Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003561.1 Hibiscus syriacus cultivar Beakdansim tig00007519_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: 63791
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1170 original size:96 final size:95
Alignment explanation
Indices: 953--1205 Score: 373
Period size: 96 Copynumber: 2.6 Consensus size: 95
943 GATCTATAAG
* *
953 CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATCATTGTA-TATATATTATAATCAC
1 CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TATTGTATATTATAATCAC
*
1017 CTTTATCAGGCTAGCTGAATATTATCCATAAAGC
62 CTTTACCAGGCTAGCTGAATATTATCCATAAAGC
*
1051 CGGAGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTT
1 CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTT
*
1116 ACCAGGCTTAGCTGAATCTTATCCATAAAGC
66 ACCAGGC-TAGCTGAATATTATCCATAAAGC
* * *
1147 CGGGGCATTTAACCGATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATATATAAT
1 CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-TATAAT
1206 TATAATTTGG
Statistics
Matches: 143, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
94 2 0.01
95 27 0.19
96 72 0.50
97 7 0.05
98 35 0.24
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (95 bp):
CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTT
ACCAGGCTAGCTGAATATTATCCATAAAGC
Found at i:3833 original size:5 final size:6
Alignment explanation
Indices: 3802--3898 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
3792 AAAGTGTTAG
*
3802 ATAAAGA ATAAAA CATAAAA ATAAAA ATAAAAA ATAGTAA AT--AA ATCAAAGA
1 ATAAA-A ATAAAA -ATAAAA ATAAAA AT-AAAA ATA-AAA ATAAAA AT-AAA-A
*
3854 ATAGAAA A-AAGA ATAAAA A-AAGAGA ATAAAA ATAAAA ATAAAA AT
1 ATA-AAA ATAAAA ATAAAA ATAA-A-A ATAAAA ATAAAA ATAAAA AT
3899 GTTAAAAGTA
Statistics
Matches: 75, Mismatches: 3, Indels: 25
0.73 0.03 0.24
Matches are distributed among these distances:
4 4 0.05
5 5 0.07
6 31 0.41
7 28 0.37
8 7 0.09
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.15
Consensus pattern (6 bp):
ATAAAA
Found at i:3833 original size:12 final size:12
Alignment explanation
Indices: 3802--3898 Score: 67
Period size: 13 Copynumber: 7.7 Consensus size: 12
3792 AAAGTGTTAG
3802 ATAAAGAATAAAA
1 ATAAA-AATAAAA
3815 CATAAAAATAAAA
1 -ATAAAAATAAAA
*
3828 ATAAAAAATAGTAA
1 AT-AAAAATA-AAA
3842 AT--AAATCAAAGA
1 ATAAAAAT-AAA-A
*
3854 ATAGAAAA-AAGA
1 ATA-AAAATAAAA
3866 ATAAAAA-AAGAGA
1 ATAAAAATAA-A-A
3879 ATAAAAATAAAA
1 ATAAAAATAAAA
3891 ATAAAAAT
1 ATAAAAAT
3899 GTTAAAAGTA
Statistics
Matches: 69, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
11 11 0.16
12 19 0.28
13 25 0.36
14 11 0.16
15 3 0.04
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.15
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:3843 original size:20 final size:19
Alignment explanation
Indices: 3802--3891 Score: 80
Period size: 19 Copynumber: 4.7 Consensus size: 19
3792 AAAGTGTTAG
* *
3802 ATAAAGAATAAAACATAAAA
1 ATAAA-AATAAAAAATAGAA
3822 ATAAAAATAAAAAATAGTAA
1 ATAAAAATAAAAAATAG-AA
*
3842 AT--AAATCAAAGAATAGAA
1 ATAAAAAT-AAAAAATAGAA
3860 A-AAAGAATAAAAAA-AGAGA
1 ATAAA-AATAAAAAATAGA-A
3879 ATAAAAATAAAAA
1 ATAAAAATAAAAA
3892 TAAAAATGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
18 10 0.17
19 34 0.58
20 15 0.25
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (19 bp):
ATAAAAATAAAAAATAGAA
Found at i:3889 original size:19 final size:19
Alignment explanation
Indices: 3821--3891 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 19
3811 AAAACATAAA
3821 AATAAAAATAAAAAATAGTA-
1 AATAAAAATAAAAAA-AG-AG
* * *
3841 AAT--AAATCAAAGAATAG
1 AATAAAAATAAAAAAAGAG
*
3858 AAAAAAGAATAAAAAAAGAG
1 AATAAA-AATAAAAAAAGAG
3878 AATAAAAATAAAAA
1 AATAAAAATAAAAA
3892 TAAAAATGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
16 1 0.03
17 3 0.08
18 8 0.21
19 9 0.23
20 18 0.46
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.14
Consensus pattern (19 bp):
AATAAAAATAAAAAAAGAG
Found at i:5176 original size:18 final size:17
Alignment explanation
Indices: 5133--5177 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
5123 AAAGGAAAAG
5133 AATAATAAATAACAAAT
1 AATAATAAATAACAAAT
* *
5150 AACTAATAAATAATACAT
1 AA-TAATAAATAACAAAT
5168 AATACATAAA
1 AATA-ATAAA
5178 GAAAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAATAAATAACAAAT
Found at i:5359 original size:70 final size:68
Alignment explanation
Indices: 5251--5622 Score: 351
Period size: 70 Copynumber: 5.3 Consensus size: 68
5241 ATGTTTTTTC
* * * *
5251 AAAACCATATATAATATA-TTTCAAAAAAATATATTTAAAATTATATATTATATATTTTCCAATA
1 AAAACTATATATTATATATTTTC--AAAAATAT-TTTAAAACTATATATTATATATTTT-CAAAA
*
5315 TGTTTTA
62 TGATTTA
* *
5322 AAAACTATAT-TTATATAAGTTTTCAAAAATATTTTAAAAAACTATATAATATATATATTCAAAA
1 AAAACTATATATTATAT-A-TTTTCAAAAATATTTT--AAAACTATATATTATATATTTTCAAAA
*
5386 -GTTTTAAA
62 TGATTT--A
* * * *
5394 AAAACTATATA-T-TATATTTTCAAAATGTTTTTTAAAAACTATAATATATAAATGTTTTCAAAA
1 AAAACTATATATTATATATTTTCAAAA-ATATTTT-AAAACTAT-ATAT-TATATATTTTCAAAA
5457 TGATTTA
62 TGATTTA
* * * *
5464 AAAACTATATATTATATATTTTCAAAAATGTTTCAAAAAGTATATGTTATATAGTTTTCAAAATG
1 AAAACTATATATTATATATTTTCAAAAATATTT-TAAAACTATATATTATATA-TTTTCAAAATG
