 AGATTAAGCCATTCTATT
1 AGATTAAGCCATTCTATT
92385 AGATTA
1 AGATTA
92391 TGAGAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (18 bp):
AGATTAAGCCATTCTATT
Found at i:93681 original size:27 final size:27
Alignment explanation
Indices: 93643--93699 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
93633 AGGTGGAACA
93643 TCTTCTCAAAAGCATCTGCTTGTAAGC
1 TCTTCTCAAAAGCATCTGCTTGTAAGC
93670 TCTTCTCAAAAGCATCTGCTTGTAAGC
1 TCTTCTCAAAAGCATCTGCTTGTAAGC
93697 TCT
1 TCT
93700 CGGATAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (27 bp):
TCTTCTCAAAAGCATCTGCTTGTAAGC
Found at i:102486 original size:221 final size:224
Alignment explanation
Indices: 102085--102530 Score: 798
Period size: 221 Copynumber: 2.0 Consensus size: 224
102075 CTACGAGTTT
102085 AACTTCTTCTTTACATATTATGTCAGTACCGGAATTTTTTAAATCCATGACTTATATTTCTTAAA
1 AACTTCTTCTTTACATATTATGTCAGTACCGGAATTTTTTAAATCCATGACTTATATTTCTTAAA
*
102150 TAATATAATATTTTAATCCTACTTGGAATTTAAAATCGAACAACACCACCTCTCTATGTTTGTTT
66 TAATATAATATTTTAATCCTACTTGGAATTTAAAATCGAACAACACCACCTCTATATGTTTGTTT
102215 CTCTTGGTCTCTATTTGGGTGCTGAAACTCCCACTTGTCACAGGCGTTGTTTAGATTTTGTGTGT
131 CTCTTGGTCTCTATTTGGGTGCTGAAACTCCCACTTGTCACAGGCGTTGTTTAGATTTTGTGTGT
102280 TCACTTTCTTTGTTTTTCTCTTGTTTGTTCC
196 TCACTTTCTTTG--TTTCTCTTGTTTGTTCC
102311 AACTTCTTCTTTACATATTATGTCAGTTACCGGAA-TTTTTAAATCCATGACTTATATTTCTTAA
1 AACTTCTTCTTTACATATTATGTCAG-TACCGGAATTTTTTAAATCCATGACTTATATTTCTTAA
102375 AT-A-AT-ATATTTT-ATCCTACTTGGAATTTAAAAATCGAACAACACCACCTCTAT-TG-TTGT
65 ATAATATAATATTTTAATCCTACTTGGAATTT-AAAATCGAACAACACCACCTCTATATGTTTGT
102434 TTCTCTTGGTCTCTATTTGGGTGCTGAAACTCCCACTTGTCACAGGCGTTGTTTAGATTTTGTGT
129 TTCTCTTGGTCTCTATTTGGGTGCTGAAACTCCCACTTGTCACAGGCGTTGTTTAGATTTTGTGT
102499 GTTCACTTTCTTTGTTTCTCTTGTTTGTTCC
194 GTTCACTTTCTTTGTTTCTCTTGTTTGTTCC
102530 A
1 A
102531 TGCGCTCCAT
Statistics
Matches: 217, Mismatches: 1, Indels: 11
0.95 0.00 0.05
Matches are distributed among these distances:
219 18 0.08
221 83 0.38
222 18 0.08
223 30 0.14
224 2 0.01
225 1 0.00
226 57 0.26
227 8 0.04
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (224 bp):
AACTTCTTCTTTACATATTATGTCAGTACCGGAATTTTTTAAATCCATGACTTATATTTCTTAAA
TAATATAATATTTTAATCCTACTTGGAATTTAAAATCGAACAACACCACCTCTATATGTTTGTTT
CTCTTGGTCTCTATTTGGGTGCTGAAACTCCCACTTGTCACAGGCGTTGTTTAGATTTTGTGTGT
TCACTTTCTTTGTTTCTCTTGTTTGTTCC
Found at i:107623 original size:22 final size:22
Alignment explanation
Indices: 107577--107623 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
107567 CAATAGCCAA
*
107577 ATAAAGAAAAGTGTGGGGTCCT
1 ATAAAGAAAAGTGTGGGGTCAT
*
107599 ATAAAGAAAAGTGTGGGGTTAT
1 ATAAAGAAAAGTGTGGGGTCAT
107621 ATA
1 ATA
107624 TACTCTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.30, T:0.26
Consensus pattern (22 bp):
ATAAAGAAAAGTGTGGGGTCAT
Found at i:107659 original size:90 final size:85
Alignment explanation
Indices: 107504--107678 Score: 296
Period size: 90 Copynumber: 2.0 Consensus size: 85
107494 GGAATGCGAG
107504 GTGGGGTCCTATAAAGAAAAGTGTGGGTTTATATCTTTAAGAAACAATAAAATATCTTAAACTCA
1 GTGGGGTCCTATAAAGAAAAGTGTGGGTTTATATCTTTAAGAAACAATAAAATATCTTAAACTCA
107569 ATAGCCAAATAAAGAAAAGT
