Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000338.1 Hibiscus syriacus cultivar Beakdansim tig00000628_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: 98470
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:7661 original size:30 final size:29
Alignment explanation
Indices: 7627--7781 Score: 89
Period size: 30 Copynumber: 5.0 Consensus size: 29
7617 CCAAAATATA
*
7627 ACTTTTAAAATTTATATTTTTAATCCTTAC
1 ACTTTTAAAATTTA-ATTTTTAATCCCTAC
* *
7657 ACTTTTACAAATTTACA-CTTTAATCCCTAG
1 ACTTTTA-AAATTTA-ATTTTTAATCCCTAC
*
7687 ACTTTCAAAATTTACTTTTTAAGTTTTTAATCCCTAC
1 ACTTT-TAAA---A---TTTAA-TTTTTAATCCCTAC
* * *
7724 ACTTTTACAAATTTACA-CTTTGATCCCTAG
1 ACTTTTA-AAATTTA-ATTTTTAATCCCTAC
* * *
7754 ACTTTTGAAATTTACTTTTCAATCCCTA
1 ACTTTTAAAATTTAATTTTTAATCCCTA
7782 GTCGAAAATT
Statistics
Matches: 96, Mismatches: 16, Indels: 27
0.69 0.12 0.19
Matches are distributed among these distances:
29 16 0.17
30 40 0.42
31 13 0.14
32 1 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 5 0.05
37 18 0.19
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.46
Consensus pattern (29 bp):
ACTTTTAAAATTTAATTTTTAATCCCTAC
Found at i:7751 original size:67 final size:67
Alignment explanation
Indices: 7643--7772 Score: 224
Period size: 67 Copynumber: 1.9 Consensus size: 67
7633 AAAATTTATA
*
7643 TTTTTAATCCTTACACTTTTACAAATTTACACTTTAATCCCTAGACTTTCAAAATTTACTTTTTA
1 TTTTTAATCCCTACACTTTTACAAATTTACACTTTAATCCCTAGACTTTCAAAATTTACTTTTTA
7708 AG
66 AG
* **
7710 TTTTTAATCCCTACACTTTTACAAATTTACACTTTGATCCCTAGACTTTTGAAATTTACTTTT
1 TTTTTAATCCCTACACTTTTACAAATTTACACTTTAATCCCTAGACTTTCAAAATTTACTTTT
7773 CAATCCCTAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (67 bp):
TTTTTAATCCCTACACTTTTACAAATTTACACTTTAATCCCTAGACTTTCAAAATTTACTTTTTA
AG
Found at i:7778 original size:29 final size:30
Alignment explanation
Indices: 7711--7782 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
7701 CTTTTTAAGT
*
7711 TTTTAATCCCTACACTTTTACAAATTTACA
1 TTTTAATCCCTAGACTTTTACAAATTTACA
* * *
7741 CTTTGATCCCTAGACTTTT-GAAATTTAC-
1 TTTTAATCCCTAGACTTTTACAAATTTACA
7769 TTTTCAATCCCTAG
1 TTTT-AATCCCTAG
7783 TCGAAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
28 3 0.09
29 16 0.46
30 16 0.46
ACGTcount: A:0.28, C:0.24, G:0.06, T:0.43
Consensus pattern (30 bp):
TTTTAATCCCTAGACTTTTACAAATTTACA
Found at i:10429 original size:36 final size:37
Alignment explanation
Indices: 10362--10438 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
10352 TTTTTATATT
10362 TTTAATTTTGTAAAAAAATTTATATAAATATTATA-AA
1 TTTAATTTTGTAAAAAAA-TTATATAAATATTATACAA
* *
10399 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTATACAA
10436 TTT
1 TTT
10439 GTAATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 14 0.39
37 18 0.50
38 4 0.11
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATACAA
Found at i:10620 original size:20 final size:20
Alignment explanation
Indices: 10584--10621 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10574 ATCCTATTCC
**
10584 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
10604 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
10622 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:11764 original size:22 final size:21
Alignment explanation
Indices: 11730--11770 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
11720 ATAATTATTT
11730 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