5529 ATTTA
64 ATTTA
* * * *
5534 AAAACTATATATTATATATTTTCAAAAATGTTTCAAAAAGTATATGTTATATAGTTTTCAAAAAT
1 AAAACTATATATTATATATTTTCAAAAATATTT-TAAAACTATATATTATATA-TTTTC-AAAAT
5599 G-TTTA
63 GATTTA
5604 AAAACTATATATTATATAT
1 AAAACTATATATTATATAT
5623 ATATTTTCAA
Statistics
Matches: 264, Mismatches: 20, Indels: 35
0.83 0.06 0.11
Matches are distributed among these distances:
69 22 0.08
70 135 0.51
71 55 0.21
72 48 0.18
73 4 0.02
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (68 bp):
AAAACTATATATTATATATTTTCAAAAATATTTTAAAACTATATATTATATATTTTCAAAATGAT
TTA
Found at i:5403 original size:35 final size:33
Alignment explanation
Indices: 5287--5622 Score: 300
Period size: 35 Copynumber: 9.6 Consensus size: 33
5277 AAATATATTT
* *
5287 AAAATTATATATTATATATTTTCCAATATGTTTTA
1 AAAACTATATATTATATATTTT-CAA-AAGTTTTA
*
5322 AAAACTATAT-TTATATAAGTTTTCAAAAATATTTTAA
1 AAAACTATATATTATAT-A-TTTTC-AAAA-GTTTT-A
* *
5359 AAAACTATATAATATATATATTCAAAAGTTTTAAA
1 AAAACTATATATTATATATTTTCAAAAGTTTT--A
5394 AAAACTATATA-T-TATATTTTCAAAATGTTTTTTA
1 AAAACTATATATTATATATTTTCAAAA-G--TTTTA
* * *
5428 AAAACTATAATATATAAATGTTTTCAAAATGATTTA
1 AAAACTAT-ATAT-TATATATTTTCAAAA-GTTTTA
*
5464 AAAACTATATATTATATATTTTCAAAAATGTTTCA
1 AAAACTATATATTATATATTTTC-AAAA-GTTTTA
* * *
5499 AAAAGTATATGTTATATAGTTTTCAAAATGATTTA
1 AAAACTATATATTATATA-TTTTCAAAA-GTTTTA
*
5534 AAAACTATATATTATATATTTTCAAAAATGTTTCA
1 AAAACTATATATTATATATTTTC-AAAA-GTTTTA
* * *
5569 AAAAGTATATGTTATATAGTTTTCAAAAATGTTTA
1 AAAACTATATATTATATA-TTTTCAAAAGT-TTTA
5604 AAAACTATATATTATATAT
1 AAAACTATATATTATATAT
5623 ATATTTTCAA
Statistics
Matches: 254, Mismatches: 28, Indels: 39
0.79 0.09 0.12
Matches are distributed among these distances:
33 12 0.05
34 37 0.15
35 134 0.53
36 40 0.16
37 13 0.05
38 18 0.07
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (33 bp):
AAAACTATATATTATATATTTTCAAAAGTTTTA
Found at i:5621 original size:105 final size:103
Alignment explanation
Indices: 5287--5622 Score: 378
Period size: 105 Copynumber: 3.2 Consensus size: 103
5277 AAATATATTT
* *
5287 AAAATTATATATTATATATTTTCCAATATGTTTTAAAAACTATAT-TTATATAAGTTTTCAAAAA
1 AAAACTATATATTATATATTTT-CAAAATGTTTTAAAAACTATATATTATAT-A-TTTTCAAAAA
* * * *
5351 TATTTTAAAAAACTATATAATATATATATTCAAAAGT-TTTAAA
63 T-GTTT-AAAAACTATATATTATATATTTTCAAAAATGTTT-AA
* *
5394 AAAACTATATA-T-TATATTTTCAAAATGTTTTTTAAAAACTATAATATATAAATGTTTTC-AAA
1 AAAACTATATATTATATATTTTCAAAATG--TTTTAAAAACTAT-ATAT-TATATATTTTCAAAA
*
5456 ATGATTTAAAAACTATATATTATATATTTTCAAAAATGTTTCA
62 ATG-TTTAAAAACTATATATTATATATTTTCAAAAATGTTTAA
* * *
5499 AAAAGTATATGTTATATAGTTTTCAAAATGATTTAAAAACTATATATTATATATTTTCAAAAATG
1 AAAACTATATATTATATA-TTTTCAAAATGTTTTAAAAACTATATATTATATATTTTCAAAAATG
* *
5564 TTTCAAAAAGTATATGTTATATAGTTTTCAAAAATGTTT-A
65 TTT-AAAAACTATATATTATATA-TTTTCAAAAATGTTTAA
5604 AAAACTATATATTATATAT
1 AAAACTATATATTATATAT
5623 ATATTTTCAA
Statistics
Matches: 198, Mismatches: 18, Indels: 29
0.81 0.07 0.12
Matches are distributed among these distances:
104 19 0.10
105 89 0.45
106 53 0.27
107 21 0.11
108 12 0.06
109 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (103 bp):
AAAACTATATATTATATATTTTCAAAATGTTTTAAAAACTATATATTATATATTTTCAAAAATGT
TTAAAAACTATATATTATATATTTTCAAAAATGTTTAA
Found at i:10462 original size:16 final size:16
Alignment explanation
Indices: 10441--10475 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
10431 TGCCAGTTTG
*
10441 ATTTTTGGGGTGTACA
1 ATTTTTGGGATGTACA
10457 ATTTTTGGGATGTACA
1 ATTTTTGGGATGTACA
10473 ATT
1 ATT
10476 ATTCGGAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.46
Consensus pattern (16 bp):
ATTTTTGGGATGTACA
Found at i:16941 original size:13 final size:13
Alignment explanation
Indices: 16895--16932 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
16885 AGCATTGTGG
16895 AAAGAAAATAATA
1 AAAGAAAATAATA
16908 AAAGAAAATAATA
1 AAAGAAAATAATA
16921 AAAGAAAATAAT
1 AAAGAAAATAAT
16933 GAAACAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAGAAAATAATA
Found at i:19298 original size:112 final size:110
Alignment explanation
Indices: 19070--19280 Score: 293
Period size: 112 Copynumber: 1.9 Consensus size: 110
19060 ATGGGGCCCC
* * * *
19070 AAAAAAGTATATATATAGTGGCGTTTTTTCAATAAACGCCACTATAGATAGACCTATTGCGATGT
1 AAAAAAGTATATATATAGTGGCATTTTTCCAATAAACACCACTATAGATAGACCTATTGCGACGT
* * *
19135 TTTTTCAAAAAAATGCCACTATTATTGCGCATGCCCAAAAAAATCCC
66 TTTTTCAAAAAAACGCCACTATTATTGCGCA--CCAAAAAAAATCCA
*
19182 AAAAAAGTATATATATAGTGGCATTTTTCCAATAAACACCACTATAGATGGACCTATTGCGACGT
1 AAAAAAGTATATATATAGTGGCATTTTTCCAATAAACACCACTATAGATAGACCTATTGCGACGT
* *
19247 TTTTTC-AAAAAACGCCATTATTGTTGC-C-CCAAAA
66 TTTTTCAAAAAAACGCCACTATTATTGCGCACCAAAA
19281 TTGAATATAT
Statistics
Matches: 90, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
107 5 0.06
110 1 0.01
111 18 0.20
112 66 0.73
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.30
Consensus pattern (110 bp):
AAAAAAGTATATATATAGTGGCATTTTTCCAATAAACACCACTATAGATAGACCTATTGCGACGT
TTTTTCAAAAAAACGCCACTATTATTGCGCACCAAAAAAAATCCA
Found at i:27551 original size:22 final size:22
Alignment explanation
Indices: 27505--27572 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