66 ATAGCCAAATAAAGAAAAGT
107589 GTGGGGTCCTATAAAGAAAAGTGTGGGGTTATATATACTCTTTAAGAAACAATAAAATATCTTAA
1 GTGGGGTCCTATAAAGAAAAGTGT-GGG-T-T-TATA-TCTTTAAGAAACAATAAAATATCTTAA
*
107654 ACTCAATAGCCAAATAAAGCAAAGT
61 ACTCAATAGCCAAATAAAGAAAAGT
107679 TCCTAAGAAG
Statistics
Matches: 84, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
85 24 0.29
86 3 0.04
87 1 0.01
88 1 0.01
89 4 0.05
90 51 0.61
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (85 bp):
GTGGGGTCCTATAAAGAAAAGTGTGGGTTTATATCTTTAAGAAACAATAAAATATCTTAAACTCA
ATAGCCAAATAAAGAAAAGT
Found at i:109129 original size:35 final size:35
Alignment explanation
Indices: 109074--109144 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
109064 TTGTATTAAA
* *
109074 AGTAAAAAATATCCAGAATTATAATAAAGAATTAC
1 AGTAAAAAATATCCAAAATTACAATAAAGAATTAC
* *
109109 AGTATAAAATATCCAAAATTACAATAAAGATTTAC
1 AGTAAAAAATATCCAAAATTACAATAAAGAATTAC
109144 A
1 A
109145 AATATAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (35 bp):
AGTAAAAAATATCCAAAATTACAATAAAGAATTAC
Found at i:110762 original size:14 final size:13
Alignment explanation
Indices: 110743--110776 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
110733 GGAAGGGAAG
110743 TTCTTTTTTTCTT
1 TTCTTTTTTTCTT
*
110756 CTTCTTTATTTCTT
1 -TTCTTTTTTTCTT
110770 TTCTTTT
1 TTCTTTT
110777 CATGTTGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:112423 original size:10 final size:10
Alignment explanation
Indices: 112399--112436 Score: 53
Period size: 9 Copynumber: 3.9 Consensus size: 10
112389 GGCTGCTGGA
112399 AACCGGTTT-
1 AACCGGTTTC
112408 AACCGGTTTC
1 AACCGGTTTC
112418 AACCGG-TTC
1 AACCGGTTTC
112427 GAACCGGTTT
1 -AACCGGTTT
112437 GACCGGTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 12 0.46
10 12 0.46
11 2 0.08
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (10 bp):
AACCGGTTTC
Found at i:112441 original size:19 final size:20
Alignment explanation
Indices: 112400--112466 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
112390 GCTGCTGGAA
*
112400 ACCGGTT-T-AACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
112419 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
*
112438 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
112457 ACCGG-TCTGA
1 ACCGGTTCTGA
112467 CCCGACCCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.05
19 32 0.74
20 9 0.21
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:112475 original size:5 final size:5
Alignment explanation
Indices: 112465--112517 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
112455 TGACCGGTCT
* *
112465 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
112514 GACC
1 GACC
112518 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:112486 original size:17 final size:17
Alignment explanation
Indices: 112464--112524 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
112454 TTGACCGGTC
112464 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
112481 TGACCCGACCCGACCCGACCGT
1 T-----GACCCGACCCGACCGT
112503 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
112520 TGACC
1 TGACC
112525 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 22 0.56