11751 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
11771 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:22400 original size:20 final size:20
Alignment explanation
Indices: 22375--22417 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
22365 TTTTATTTTA
*
22375 TAATTGTATATTATTTAAAT
1 TAATTGTAAATTATTTAAAT
* *
22395 TAATTGTAAATTTTTTTAAT
1 TAATTGTAAATTATTTAAAT
22415 TAA
1 TAA
22418 AAAATATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TAATTGTAAATTATTTAAAT
Found at i:23696 original size:3 final size:3
Alignment explanation
Indices: 23690--23748 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
23680 TCCCATTTGG
23690 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23738 TTA TTA TTA TT
1 TTA TTA TTA TT
23749 TCATTTCAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25103 original size:14 final size:13
Alignment explanation
Indices: 25078--25118 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
25068 CCATGTTTAG
25078 TTATATTTTAATT
1 TTATATTTTAATT
25091 TTATATGTTTAATT
1 TTATAT-TTTAATT
**
25105 AAATATTTTAATT
1 TTATATTTTAATT
25118 T
1 T
25119 ATTATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TTATATTTTAATT
Found at i:25153 original size:21 final size:21
Alignment explanation
Indices: 25107--25153 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
25097 GTTTAATTAA
* *
25107 ATATTTTAATTTATTATTATT
1 ATATTTTAATATATTAATATT
*
25128 TTATTTTAATCATATTAATA-T
1 ATATTTTAAT-ATATTAATATT
25149 ATATT
1 ATATT
25154 ATTTGATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTTTAATATATTAATATT
Found at i:25326 original size:2 final size:2
Alignment explanation
Indices: 25271--25308 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
25261 ATATCATGCT
25271 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25309 TTAATTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26960 original size:20 final size:20
Alignment explanation
Indices: 26924--26961 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
26914 ATCCTATTCC
**
26924 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
26944 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
26962 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:37148 original size:18 final size:18
Alignment explanation
Indices: 37122--37159 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
37112 CAAGTTTATC
*
37122 TTTTTGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
37140 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
37158 TT
1 TT
37160 CTTTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:38289 original size:23 final size:22
Alignment explanation
Indices: 38247--38292 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
38237 GTTCATAATG
*
38247 AGAAGAATTCATCTGAAGAAGA
1 AGAAGAATTCATATGAAGAAGA
38269 AGAAGAAGTTCATAATG-AGAAGA
1 AGAAGAA-TTCAT-ATGAAGAAGA
38292 A
1 A
38293 TTTGTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 12 0.57
24 2 0.10
ACGTcount: A:0.52, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AGAAGAATTCATATGAAGAAGA
Found at i:38436 original size:122 final size:122
Alignment explanation
Indices: 38219--38800 Score: 771
Period size: 122 Copynumber: 4.7 Consensus size: 122
38209 CACTCGATGG
*
38219 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAGAAGAAGTTCATAA
* * * *
38284 TGAGAAGAATTTGTTCAACTTTTTGC-TCGATTCTATAACAGAAGGAGATAGATCAAC
66 TGAGAAGAACTTGTTCAACCTTTTGCAT-GATTCTATCACAGAAGGAGATAGATCAGC