27495 ATATTTATTA
* **
27505 ATATTTTTAATAATATAATGTT
1 ATATTTTTAATATTATAATAAT
*
27527 ATATTTTTAATATTAGAATAAT
1 ATATTTTTAATATTATAATAAT
27549 ATATTCATTT-ATATTATAATAAT
1 ATATT--TTTAATATTATAATAAT
27572 A
1 A
27573 AATTATATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 23 0.59
23 13 0.33
24 3 0.08
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
ATATTTTTAATATTATAATAAT
Found at i:27564 original size:23 final size:23
Alignment explanation
Indices: 27536--27586 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
27526 TATATTTTTA
*
27536 ATATTAGAATAATATATTCAT-TT
1 ATATTAGAATAATAAATT-ATATT
*
27559 ATATTATAATAATAAATTATATT
1 ATATTAGAATAATAAATTATATT
27582 ATATT
1 ATATT
27587 TTTATTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTAGAATAATAAATTATATT
Found at i:27647 original size:47 final size:44
Alignment explanation
Indices: 27559--27664 Score: 124
Period size: 47 Copynumber: 2.3 Consensus size: 44
27549 ATATTCATTT
* * *
27559 ATATTATAATAATAAATTATATTATATTTTTATTTTGATAAAATATA
1 ATATTAT--TAATAAATTATATTATATTATTAATTTCATAAAA-ATA
27606 ATAAATTATTAATAAATTTATATTAT-TTATTAATTTCATAAAAATA
1 AT--ATTATTAATAAA-TTATATTATATTATTAATTTCATAAAAATA
27652 ATATTATTAATAA
1 ATATTATTAATAA
27665 TGAATAACAT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
44 11 0.21
46 5 0.09
47 23 0.43
48 9 0.17
49 5 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (44 bp):
ATATTATTAATAAATTATATTATATTATTAATTTCATAAAAATA
Found at i:27833 original size:55 final size:55
Alignment explanation
Indices: 27768--28009 Score: 147
Period size: 55 Copynumber: 4.3 Consensus size: 55
27758 TATAGTATTC
*
27768 TTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATA
1 TTATCTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATA
** * * * * * ** *
27823 TTATCTTAATATTGTTATTTACA-AAATTATAGA-AATAATATTTT-CTAGTAATAT-
1 TTATCTTAATA-AATAATTAATATAATTTATA-ATATTTTTATTTTAATAG-AATATA
** * * * * * * * *
27877 TT-TAATAA-AAATACTTAAAATATATTCATTAATAATTTTCAAAATGTAGTATAATATTA
1 TTATCTTAATAAATAATTAATATA-ATTTA-TAAT-ATTTT--TATTTTAATAGAATA-TA
*
27936 TTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATA
1 TTATCTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATA
27991 TTATCTTAATACAA-AATTA
1 TTATCTTAATA-AATAATTA
28010 TAAGAATAAT
Statistics
Matches: 131, Mismatches: 40, Indels: 32
0.65 0.20 0.16
Matches are distributed among these distances:
51 5 0.04
52 2 0.02
53 8 0.06
54 7 0.05
55 49 0.37
56 19 0.15
57 7 0.05
58 8 0.06
59 6 0.05
60 8 0.06
61 12 0.09
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (55 bp):
TTATCTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATA
Found at i:27892 original size:167 final size:169
Alignment explanation
Indices: 27698--28001 Score: 549
Period size: 168 Copynumber: 1.8 Consensus size: 169
27688 AATATAATAA
* *
27698 TCTAGTAATGTTTTTAATAGAAATACTTAAAATATATTCATTAATAA-TTTCAAAATGTAATATA
1 TCTAGTAATGATTTTAATAAAAATACTTAAAATATATTCATTAATAATTTTCAAAATGTAATATA
* *
27762 GTATTCTTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATATTAT
66 ATATTATTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATATTAT
27827 CTTAATATTGTTATTTACAAAATTATAGAAATAATATTT
131 CTTAATATTGTTATTTACAAAATTATAGAAATAATATTT
*
27866 TCTAGTAAT-ATTTTAATAAAAATACTTAAAATATATTCATTAATAATTTTCAAAATGTAGTATA
1 TCTAGTAATGATTTTAATAAAAATACTTAAAATATATTCATTAATAATTTTCAAAATGTAATATA
27930 ATATTATTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATATTAT
66 ATATTATTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATATTAT
27995 CTTAATA
131 CTTAATA
28002 CAAAATTATA
Statistics
Matches: 130, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
167 35 0.27
168 95 0.73
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (169 bp):
TCTAGTAATGATTTTAATAAAAATACTTAAAATATATTCATTAATAATTTTCAAAATGTAATATA
ATATTATTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATATTAT
CTTAATATTGTTATTTACAAAATTATAGAAATAATATTT
Found at i:28048 original size:19 final size:17
Alignment explanation
Indices: 28007--28092 Score: 70
Period size: 16 Copynumber: 5.1 Consensus size: 17
27997 TAATACAAAA
*
28007 TTATAAGAA-TAATATTT
1 TTATAATAATTAAT-TTT
*
28024 TAATAAT-ATTAATTTT
1 TTATAATAATTAATTTT
28040 TTATAATAATTAATATTAT
1 TTATAATAATTAAT-TT-T
* * *
28059 TTATTATATTTAA-TAT
1 TTATAATAATTAATTTT
*
28075 TTATAATAAATAATTTT
1 TTATAATAATTAATTTT
28092 T
1 T
28093 AAAAACAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
16 21 0.39
17 19 0.35
18 2 0.04
19 12 0.22
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (17 bp):
TTATAATAATTAATTTT
Found at i:32391 original size:2 final size:2
Alignment explanation
Indices: 32384--32415 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32374 ATTAACATAG
32384 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32416 AAATAACTTA
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):
TA
Found at i:36130 original size:35 final size:35
Alignment explanation
Indices: 36063--36132 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
36053 AAAGATCTAG
* * *
36063 AACAAACTGAACTGCTGAAGAGCACACGGAAAACT
1 AACAAACTGAACAGCTGAAGAACACACAGAAAACT
* * *