22 17 0.44
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:112491 original size:22 final size:22
Alignment explanation
Indices: 112465--112531 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
112455 TGACCGGTCT
112465 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
112487 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
112509 GACCCGACCGTTGACCGTTGACC
1 GACCCGACC--CGACCGTTGACC
112532 GTTGACCGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.18, C:0.46, G:0.24, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:112524 original size:7 final size:7
Alignment explanation
Indices: 112514--112544 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
112504 GACCCGACCC
112514 GACCGTT
1 GACCGTT
112521 GACCGTT
1 GACCGTT
112528 GACCGTT
1 GACCGTT
112535 GACCGTT
1 GACCGTT
112542 GAC
1 GAC
112545 TATTGACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:119727 original size:20 final size:21
Alignment explanation
Indices: 119702--119740 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
119692 GGCTGCTGGA
119702 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
119722 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
119741 GATCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:119738 original size:10 final size:9
Alignment explanation
Indices: 119703--119801 Score: 72
Period size: 10 Copynumber: 10.3 Consensus size: 9
119693 GCTGCTGGAA
*
119703 ACCGGTTTA
1 ACCGGTTTG
*
119712 ACCGGTTTTCA
1 ACCGG-TTT-G
119723 ACCGGTTCTG
1 ACCGGTT-TG
119733 ACCGGTTTG
1 ACCGGTTTG
* *
119742 ATCGGTTTCA
1 ACCGGTTT-G
*
119752 ACCGGTTCG
1 ACCGGTTTG
119761 AACCGGTTTG
1 -ACCGGTTTG
*
119771 ACCGGTCTG
1 ACCGGTTTG
*
119780 AATCGGTTTG
1 -ACCGGTTTG
*
119790 ACCGGTCTG
1 ACCGGTTTG
119799 ACC
1 ACC
119802 CGACCCGACC
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
9 32 0.44
10 33 0.46
11 7 0.10
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:119765 original size:29 final size:30
Alignment explanation
Indices: 119702--119801 Score: 109
Period size: 29 Copynumber: 3.4 Consensus size: 30
119692 GGCTGCTGGA
*
119702 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
*
119733 -ACCGGTTTGATCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
119761 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
119790 -ACCGGTCTGACC
1 AACCGGTTTGACC
119802 CGACCCGACC
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
28 12 0.20
29 36 0.60
30 12 0.20
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:119774 original size:19 final size:19
Alignment explanation
Indices: 119702--119795 Score: 77
Period size: 19 Copynumber: 4.8 Consensus size: 19
119692 GGCTGCTGGA
*
119702 AACCGGTTTAACCGGTTTTC-
1 AACCGGTTTGACCGG--TTCG
*
119722 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTTCG
* *
119742 -ATCGGTTTCAACCGGTTCG
1 AACCGGTTT-GACCGGTTCG
119761 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
119780 AATCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
119796 CTGACCCGAC
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
18 3 0.05
19 36 0.60
20 15 0.25
21 6 0.10