38341 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAGAAGAAGTTCATAA
* ** *
38406 TGAGAATAACTTGTTCAAATTTTTGC-TCGATTCTATCACAGAAGGAGATAGATCAGT
66 TGAGAAGAACTTGTTCAACCTTTTGCAT-GATTCTATCACAGAAGGAGATAGATCAGC
* * * * *
38463 ATCAACATTTCTAGAAGTGTTCATAATGAGAAAAACTCATCTGAAG-AGGAAAAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGG-AGAAGAAGTTCATA
*
38527 ATGAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAAGAGATAGATCAGC
65 ATGAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAGC
* *
38585 AT-ACACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTT-ATCTGAAG-AGGAAGAAGAAGTTC
1 ATCA-ACATTTCCAGAAG-AGTTCATAATGAGAAGAA-TTCATCTGAAGAAGG-AGAAGAAGTTC
* * * *
38647 ATAATAAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATATATCAGC
62 ATAATGAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAGC
* * * *
38708 ATCAACATTCATTTCCCAAAGAGAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAGAAAAAGT
1 ATC-A-A--CATTT-CCAGA-AGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAGAAGAAGT
*
38773 TCATAATGAGAAGAATTTGTTCAACCTT
60 TCATAATGAGAAGAACTTGTTCAACCTT
38801 GCCTTAATTC
Statistics
Matches: 410, Mismatches: 37, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
121 4 0.01
122 233 0.57
123 97 0.24
124 1 0.00
125 3 0.01
127 5 0.01
128 63 0.15
129 4 0.01
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (122 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAGC
Found at i:40420 original size:14 final size:13
Alignment explanation
Indices: 40395--40433 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
40385 CCATGTTTAG
40395 TTATATTTTAATT
1 TTATATTTTAATT
40408 TTATATGTTTAATT
1 TTATAT-TTTAATT
*
40422 TAATATTTTAAT
1 TTATATTTTAAT
40434 CTATTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
TTATATTTTAATT
Found at i:40709 original size:149 final size:145
Alignment explanation
Indices: 40472--40869 Score: 385
Period size: 149 Copynumber: 2.7 Consensus size: 145
40462 TATAAGTTAA
* * ** * *
40472 TAATATTTATTTATTTTTAAAATATTAAGAAATGATAGTCTTAAAATAACTAGATGTCCTATTCT
1 TAATATTTATTTATTTTT-TAATATTAAGAAAAGGCAGTCTTAAAATAACTAGATGTCATTTTCT
* * * * *
40537 GGTA-TCTTAAAAATAATAAATATCATGCTTATAAAAATATATATTTATTTAATTTAATTTTATA
65 GATATTTTTAAATA-AATAAATATCATACTTATAAAAAT-TATATATA-TTAATTTAA-TTTAT-
*
40601 TAAATTATTTTA-A-TCATG-TT-T
125 T--A-T-TTTTAGAGACATGTTTAT
* *
40622 TAATATTTACTTATTTTTTAATATTAAGAAAAGGCAGTCTTAAAATAACTGGATGTCATTTTCTG
1 TAATATTTATTTATTTTTTAATATTAAGAAAAGGCAGTCTTAAAATAACTAGATGTCATTTTCTG
* * * * *
40687 ATATTTTTAAGTAAATAGATATCCTACTTTTATAAATTATATATATTAATTTAATTTATTATTTT
66 ATATTTTTAAATAAATAAATATCATACTTATAAAAATTATATATATTAATTTAATTTATTATTTT
40752 TAGAGACATGTTTTAT
131 TAGAGACATG-TTTAT
* * * * *
40768 TAATATTTATTTATTTTTTAATATTAAGAAAGGGGATGTCTTAAAACAGCTAGAAGAT-ATTTTC
1 TAATATTTATTTATTTTTTAATATTAAGAAAAGGCA-GTCTTAAAATAACTAGATG-TCATTTTC
* ** *
40832 TGATATTTCTAAATAAATAAATATTTTATTTATAAAAA
64 TGATATTTTTAAATAAATAAATATCATACTTATAAAAA
40870 CTTAAAATAT
Statistics
Matches: 206, Mismatches: 34, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
141 5 0.02
142 2 0.01
143 5 0.02
145 3 0.01
146 39 0.19
147 60 0.29
148 8 0.04
149 61 0.30
150 23 0.11
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (145 bp):
TAATATTTATTTATTTTTTAATATTAAGAAAAGGCAGTCTTAAAATAACTAGATGTCATTTTCTG
ATATTTTTAAATAAATAAATATCATACTTATAAAAATTATATATATTAATTTAATTTATTATTTT
TAGAGACATGTTTAT
Found at i:40898 original size:21 final size:23