36098 AACACACTGAACAGCTGAATAACACATAGAAAACT
1 AACAAACTGAACAGCTGAAGAACACACAGAAAACT
36133 GACATAGTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.13
Consensus pattern (35 bp):
AACAAACTGAACAGCTGAAGAACACACAGAAAACT
Found at i:39081 original size:127 final size:126
Alignment explanation
Indices: 38847--39213 Score: 429
Period size: 127 Copynumber: 2.9 Consensus size: 126
38837 GAATTTATCC
* * * * * * * * *
38847 GCTTCACTGCTCTTCAGGAAGACCATATATGGAAATTTGGACTCACTCCACTACTCTTTA-GGAG
1 GCTTTACTGCTCTTCAAGAAAATCAGATATGGAAATTT-GATTCATTTCACTACTCTTCAGGGA-
* * * * *
38911 AGGTTGAATCGAGGTTGATTTTCTTTACTGCTCTTCAGGAAGATTAAAT-TTAAAAAAGAATCT
64 AAGTTGAATCGAGGTTGATTTGCTTCACTGCTCTTCAGAAAGATCAAATCTT-AAAAAGAATCT
*
38974 GCTTTACTGCTCTTCAAGAAAATCAGATATGGAAACTTTGATTCATTTCACTATTCTTCAGGGAA
1 GCTTTACTGCTCTTCAAGAAAATCAGATATGGAAA-TTTGATTCATTTCACTACTCTTCAGGGAA
* * *
39039 AGTTGAATCGAGGTTGATTTGCTTCACTGCTCTTTAGAAAGATCAAATCTTAAAAAGGATTT
65 AGTTGAATCGAGGTTGATTTGCTTCACTGCTCTTCAGAAAGATCAAATCTTAAAAAGAATCT
39101 G-TTTCACTAG-TCATT-AAGAAAATCAGATATGGAAAATTTGATTCATTTCACTACTCTTCAGG
1 GCTTT-ACT-GCTC-TTCAAGAAAATCAGATATGG-AAATTTGATTCATTTCACTACTCTTCAGG
* * * *
39163 GAAAGTTGAATTGAGATTGATTTGCTTCACTACTCTTCAAAAAGATCAAAT
62 GAAAGTTGAATCGAGGTTGATTTGCTTCACTGCTCTTCAGAAAGATCAAAT
39214 ATGAAAAACA
Statistics
Matches: 209, Mismatches: 24, Indels: 14
0.85 0.10 0.06
Matches are distributed among these distances:
126 3 0.01
127 192 0.92
128 14 0.07
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (126 bp):
GCTTTACTGCTCTTCAAGAAAATCAGATATGGAAATTTGATTCATTTCACTACTCTTCAGGGAAA
GTTGAATCGAGGTTGATTTGCTTCACTGCTCTTCAGAAAGATCAAATCTTAAAAAGAATCT
Found at i:39988 original size:45 final size:44
Alignment explanation
Indices: 39928--40289 Score: 314
Period size: 45 Copynumber: 8.1 Consensus size: 44
39918 AGTCAAGTTG
* * *
39928 AGAATGACATCACTAAAAGGTTGACTCATCTTCCTGAGAAAGTCA
1 AGAAGGACAACACTAAAAGGTTGACTCCTCTTCC-GAGAAAGTCA
** * ** * * *
39973 AGAATCATATTACTAAAAGGTTGACTCTTTTTTACGAGAAAGTCA
1 AGAAGGACAACACTAAAAGGTTGACTC-CTCTTCCGAGAAAGTCA
* * * *
40018 AGAATGAGATA-ACTAAAAGTTTGACTCCTGTTCGCGAGAAAGTCA
1 AGAAGGACA-ACACTAAAAGGTTGACTCCTCTTC-CGAGAAAGTCA
* * * *
40063 ATAAGGACAACACTGAAAGGTTAACTCCTCTTCAAGAGAAAGTCA
1 AGAAGGACAACACTAAAAGGTTGACTCCTCTTC-CGAGAAAGTCA
** **
40108 AGAAGGACAACACTAAAATATTGACTCCTCTTTGTGAGAAAGTCA
1 AGAAGGACAACACTAAAAGGTTGACTCCTC-TTCCGAGAAAGTCA
* * *
40153 AGAAGGACAACACTAAAAGATTGACTTCTCTTTGCGAGAAAGTCA
1 AGAAGGACAACACTAAAAGGTTGACTCCTC-TTCCGAGAAAGTCA
* ** * * *
40198 TGAATAACATCACCAAAAGGTTGACTCCTCTTCACAAGAAA-TCA
1 AGAAGGACAACACTAAAAGGTTGACTCCTCTTC-CGAGAAAGTCA
* **
40242 AGAAGGACAACACTAAAAGATTGACTTATCTTCACGAGAAAGTCA
1 AGAAGGACAACACTAAAAGGTTGACTCCTCTTC-CGAGAAAGTCA
40287 AGA
1 AGA
40290 CTAAAAGATT
Statistics
Matches: 260, Mismatches: 50, Indels: 14
0.80 0.15 0.04
Matches are distributed among these distances:
44 41 0.16
45 213 0.82
46 6 0.02
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (44 bp):
AGAAGGACAACACTAAAAGGTTGACTCCTCTTCCGAGAAAGTCA
Found at i:40057 original size:90 final size:90
Alignment explanation
Indices: 39928--40289 Score: 363
Period size: 90 Copynumber: 4.0 Consensus size: 90
39918 AGTCAAGTTG
* * ** * **
39928 AGAATGACATCACTAAAAGGTTGACTCATCTTC-CTGAGAAAGTCAAGAATCATATTACTAAAAG
1 AGAATGACATAACTAAAAGGTTGACTCCTCTTCGC-GAGAAAGTCAAGAAGGACAACACTAAAAG
* * *
39992 GTTGACTCT-TTTTTACGAGAAAGTCA
65 ATTGACT-TATCTTCACGAGAAAGTCA
* * * * * *
40018 AGAATGAGATAACTAAAAGTTTGACTCCTGTTCGCGAGAAAGTCAATAAGGACAACACTGAAAGG
1 AGAATGACATAACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGA
* ** *
40083 TTAACTCCTCTTCAAGAGAAAGTCA
66 TTGACTTATCTTCACGAGAAAGTCA
* ** * *
40108 AGAAGGACA-ACACTAAAATATTGACTCCTCTTTGTGAGAAAGTCAAGAAGGACAACACTAAAAG
1 AGAATGACATA-ACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAG
* **
40172 ATTGACTTCTCTTTGCGAGAAAGTCA
65 ATTGACTTATCTTCACGAGAAAGTCA
* * * * * *
40198 TGAATAACATCACCAAAAGGTTGACTCCTCTTCACAAGAAA-TCAAGAAGGACAACACTAAAAGA
1 AGAATGACATAACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGA
40262 TTGACTTATCTTCACGAGAAAGTCA
66 TTGACTTATCTTCACGAGAAAGTCA
40287 AGA
1 AGA
40290 CTAAAAGATT
Statistics
Matches: 221, Mismatches: 47, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
89 48 0.22
90 172 0.78
91 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (90 bp):
AGAATGACATAACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGA
TTGACTTATCTTCACGAGAAAGTCA
Found at i:40124 original size:135 final size:135
Alignment explanation
Indices: 39893--40289 Score: 401
Period size: 135 Copynumber: 2.9 Consensus size: 135
39883 GATACAACTG
* * * *
39893 AAAAG-TTGACTCATCTCCGCGAGAAAGTCAAGTTGAGAATGACATCACTAAAAGGTTGACTCAT
1 AAAAGATTGACTCCTCTTCGCGAGAAAGTC-A--T--GAAGGACATCACTAAAAGGTTGACTCCT
** ** * ** * *
39957 CTTCCTGAGAAAGTCAAGAATCATATTACTAAAAGGTTGACTCTTTTTTACGAGAAAGTCAAGAA
61 CTTCAAGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCTTCTTTACGAGAAAGTCAAGAA
* *
40022 TGAGATA-ACT
126 GGACA-ACACT
* * * * *
40032 AAAAGTTTGACTCCTGTTCGCGAGAAAGTCAAT-AAGGACAACACTGAAAGGTTAACTCCTCTTC
1 AAAAGATTGACTCCTCTTCGCGAGAAAGTC-ATGAAGGACATCACTAAAAGGTTGACTCCTCTTC
* * **