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:119796 original size:19 final size:19
Alignment explanation
Indices: 119725--119799 Score: 82
Period size: 19 Copynumber: 3.9 Consensus size: 19
119715 GGTTTTCAAC
*
119725 CGGTTCTGACCGGTTTG-AT
1 CGGTT-TGACCGGTCTGAAT
* *
119744 CGGTTTCAACCGGT-TCGAAC
1 CGGTTT-GACCGGTCT-GAAT
119764 CGGTTTGACCGGTCTGAAT
1 CGGTTTGACCGGTCTGAAT
119783 CGGTTTGACCGGTCTGA
1 CGGTTTGACCGGTCTGA
119800 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.04
19 38 0.79
20 8 0.17
ACGTcount: A:0.15, C:0.24, G:0.31, T:0.31
Consensus pattern (19 bp):
CGGTTTGACCGGTCTGAAT
Found at i:119808 original size:5 final size:5
Alignment explanation
Indices: 119798--119855 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
119788 TGACCGGTCT
* *
119798 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
119847 GACCC GACC
1 GACCC GACC
119856 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:119824 original size:22 final size:22
Alignment explanation
Indices: 119798--119862 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
119788 TGACCGGTCT
119798 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
119820 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
119842 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
119863 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:119864 original size:7 final size:7
Alignment explanation
Indices: 119852--119882 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
119842 GACCCGACCC
119852 GACCGTT
1 GACCGTT
119859 GACCGTT
1 GACCGTT
119866 GACCGTT
1 GACCGTT
*
119873 GACCATT
1 GACCGTT
119880 GAC
1 GAC
119883 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:129489 original size:22 final size:21
Alignment explanation
Indices: 129460--129508 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
129450 AGAAAAAATA
*
129460 TGAATTCGTCAATTTCGCAAC
1 TGAATTCGCCAATTTCGCAAC
*
129481 TCGAATTCGCCAATTTCGTAAC
1 T-GAATTCGCCAATTTCGCAAC
129503 TGAATT
1 TGAATT
129509 ACCGATATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (21 bp):
TGAATTCGCCAATTTCGCAAC
Found at i:129767 original size:22 final size:22
Alignment explanation
Indices: 129738--129821 Score: 125
Period size: 22 Copynumber: 3.9 Consensus size: 22
129728 CTATACTGGT
129738 AATT-GAGTTGCGAATTTGGCG
1 AATTCGAGTTGCGAATTTGGCG
129759 AATTCGAGTTGCGAATTTGGCG
1 AATTCGAGTTGCGAATTTGGCG
* * *
129781 AATTCGAGTTACGAAATTGACG
1 AATTCGAGTTGCGAATTTGGCG
*
129803 AATTCGCGTTGCGAATTTG
1 AATTCGAGTTGCGAATTTG
129822 AAAACTGTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
21 4 0.07
22 52 0.93
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (22 bp):
AATTCGAGTTGCGAATTTGGCG
Found at i:130202 original size:24 final size:25
Alignment explanation
Indices: 130151--130210 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
130141 ATTTTTTATT
*
130151 AATTTTTTAATTTCATAATTCTTAA
1 AATTTTTTAATTTCACAATTCTTAA
* *
130176 AATTTTATAATTTCACACTTCTT-A
1 AATTTTTTAATTTCACAATTCTTAA
130200 AATTTTTTAAT
1 AATTTTTTAAT
130211 ATAATTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (25 bp):
AATTTTTTAATTTCACAATTCTTAA