Alignment explanation
Indices: 40874--40917 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
40864 TAAAAACTTA
*
40874 AAATATATATATA-T-ATATATT
1 AAATATATAGATATTAATATATT
40895 AAATATATAGATATTAATATATT
1 AAATATATAGATATTAATATATT
40918 TTCTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
23 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATATATAGATATTAATATATT
Found at i:40902 original size:15 final size:14
Alignment explanation
Indices: 40882--40916 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
40872 TAAAATATAT
*
40882 ATATATATATATTAA
1 ATATATAGATATT-A
40897 ATATATAGATATTA
1 ATATATAGATATTA
40911 ATATAT
1 ATATAT
40917 TTTCTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
ATATATAGATATTA
Found at i:40902 original size:23 final size:22
Alignment explanation
Indices: 40871--40917 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
40861 TTATAAAAAC
*
40871 TTAAAATATATATA-TATATATA
1 TTAAAATATAGATATTA-ATATA
40893 TTAAATATATAGATATTAATATA
1 TTAAA-ATATAGATATTAATATA
40916 TT
1 TT
40918 TTCTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 15 0.68
24 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAAAATATAGATATTAATATA
Found at i:41464 original size:2 final size:2
Alignment explanation
Indices: 41457--41488 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41447 TTTTCATAGA
41457 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
41489 TAAAGTTGTG
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:42701 original size:2 final size:2
Alignment explanation
Indices: 42694--42721 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42684 AAATAATTTA
42694 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
42722 CATTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43278 original size:39 final size:38
Alignment explanation
Indices: 43235--43309 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 38
43225 CGAGAGATAT
43235 ATAAA-TT-ATTTTTCAAATAACTAAAAAATTAAATTTTCA
1 ATAAATTTGATTTTT-AAATAA-TAAAAAATT-AATTTTCA
**
43274 ATAAATTTGATTTTTATTTAATAAAAAATTAATTTT
1 ATAAATTTGATTTTTAAATAATAAAAAATTAATTTT
43310 ATTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 6 0.19
39 14 0.44
40 6 0.19
41 6 0.19
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (38 bp):
ATAAATTTGATTTTTAAATAATAAAAAATTAATTTTCA
Found at i:43600 original size:16 final size:16
Alignment explanation
Indices: 43575--43605 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43565 CTTAACATCC
*
43575 TCTCTGCTTCTTCCAT
1 TCTCTACTTCTTCCAT
43591 TCTCTACTTCTTCCA
1 TCTCTACTTCTTCCA
43606 GTGACACAAC
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:0.10, C:0.39, G:0.03, T:0.48
Consensus pattern (16 bp):
TCTCTACTTCTTCCAT
Found at i:44569 original size:43 final size:43
Alignment explanation
Indices: 44509--44653 Score: 191
Period size: 43 Copynumber: 3.3 Consensus size: 43
44499 TTTTTTGCAA
** *
44509 AAAATGGTCAGATCTATAGTGGCGTTTTTGGATACAAACACCGC
1 AAAA-GGTCAGATCTATAGCAGCGTTTTTGGATACAAACGCCGC
* * * **
44553 AAAAGGTCAGTTCTATAGCAGCGTTTTTGCATATAAACGTTGC
1 AAAAGGTCAGATCTATAGCAGCGTTTTTGGATACAAACGCCGC
* *
44596 AAAATGTCAGATCTATAGCAGCGTTTTTGGATACAAATGCCGC
1 AAAAGGTCAGATCTATAGCAGCGTTTTTGGATACAAACGCCGC
44639 AAAAGGTCAGATCTA
1 AAAAGGTCAGATCTA
44654 GCACTCTGTT
Statistics
Matches: 85, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
43 81 0.95
44 4 0.05
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (43 bp):