40096 AAGAGAAAGTCAAGAAGGACAACACTAAAATATTGACTCCTCTTTGTGAGAAAGTCAAGAAGGAC
65 AAGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCTTCTTTACGAGAAAGTCAAGAAGGAC
40161 AACACT
130 AACACT
* * ** *
40167 AAAAGATTGACTTCTCTTTGCGAGAAAGTCATGAATAACATCACCAAAAGGTTGACTCCTCTTCA
1 AAAAGATTGACTCCTCTTCGCGAGAAAGTCATGAAGGACATCACTAAAAGGTTGACTCCTCTTCA
*
40232 CA-AGAAA-TCAAGAAGGACAACACTAAAAGATTGACT-TATCTTCACGAGAAAGTCAAGA
66 -AGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCT-TCTTTACGAGAAAGTCAAGA
40290 CTAAAAGATT
Statistics
Matches: 215, Mismatches: 38, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
134 48 0.22
135 137 0.64
136 1 0.00
138 1 0.00
139 5 0.02
140 23 0.11
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (135 bp):
AAAAGATTGACTCCTCTTCGCGAGAAAGTCATGAAGGACATCACTAAAAGGTTGACTCCTCTTCA
AGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCTTCTTTACGAGAAAGTCAAGAAGGACA
ACACT
Found at i:40351 original size:41 final size:41
Alignment explanation
Indices: 40106--40352 Score: 150
Period size: 45 Copynumber: 5.9 Consensus size: 41
40096 AAGAGAAAGT
* * * *
40106 CAAGAAGGACAACACTAAAATATTGACTCCTCTTTGTGA-GAAA
1 CAAGAATGACAACACTAAAAGATTGACTCATC--T-TCACGAAA
*
40149 GTCAAGAAGGACAACACTAAAAGATTGACTTC-TCTTTGCGA-GAAA
1 --CAAGAATGACAACACTAAAAGATTGAC-TCATC-TT-C-ACGAAA
* * * * * *
40194 GTCATGAATAACATCACCAAAAGGTTGACTCCTCTTCACAAGAAA
1 --CAAGAATGACAACACTAAAAGATTGACTCATCTTCAC--GAAA
* * *
40239 TCAAGAAGGACAACACTAAAAGATTGACTTATCTTCACGAGA
1 -CAAGAATGACAACACTAAAAGATTGACTCATCTTCACGAAA
*
40281 -AAG--T--CAAGACTAAAAGATTGACTCATCTTCACGAAA
1 CAAGAATGACAACACTAAAAGATTGACTCATCTTCACGAAA
* * *
40317 CAAGAATGACAACACTGAAAGATTGTCTCCTCTTCA
1 CAAGAATGACAACACTAAAAGATTGACTCATCTTCA
40353 TGAGAAAGTC
Statistics
Matches: 165, Mismatches: 25, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
36 29 0.18
37 3 0.02
39 1 0.01
40 3 0.02
41 23 0.14
42 4 0.02
43 2 0.01
44 36 0.22
45 62 0.38
46 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.23
Consensus pattern (41 bp):
CAAGAATGACAACACTAAAAGATTGACTCATCTTCACGAAA
Found at i:40351 original size:77 final size:79
Alignment explanation
Indices: 40212--40365 Score: 213
Period size: 77 Copynumber: 2.0 Consensus size: 79
40202 TAACATCACC
* * *
40212 AAAAGGTTGACTCCTCTTCACAAGAAATCAAGAAGGACAACACTAAAAGATTGACTTATCTTCAC
1 AAAAGATTGACTCATCTTCAC-AGAAATCAAGAAGGACAACACTAAAAGATTGACTCATCTTCAC
40277 GAGAAAGTCAAGACT
65 GAGAAAGTCAAGACT
* * * * *
40292 AAAAGATTGACTCATCTTCAC-GAAA-CAAGAATGACAACACTGAAAGATTGTCTCCTCTTCATG
1 AAAAGATTGACTCATCTTCACAGAAATCAAGAAGGACAACACTAAAAGATTGACTCATCTTCACG
40355 AGAAAGTCAAG
66 AGAAAGTCAAG
40366 TTGAGGTTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
77 43 0.65
78 4 0.06
80 19 0.29
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (79 bp):
AAAAGATTGACTCATCTTCACAGAAATCAAGAAGGACAACACTAAAAGATTGACTCATCTTCACG
AGAAAGTCAAGACT
Found at i:40490 original size:37 final size:38
Alignment explanation
Indices: 40449--40543 Score: 113
Period size: 37 Copynumber: 2.5 Consensus size: 38
40439 ATCAAATTTA
* *
40449 TATAGAAACGATCCTAAGAAGGACAAAAATGA-GTTTC
1 TATAGAAACCATCCTAAAAAGGACAAAAATGAGGTTTC
* *
40486 TATAGAAACCATCCTAAAAAGGACTAGAATGAGGTTTC
1 TATAGAAACCATCCTAAAAAGGACAAAAATGAGGTTTC
* *
40524 TA-AGGAAACAATCTTAAAAA
1 TATA-GAAACCATCCTAAAAA
40544 ATAAAATGGT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
37 29 0.58
38 21 0.42
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (38 bp):
TATAGAAACCATCCTAAAAAGGACAAAAATGAGGTTTC
Found at i:41763 original size:20 final size:20
Alignment explanation
Indices: 41738--41787 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
41728 GACCAACAAA
41738 TTCGCAACGCAAACTCCAAT
1 TTCGCAACGCAAACTCCAAT
* ** *
41758 TTCGCAACCCAATTTCTAAT
1 TTCGCAACGCAAACTCCAAT
41778 TTCGCAACGC
1 TTCGCAACGC
41788 GAATCTGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.34, G:0.10, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCAAACTCCAAT
Found at i:41842 original size:60 final size:60
Alignment explanation
Indices: 41778--42005 Score: 223
Period size: 60 Copynumber: 3.8 Consensus size: 60
41768 AATTTCTAAT
* * *
41778 TTCGCAACGCGAATCTGTAAATCGCAACATAGAAGTCAAATTTGCAACACAAAAGTCAAA
1 TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAA
* * * ** * *
41838 TTCGCAATGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCACAATGCGATAGTCAAA
1 TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAA
* * * * *
41898 TTCGCAACAC-AA-AAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACTCAAAAGTTAAA
1 TTCGCAACGCGAATATGT-AAA-TCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAA
* *
41958 TTCGCAACGCG-ATA-GTCAAATTCACAACGC-GAAAGTCAAATTCGCAAC
1 TTCGCAACGCGAATATGT-AAA-TCGCAACACAG-AAGTCAAATTCGCAAC
42006 GCGAAACACA
Statistics
Matches: 139, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
58 2 0.01
59 5 0.04
60 131 0.94
61 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (60 bp):
TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAA
Found at i:42006 original size:20 final size:20
Alignment explanation
Indices: 41810--42011 Score: 194
Period size: 20 Copynumber: 10.1 Consensus size: 20
41800 CGCAACATAG