Found at i:135261 original size:24 final size:25
Alignment explanation
Indices: 135191--135289 Score: 96
Period size: 24 Copynumber: 4.0 Consensus size: 25
135181 CACAATAAGT
*
135191 AGTCATAATTGCTTAAATTGAACGC
1 AGTCATAATTGCTAAAATTGAACGC
* * * * *
135216 AGACGTAACTACTAAAATTGAACAC
1 AGTCATAATTGCTAAAATTGAACGC
*
135241 AGTCATAATTGC-AAAATTGAACGT
1 AGTCATAATTGCTAAAATTGAACGC
*
135265 AGTCATAACTT-C-AAAACTGAACGC
1 AGTCATAA-TTGCTAAAATTGAACGC
135289 A
1 A
135290 CCCTTGGTGA
Statistics
Matches: 59, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
24 30 0.51
25 29 0.49
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.25
Consensus pattern (25 bp):
AGTCATAATTGCTAAAATTGAACGC
Found at i:136876 original size:13 final size:13
Alignment explanation
Indices: 136854--136885 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
136844 ATTCTTAATC
136854 CAAC-TTAAAATT
1 CAACATTAAAATT
136866 CAACATTAAAATT
1 CAACATTAAAATT
136879 CAACATT
1 CAACATT
136886 GAACACCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (13 bp):
CAACATTAAAATT
Found at i:139235 original size:14 final size:15
Alignment explanation
Indices: 139204--139310 Score: 67
Period size: 17 Copynumber: 6.6 Consensus size: 15
139194 AGGCTCCTCT
139204 TCCTTCTTCGGTTCTTC
1 TCCTTCTTCGG--CTTC
139221 TCCTTCTTCGGTTCTTC
1 TCCTTCTTCGG--CTTC
*
139238 TTCCTTCTTCGGCTCCTT
1 -TCCTTCTTCGGCT--TC
139256 TCCTTCTTCGG-TTC
1 TCCTTCTTCGGCTTC
*
139270 -CTCTTCTTCGGTTCCTC
1 TC-CTTCTTCGG--CTTC
*
139287 TTCCTTCTTCGGCTCC
1 -TCCTTCTTCGGCTTC
139303 T-CTTCTTC
1 TCCTTCTTC
139311 TTGGGTTCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 21
0.75 0.05 0.21
Matches are distributed among these distances:
13 1 0.01
14 17 0.22
15 1 0.01
16 5 0.07
17 30 0.39
18 21 0.28
19 1 0.01
ACGTcount: A:0.00, C:0.38, G:0.11, T:0.50
Consensus pattern (15 bp):
TCCTTCTTCGGCTTC
Found at i:139247 original size:35 final size:35
Alignment explanation
Indices: 139201--139344 Score: 165
Period size: 35 Copynumber: 4.2 Consensus size: 35
139191 CCTAGGCTCC
*
139201 TCTTCCTTCTTCGGTTCTTC-TCCTTCTTCGGTTCT
1 TCTT-CTTCTTCGGTTCCTCTTCCTTCTTCGGTTCT
*
139236 TCTTCCTTCTTCGGCTCCT-TTCCTTCTTCGGTTC-
1 TCTT-CTTCTTCGGTTCCTCTTCCTTCTTCGGTTCT
* *
139270 -C-TCTTCTTCGGTTCCTCTTCCTTCTTCGGCTCC
1 TCTTCTTCTTCGGTTCCTCTTCCTTCTTCGGTTCT
* *
139303 TCTTCTTCTTGGGTTCCTCTTCTTTCTT-GGTTCT
1 TCTTCTTCTTCGGTTCCTCTTCCTTCTTCGGTTCT
139337 TCCTTCTT
1 T-CTTCTT
139345 GGCTCCTCCT
Statistics
Matches: 95, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
31 13 0.14
32 15 0.16
33 1 0.01
34 6 0.06
35 60 0.63
ACGTcount: A:0.00, C:0.35, G:0.12, T:0.53
Consensus pattern (35 bp):
TCTTCTTCTTCGGTTCCTCTTCCTTCTTCGGTTCT
Found at i:139280 original size:49 final size:50
Alignment explanation
Indices: 139145--139352 Score: 228
Period size: 49 Copynumber: 4.1 Consensus size: 50
139135 TGCAGCTGTT
*** * * * * *
139145 GCTCCTCTTCCTTCTTCTCCTCCTCTTTCTTAGCTTCTTCTTCTTTCCTAG
1 GCTCCTCTTCCTTCTTCGGTTCCTC-TTCTTCGGTTCTTCTTCCTTCTTCG
139196 GCTCCTCTTCCTTCTTCGGTTCTTCTCCTTCTTCGGTTCTTCTTCCTTCTTCG
1 GCTCCTCTTCCTTCTTCGGTTC--CT-CTTCTTCGGTTCTTCTTCCTTCTTCG
*