AAAAGGTCAGATCTATAGCAGCGTTTTTGGATACAAACGCCGC
Found at i:48547 original size:41 final size:41
Alignment explanation
Indices: 48481--48676 Score: 239
Period size: 41 Copynumber: 4.7 Consensus size: 41
48471 ATAAATTTAC
* * * *
48481 GGCGTTTGTAAACACAAACACCACTAAAGTATGATTCTATAGC
1 GGCGTTTGTATA-A-AAACGCCACTAAAGTACGATTCTATAGT
* * * *
48524 GGCGTATGTATATAAACGCCACTAAAGTACAATTGTATAGT
1 GGCGTTTGTATAAAAACGCCACTAAAGTACGATTCTATAGT
* *
48565 GGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTATAGT
1 GGCGTTTGTATAAAAACGCCACTAAAGTACGATTCTATAGT
* * *
48606 GGTGTTTGTATAAAAACGCCACTAAAGTACGAATGTATAGT
1 GGCGTTTGTATAAAAACGCCACTAAAGTACGATTCTATAGT
**
48647 GGCGTTTGTATAAAAATACCACTAAAGTAC
1 GGCGTTTGTATAAAAACGCCACTAAAGTAC
48677 TACTCTGTTG
Statistics
Matches: 132, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
41 122 0.92
43 10 0.08
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (41 bp):
GGCGTTTGTATAAAAACGCCACTAAAGTACGATTCTATAGT
Found at i:48692 original size:41 final size:41
Alignment explanation
Indices: 48480--48759 Score: 235
Period size: 41 Copynumber: 6.8 Consensus size: 41
48470 TATAAATTTA
* * * *
48480 CGGCGTTTGTAAACACAAACACCACTAAAGTATGATTCTATAG
1 CGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAATCTATAG
* * *
48523 CGGCGTATGTATATAAACGCCACTAAAGTAC-AATTGTATAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAA-TCTATAG
* * *
48564 TGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTATAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAATCTATAG
* * *
48605 TGGTGTTTGTATAAAAACGCCACTAAAGTACGAATGTATAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAATCTATAG
* ** * * * *
48646 TGGCGTTTGTATAAAAATACCACTAAAGTACTACTCTGTTG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAATCTATAG
* * * *
48687 CGGCGTTTGTTGAAAAAAAATGCCACTATAA-T--GAACCTATTG
1 CGGCGTTTG-T--ATAAAAACGCCACTA-AAGTACGAATCTATAG
* *
48729 CGGCATTTGTATAAAAACGCCGCTAAAGTAC
1 CGGCGTTTGTATAAAAACGCCACTAAAGTAC
48760 TACTTTATAG
Statistics
Matches: 192, Mismatches: 36, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
38 2 0.01
39 13 0.07
40 1 0.01
41 133 0.69
42 16 0.08
43 11 0.06
44 14 0.07
45 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (41 bp):
CGGCGTTTGTATAAAAACGCCACTAAAGTACGAATCTATAG
Found at i:48703 original size:82 final size:82
Alignment explanation
Indices: 48481--48696 Score: 281
Period size: 82 Copynumber: 2.6 Consensus size: 82
48471 ATAAATTTAC
* * * * * *
48481 GGCGTTTGTAAACACAAACACCACTAAAGTATGATTCTATAGCGGCGTATGTATATAAACGCCAC
1 GGCGTTTGTATA-A-AAATACCACTAAAGTACGACTCTATAGCGGCGTTTGTATAAAAACGCCAC
48546 TAAAGTACAATTGTATAGT
64 TAAAGTACAATTGTATAGT
* * * *
48565 GGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTATAGTGGTGTTTGTATAAAAACGCCACTA
1 GGCGTTTGTATAAAAATACCACTAAAGTACGACTCTATAGCGGCGTTTGTATAAAAACGCCACTA
48630 AAGTACGAA-TGTATAGT
66 AAGTAC-AATTGTATAGT
* * *
48647 GGCGTTTGTATAAAAATACCACTAAAGTACTACTCTGTTGCGGCGTTTGT
1 GGCGTTTGTATAAAAATACCACTAAAGTACGACTCTATAGCGGCGTTTGT
48697 TGAAAAAAAA
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
82 101 0.88
83 3 0.03
84 11 0.10
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (82 bp):
GGCGTTTGTATAAAAATACCACTAAAGTACGACTCTATAGCGGCGTTTGTATAAAAACGCCACTA
AAGTACAATTGTATAGT
Found at i:51135 original size:12 final size:13
Alignment explanation
Indices: 51108--51140 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
51098 TAATATATCC
*
51108 TTTAAAATTATAT