* * *
41810 AAGTCAAATTTGCAACACAA
1 AAGTCAAATTCGCAACGCGA
*
41830 AAGTCAAATTCGCAATGCGA
1 AAGTCAAATTCGCAACGCGA
* *
41850 ATTTGT-AAA-TCGCAACAC-A
1 A--AGTCAAATTCGCAACGCGA
* *
41869 GAAGTCAAATTCACAATGCGA
1 -AAGTCAAATTCGCAACGCGA
* * *
41890 TAGTCAAATTCGCAACACAA
1 AAGTCAAATTCGCAACGCGA
* *
41910 AAGTCAAATTCGCAACACAA
1 AAGTCAAATTCGCAACGCGA
* *
41930 AAGTCAAATTCGCAACTCAA
1 AAGTCAAATTCGCAACGCGA
*
41950 AAGTTAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
* *
41970 TAGTCAAATTCACAACGCGA
1 AAGTCAAATTCGCAACGCGA
41990 AAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
42010 AA
1 AA
42012 CACAATATTA
Statistics
Matches: 150, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
18 2 0.01
19 4 0.03
20 138 0.92
21 4 0.03
22 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.19
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:42006 original size:40 final size:40
Alignment explanation
Indices: 41811--42009 Score: 240
Period size: 40 Copynumber: 5.0 Consensus size: 40
41801 GCAACATAGA
* *
41811 AGTCAAATTTGCAACACAAAAGTCAAATTCGCAATGCGAATT
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCG-A-T
* * * *
41853 TGT-AAA-TCGCAACACAGAAGTCAAATTCACAATGCGAT
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
* * *
41891 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
* *
41931 AGTCAAATTCGCAACTCAAAAGTTAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
* * *
41971 AGTCAAATTCACAACGCGAAAGTCAAATTCGCAACGCGA
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGA
42010 AACACAATAT
Statistics
Matches: 135, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
38 3 0.02
39 4 0.03
40 123 0.91
41 3 0.02
42 2 0.01
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.20
Consensus pattern (40 bp):
AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
Found at i:42146 original size:22 final size:22
Alignment explanation
Indices: 42121--42171 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
42111 CTACGGCGAC
42121 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
42143 ATCCATCCCCATCTCTGACGAA
1 ATCCGTCCCCATCTCCGACGAA
42165 ATCCGTC
1 ATCCGTC
42172 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.43, G:0.12, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:42591 original size:20 final size:20
Alignment explanation
Indices: 42556--42603 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
42546 AAATCGCAAC
42556 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
42575 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
42595 TCGATTTTC
1 GCGATTTTC
42604 TCATTGCGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.10, C:0.19, G:0.21, T:0.50
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:42621 original size:20 final size:21
Alignment explanation
Indices: 42593--42632 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
42583 CATTTTCGCG
*
42593 TTTCGATTTTCTCATTGCGAT
1 TTTCGATTTTCGCATTGCGAT
42614 TTTC-ATTTTCGCATTGCGA
1 TTTCGATTTTCGCATTGCGA
42633 ATTTAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (21 bp):
TTTCGATTTTCGCATTGCGAT
Found at i:42643 original size:20 final size:20
Alignment explanation
Indices: 42600--42643 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
42590 GCGTTTCGAT
* * * *
42600 TTTCTCATTGCGATTTTCAT
1 TTTCGCATTGCGAATTTAAG
42620 TTTCGCATTGCGAATTTAAG
1 TTTCGCATTGCGAATTTAAG
42640 TTTC
1 TTTC
42644 AGAAACTACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (20 bp):
TTTCGCATTGCGAATTTAAG
Found at i:44382 original size:42 final size:42
Alignment explanation
Indices: 44319--44399 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
44309 GATACACCTA
* * *
44319 TCATCATTCAAGAGGCACCTCATATCGTTCAAGAGGCCCTTC
1 TCATCATTCAAGAAGCACCTCACACCGTTCAAGAGGCCCTTC
*
44361 TCATCA-TCGAAGAAGCCCCTCACACCGTTCAAGAGGCCC
1 TCATCATTC-AAGAAGCACCTCACACCGTTCAAGAGGCCC
44400 CAATCATCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.21
Consensus pattern (42 bp):
TCATCATTCAAGAAGCACCTCACACCGTTCAAGAGGCCCTTC
Found at i:44407 original size:42 final size:42
Alignment explanation
Indices: 44318--44415 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
44308 CGATACACCT
* * * **
44318 ATCATCATTCAAGAGGCACCTCATATCGTTCAAGAGGCCCTT
1 ATCATCATTCAAGAAGCACCTCACACCGTTCAAGAGGCCCCA
* *
44360 CTCATCA-TCGAAGAAGCCCCTCACACCGTTCAAGAGGCCCCA
1 ATCATCATTC-AAGAAGCACCTCACACCGTTCAAGAGGCCCCA
*
44402 ATCATCGTTCAAGA
1 ATCATCATTCAAGA
44416 GGTCCTACCC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
41 2 0.04
42 41 0.91
43 2 0.04
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (42 bp):
ATCATCATTCAAGAAGCACCTCACACCGTTCAAGAGGCCCCA
Found at i:44410 original size:21 final size:20
Alignment explanation
Indices: 44318--44417 Score: 64
Period size: 21 Copynumber: 4.8 Consensus size: 20
44308 CGATACACCT
*
44318 ATCATCATTCAAGAGGCACCTC
1 ATCATCGTTCAAGAGGC-CC-C
44340 AT-ATCGTTCAAGAGGCCCTTC
1 ATCATCGTTCAAGAGGCCC--C
* *
44361 -TCATC-ATCGAAGAAGCCCC
1 ATCATCGTTC-AAGAGGCCCC
*
44380 -TCACACCGTTCAAGAGGCCCC
1 AT--CATCGTTCAAGAGGCCCC
44401 AATCATCGTTCAAGAGG
1 -ATCATCGTTCAAGAGG
44418 TCCTACCCGC
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