139249 GCTCCT-TTCCTTCTTCGGTTCCTCTTCTTCGGTTCCTCTTCCTTCTTCG
1 GCTCCTCTTCCTTCTTCGGTTCCTCTTCTTCGGTTCTTCTTCCTTCTTCG
* *
139298 GCTCCTCTT-CTTCTTGGGTTCCTCTTCTTTC--TTGGTTCTTCCTTCTT-G
1 GCTCCTCTTCCTTCTTCGGTTCCTCTTC-TTCGGTT-CTTCTTCCTTCTTCG
139346 GCTCCTC
1 GCTCCTC
139353 CTTCTTTGGT
Statistics
Matches: 139, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
48 10 0.07
49 59 0.42
50 7 0.05
51 19 0.14
52 15 0.11
53 28 0.20
54 1 0.01
ACGTcount: A:0.01, C:0.38, G:0.11, T:0.50
Consensus pattern (50 bp):
GCTCCTCTTCCTTCTTCGGTTCCTCTTCTTCGGTTCTTCTTCCTTCTTCG
Found at i:139337 original size:14 final size:14
Alignment explanation
Indices: 139320--139372 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
139310 CTTGGGTTCC
*
139320 TCTTCTTTCTTGGT
1 TCTTCCTTCTTGGT
*
139334 TCTTCCTTCTTGGC
1 TCTTCCTTCTTGGT
*
139348 TCCTCCTTCTTTGGT
1 TCTTCCTTC-TTGGT
139363 TCTTCCTTCT
1 TCTTCCTTCT
139373 CCGGCTCCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.00, C:0.32, G:0.11, T:0.57
Consensus pattern (14 bp):
TCTTCCTTCTTGGT
Found at i:139344 original size:18 final size:18
Alignment explanation
Indices: 139162--139332 Score: 104
Period size: 18 Copynumber: 9.9 Consensus size: 18
139152 TTCCTTCTTC
* * *
139162 TCCTCCTCTTTCTTAGCT
1 TCCTCTTCTTTCTTGGGT
* * * *
139180 TCTTCTTCTTTCCTAGGC
1 TCCTCTTCTTTCTTGGGT
* *
139198 TCCTCTTCCTTCTTCGGT
1 TCCTCTTCTTTCTTGGGT
* * *
139216 TCTTC-TCCTTCTTCGGT
1 TCCTCTTCTTTCTTGGGT
* * * *
139233 TCTTCTTCCTTCTTCGGC
1 TCCTCTTCTTTCTTGGGT
* *
139251 TCCT-TTCCTTCTTCGGT
1 TCCTCTTCTTTCTTGGGT
139268 TCCTCTTC-TTC---GGT
1 TCCTCTTCTTTCTTGGGT
* * *
139282 TCCTCTTCCTTCTTCGGC
1 TCCTCTTCTTTCTTGGGT
139300 TCCTCTTC-TTCTTGGGT
1 TCCTCTTCTTTCTTGGGT
139317 TCCTCTTCTTTCTTGG
1 TCCTCTTCTTTCTTGG
139333 TTCTTCCTTC
Statistics
Matches: 129, Mismatches: 17, Indels: 14
0.81 0.11 0.09
Matches are distributed among these distances:
14 11 0.09
15 3 0.02
17 51 0.40
18 64 0.50
ACGTcount: A:0.01, C:0.36, G:0.12, T:0.51
Consensus pattern (18 bp):
TCCTCTTCTTTCTTGGGT
Found at i:139357 original size:32 final size:33
Alignment explanation
Indices: 139201--139381 Score: 164
Period size: 35 Copynumber: 5.6 Consensus size: 33
139191 CCTAGGCTCC
* *
139201 TCTTCCTTCTTCGGTTCTTC-TCCTTCTTCGGTTCT
1 TCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGG---T
139236 TCTTCCTTCTTCGGCTCCT-TTCCTTCTTCGGT
1 TCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGGT
* *
139268 TCCT-CTTCTTCGGTTCCTCTTCCTTCTTCGGCT
1 TCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGG-T
* * *
139301 CCTCTT-CTTCTTGGGTTCCTCTTCTTTCTT-GGT
1 --TCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGGT
*
139334 TCTTCCTTCTT-GGCT-C-C-TCCTTCTTTGGT
1 TCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGGT
*
139363 TCTTCCTTCTCCGGCTCCT
1 TCTTCCTTCTTCGGCTCCT
139382 TCGCTGGCCC
Statistics
Matches: 126, Mismatches: 10, Indels: 23
0.79 0.06 0.14
Matches are distributed among these distances:
28 7 0.06
29 14 0.11
30 5 0.04
31 21 0.17
32 22 0.17
33 2 0.02
34 2 0.02
35 53 0.42
ACGTcount: A:0.00, C:0.36, G:0.13, T:0.51
Consensus pattern (33 bp):
TCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGGT
Done.