1 TTTAAAAATATAT
51121 TTTAAAAAT-TAT
1 TTTAAAAATATAT
51133 TTTAAAAA
1 TTTAAAAA
51141 ATAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAAAATATAT
Found at i:51287 original size:71 final size:70
Alignment explanation
Indices: 51194--51344 Score: 189
Period size: 71 Copynumber: 2.1 Consensus size: 70
51184 TCATTGTCTG
* * *
51194 AAAAAAAATTCTGCTTTTACTCTCAACTCTCCACTCCCCCTT-CTTCATCCCCCGA-TTTCATTG
1 AAAAAAAATTCTACTTTCACTCTCAACTC-CC-CCCCCCCTTCCTTC-TCCCCCGACTTTCATTG
51257 TCTGAAAC
63 TCTGAAAC
* * *
51265 AAAAAAAATTCTACTTTCACTCTCAACTCCCCCCCCCCTTCCTTCTCCCTCGACCTTTCATTTTT
1 AAAAAAAATTCTACTTTCACTCTCAACTCCCCCCCCCCTTCCTTCTCCCCCGA-CTTTCATTGTC
51330 TGAAAC
65 TGAAAC
51336 AAAGAAAAA
1 AAA-AAAAA
51345 ATTGCGATTG
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
69 15 0.21
70 6 0.09
71 44 0.63
72 5 0.07
ACGTcount: A:0.28, C:0.35, G:0.05, T:0.32
Consensus pattern (70 bp):
AAAAAAAATTCTACTTTCACTCTCAACTCCCCCCCCCCTTCCTTCTCCCCCGACTTTCATTGTCT
GAAAC
Found at i:58579 original size:17 final size:18
Alignment explanation
Indices: 58546--58580 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
58536 CTCTAATGAA
*
58546 TTTTTAATATGATTTTAT
1 TTTTTAATATGAATTTAT
58564 TTTTTAATAT-AATTTAT
1 TTTTTAATATGAATTTAT
58581 ATATAATTAC
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:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTAATATGAATTTAT
Found at i:67948 original size:23 final size:26
Alignment explanation
Indices: 67898--67948 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
67888 ATTTTATTTT
67898 AATAATTTAATATTAATATCATTAAA
1 AATAATTTAATATTAATATCATTAAA
* *
67924 AATAATTT-ATTTTAATTTC-TTAAA
1 AATAATTTAATATTAATATCATTAAA
67948 A
1 A
67949 GTAAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 6 0.26
25 9 0.39
26 8 0.35
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
AATAATTTAATATTAATATCATTAAA
Found at i:69290 original size:2 final size:2
Alignment explanation
Indices: 69234--69270 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
69224 CAAAAACCAG
69234 GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
69271 AGGTGGGGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:71186 original size:20 final size:20
Alignment explanation
Indices: 71161--71207 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
71151 TATTCCCTGA
71161 TAATCTTGTATTCTCACTAG
1 TAATCTTGTATTCTCACTAG
* *
71181 TAATCTTTTATTCTCACTGG
1 TAATCTTGTATTCTCACTAG
71201 TAATCTT
1 TAATCTT
71208 ACATTTTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (20 bp):
TAATCTTGTATTCTCACTAG
Found at i:71217 original size:20 final size:20
Alignment explanation
Indices: 71174--71234 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
71164 TCTTGTATTC
* ** *
71174 TCACTAGTAATCTTTTATTC
1 TCACTGGTAATCTTACATTT
71194 TCACTGGTAATCTTACATTT
1 TCACTGGTAATCTTACATTT
*
71214 TCACTGATAATCTTACATTT
1 TCACTGGTAATCTTACATTT
71234 T
1 T
71235 AACGCACTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.48
Consensus pattern (20 bp):
TCACTGGTAATCTTACATTT
Found at i:74874 original size:21 final size:20
Alignment explanation
Indices: 74842--74895 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
74832 TGACTCCAGG
74842 CGCATTCTCAAGGCCACTTGC
1 CGCATTC-CAAGGCCACTTGC
*
74863 CGCATCTCCAAGGCCATTTGC
1 CGCAT-TCCAAGGCCACTTGC
*
74884 CACATTTCCAAG
1 CGCA-TTCCAAG
74896 AGAGATGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (20 bp):
CGCATTCCAAGGCCACTTGC