19 2 0.03
20 5 0.08
21 51 0.81
22 4 0.06
23 1 0.02
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCATCGTTCAAGAGGCCCC
Found at i:45897 original size:66 final size:65
Alignment explanation
Indices: 45733--45908 Score: 255
Period size: 66 Copynumber: 2.6 Consensus size: 65
45723 TGGCGTACAC
*
45733 TTTTTTTGCTTGTTTAATTGAATTTTACATTGAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
1 TTTTTTTGCTTGTTTAATTG-A-TTT---TTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
45798 AATTA
61 AATTA
* * *
45803 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATT
45867 A
65 A
45868 TTTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTT
45909 GTTTTAAATT
Statistics
Matches: 99, Mismatches: 5, Indels: 8
0.88 0.04 0.07
Matches are distributed among these distances:
64 18 0.18
65 19 0.19
66 39 0.39
67 3 0.03
68 1 0.01
69 19 0.19
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.53
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:46402 original size:18 final size:18
Alignment explanation
Indices: 46379--46414 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
46369 AAGCCGGTTG
*
46379 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
46397 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
46415 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:47391 original size:18 final size:18
Alignment explanation
Indices: 47368--47404 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47358 CGAAATTTAT
47368 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
47386 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
47404 A
1 A
47405 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:47818 original size:25 final size:25
Alignment explanation
Indices: 47790--47839 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
47780 CATTATTTTC
* *
47790 CAAATAATGTACCCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
47815 CAAATAATATACCCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
47840 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:48402 original size:18 final size:18
Alignment explanation
Indices: 48379--48414 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
48369 AAGCCGGTTG
48379 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
48397 TGATTGTGATTTTGATTT
1 TGATTGAGATTTTGATTT
48415 CCTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.58
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:51738 original size:60 final size:60
Alignment explanation
Indices: 51674--51816 Score: 146
Period size: 60 Copynumber: 2.4 Consensus size: 60
51664 AAATTCCGCG
*
51674 TTGCGAATTTGACTTTTGTGTTGTGAATTTGACTTATATGTTACG-ATTT-ACAAATTCACA
1 TTGCGAATTTGACTTTTGTGTTGTGAAATTGACTTATATGTTACGAATTTGAC-AA-TCACA
* * * * * * * * * *
51734 TTGCGAAATTGACTATCGCGTTGTGAAATTGACTTTTGTGTTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTTGTGTTGTGAAATTGACTTATATGTTACGAATTTGACAATCACA
*
51794 TTGCGAATTTGACTTCTGTGTTG
1 TTGCGAATTTGACTTTTGTGTTG
51817 CGATTTATAG
Statistics
Matches: 65, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
60 58 0.89
61 5 0.08
62 2 0.03
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (60 bp):
TTGCGAATTTGACTTTTGTGTTGTGAAATTGACTTATATGTTACGAATTTGACAATCACA
Found at i:51763 original size:20 final size:20
Alignment explanation
Indices: 51734--51807 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
51724 CAAATTCACA
51734 TTGCGAAATTGACTATCGCG
1 TTGCGAAATTGACTATCGCG
* * * *
51754 TTGTGAAATTGACTTTTGTG
1 TTGCGAAATTGACTATCGCG
*
51774 TTGCGAATTTGACTATCGCG
1 TTGCGAAATTGACTATCGCG
*
51794 TTGCGAATTTGACT
1 TTGCGAAATTGACT
51808 TCTGTGTTGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (20 bp):
TTGCGAAATTGACTATCGCG
Found at i:51778 original size:40 final size:40
Alignment explanation
Indices: 51734--51819 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
51724 CAAATTCACA
* *
51734 TTGCGAAATTGACTATCGCGTTGTGAAATTGACTTTTGTG
1 TTGCGAAATTGACTATCGCGTTGCGAAATTGACTTCTGTG
* *
51774 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTG
1 TTGCGAAATTGACTATCGCGTTGCGAAATTGACTTCTGTG
51814 TTGCGA
1 TTGCGA
51820 TTTATAGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.40
Consensus pattern (40 bp):
TTGCGAAATTGACTATCGCGTTGCGAAATTGACTTCTGTG
Found at i:51816 original size:20 final size:20
Alignment explanation
Indices: 51673--51819 Score: 88
Period size: 20 Copynumber: 7.3 Consensus size: 20
51663 CAAATTCCGC
*
51673 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
* * *
51693 GTTGTGAATTTGACTTATAT
1 GTTGCGAATTTGACTTCTGT
* **
51713 GTTACG-ATTT-ACAAATTC-AC
1 GTTGCGAATTTGAC---TTCTGT
* * *
51733 ATTGCGAAATTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
* * *
51753 GTTGTGAAATTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
*
51773 GTTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
51793 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
51813 GTTGCGA
1 GTTGCGA
51820 TTTATAGATT
Statistics
Matches: 98, Mismatches: 20, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
18 2 0.02
19 8 0.08
20 80 0.82
21 6 0.06
22 2 0.02
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:52288 original size:76 final size:73
Alignment explanation
Indices: 52137--52347 Score: 284
Period size: 75 Copynumber: 2.9 Consensus size: 73
52127 ATTTTAAACA
* * *
52137 TTATATTTTATCTTTTCTTTATGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGTTTTAG
1 TTATATTTTATCTTTT-TTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTAG
*
52202 GATATTATTT
65 AATATTA-TT
52212 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTT-TTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAGGATTTA
52277 GAATATTATT
64 GAATATTATT
* * * *
52287 TTAAATATTA---TTTTTTAGTTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 TTATATTTTATCTTTTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAGGATTTA
52348 AGATGTTTTA
Statistics
Matches: 125, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
70 5 0.04
71 41 0.33
72 2 0.02
75 46 0.37
76 31 0.25
ACGTcount: A:0.28, C:0.01, G:0.11, T:0.59
Consensus pattern (73 bp):
TTATATTTTATCTTTTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTAGA
ATATTATT
Found at i:53044 original size:16 final size:15
Alignment explanation
Indices: 53016--53097 Score: 66
Period size: 14 Copynumber: 5.5 Consensus size: 15
53006 GAAACCCCCC
53016 TTTTATATTATTACTT
1 TTTTATATTATTA-TT
53032 TTTTA-ATTCATTATT
1 TTTTATATT-ATTATT
*
53047 TTTTAT-TTTTTATT
1 TTTTATATTATTATT
*
53061 TTTTAT-TTTTTA-T
1 TTTTATATTATTATT
*
53074 TTATA-ATTACTTATT
1 TTTTATATTA-TTATT
53089 TTATTATAT
1 TT-TTATAT
53098 CTTTTCAACT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
13 7 0.13
14 20 0.36
15 15 0.27
16 11 0.20
17 2 0.04
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATATTATTATT
Found at i:53054 original size:7 final size:7
Alignment explanation
Indices: 53042--53075 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
53032 TTTTAATTCA
53042 TTATTTT
1 TTATTTT
53049 TTATTTT
1 TTATTTT
53056 TTATTTT
1 TTATTTT
53063 TTATTTT
1 TTATTTT
53070 TTATTT
1 TTATTT
53076 ATAATTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTATTTT
Found at i:53087 original size:21 final size:21
Alignment explanation
Indices: 53042--53095 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
53032 TTTTAATTCA
* * **
53042 TTATTTTTTATTTTTTATTTT
1 TTATTTTTTATTTATAATTAC
53063 TTATTTTTTATTTATAATTAC
1 TTATTTTTTATTTATAATTAC
53084 TTATTTTATTAT
1 TTATTTT-TTAT
53096 ATCTTTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATTTTTTATTTATAATTAC
Found at i:60359 original size:44 final size:43
Alignment explanation
Indices: 60306--60435 Score: 122
Period size: 44 Copynumber: 3.2 Consensus size: 43
60296 ATTTTAAACA
60306 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTT
1 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTT
*
60349 TTAGTATTTTA-ATTAAGTTTTAGG-A---TA---T---TA-GTT
1 TTA-TATTTTATATT-TGTTTTAGGTATTTTAGTTTAAATAGGTT
* *
60382 TTATATTTTATCTTTTTTTTAGGTATTTTAGTTTAAATAGGTT
1 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTT
60425 TTAATATTTTA
1 TT-ATATTTTA
60436 ATTAGGATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 29
0.67 0.04 0.29
Matches are distributed among these distances:
32 14 0.21
33 9 0.13
34 2 0.03
36 2 0.03
37 1 0.01
39 1 0.01
40 2 0.03
42 2 0.03
43 12 0.18
44 23 0.34
ACGTcount: A:0.27, C:0.01, G:0.12, T:0.60
Consensus pattern (43 bp):
TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTT
Found at i:60416 original size:76 final size:74
Alignment explanation
Indices: 60306--60510 Score: 263
Period size: 76 Copynumber: 2.8 Consensus size: 74
60296 ATTTTAAACA
* *
60306 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTAT-TTTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
* *
60371 GGATATTAGTT
65 GAATATTA-AT
* *
60382 TTATATTTTATCTTTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAATATTTTAATTAGGATTTA
1 TTATATTTTAT-TTTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
60447 GAATATTAAT
65 GAATATTAAT
* * * * *
60457 TTA-A--ATATTATTTTTTAAGTATTTTAGTTTAAATAGGTTTAAGTGTTTTAATTA
1 TTATATTTTATTTTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTA
60511 GTATTAAGAT
Statistics
Matches: 116, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
71 41 0.35
72 3 0.03
74 1 0.01
75 4 0.03
76 67 0.58
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (74 bp):
TTATATTTTATTTTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAG
AATATTAAT
Found at i:61798 original size:3 final size:3
Alignment explanation
Indices: 61792--61841 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
61782 TTCTCTTTTT
*
61792 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTA TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
61840 TT
1 TT
61842 TTTCCTTTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:61880 original size:21 final size:22
Alignment explanation
Indices: 61854--61901 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
61844 TCCTTTCTCA
* *
61854 TTTTTCTTTCTTTT-TTTTTTT
1 TTTTTCTATCTTTTCTCTTTTT
61875 TTTTTCTATCTTTTCTCTTTTT
1 TTTTTCTATCTTTTCTCTTTTT
61897 TTTTT
1 TTTTT
61902 GAATATGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.85
Consensus pattern (22 bp):
TTTTTCTATCTTTTCTCTTTTT
Done.