Found at i:83455 original size:18 final size:18
Alignment explanation
Indices: 83434--83490 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
83424 TTAAAATTAA
83434 ATATTATTTTAAATAATT
1 ATATTATTTTAAATAATT
83452 ATA-T-TTTTACAACT-A-T
1 ATATTATTTTA-AA-TAATT
83468 AT-TATATTTTAAATAATT
1 ATAT-TATTTTAAATAATT
83486 ATATT
1 ATATT
83491 TTAACAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 16
0.66 0.00 0.34
Matches are distributed among these distances:
16 9 0.29
17 8 0.26
18 13 0.42
19 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTATTTTAAATAATT
Found at i:83458 original size:15 final size:15
Alignment explanation
Indices: 83438--83494 Score: 78
Period size: 15 Copynumber: 3.5 Consensus size: 15
83428 AATTAAATAT
83438 TATTTTAAATAATTA
1 TATTTTAAATAATTA
83453 TATTTTTACAACTATATTA
1 TA-TTTTA-AA-TA-ATTA
83472 TATTTTAAATAATTA
1 TATTTTAAATAATTA
83487 TATTTTAA
1 TATTTTAA
83495 CAATAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
15 14 0.37
16 7 0.18
17 4 0.11
18 7 0.18
19 6 0.16
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTTTAAATAATTA
Found at i:83478 original size:34 final size:34
Alignment explanation
Indices: 83438--83510 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
83428 AATTAAATAT
*
83438 TATTTTAAATAATTATATTTTTACAACT-ATATTA
1 TATTTTAAATAATTATATTTTAACAA-TAATATTA
83472 TATTTTAAATAATTATATTTTAACAATAATATTA
1 TATTTTAAATAATTATATTTTAACAATAATATTA
83506 T-TTTT
1 TATTTT
83511 CACCCCATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
33 5 0.14
34 32 0.86
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (34 bp):
TATTTTAAATAATTATATTTTAACAATAATATTA
Found at i:88308 original size:16 final size:17
Alignment explanation
Indices: 88275--88308 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
88265 TATTATTATA
88275 AAAATAATATAATTAATT
1 AAAATAATAT-ATTAATT
88293 AAAATAATAT-TTAATT
1 AAAATAATATATTAATT
88309 TTGAGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATAATATATTAATT
Found at i:88966 original size:19 final size:19
Alignment explanation
Indices: 88944--88979 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
88934 GACGTTGCAT
*
88944 TTTTTA-ATTATTTTTTAA
1 TTTTTATATTATTATTTAA
88962 TTTTTATATTATTATTTA
1 TTTTTATATTATTATTTA
88980 TATTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTATATTATTATTTAA
Found at i:88981 original size:12 final size:12
Alignment explanation
Indices: 88964--89002 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
88954 TTTTTTAATT
88964 TTTATATTATTA
1 TTTATATTATTA
88976 TTTATATTA-TA
1 TTTATATTATTA
*
88987 TTTAAATTAATTA
1 TTTATATT-ATTA
89000 TTT
1 TTT
89003 TCAACTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:89483 original size:10 final size:10
Alignment explanation
Indices: 89470--89494 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
89460 ATAATAATAT
89470 AAAAAATTTA
1 AAAAAATTTA
89480 AAAAAATTTA
1 AAAAAATTTA
89490 AAAAA
1 AAAAA
89495 TGCAACGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:91097 original size:60 final size:59
Alignment explanation
Indices: 91033--91147 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
91023 CATTACAACA
* * **
91033 TAGTAAGTAACTCATTTTTTTATGTGAACCGTTTAAGTTATAAGTATGAAACCGTTAACG
1 TAGTAAGTAACAC-CTTTTTTATGTGAACAATTTAAGTTATAAGTATGAAACCGTTAACG
* *
91093 TAGTAGGTAACACCTTTTTTATGTTAACAATTTAAGTTATAAGTATGAAACCGTT
1 TAGTAAGTAACACCTTTTTTATGTGAACAATTTAAGTTATAAGTATGAAACCGTT
91148 TATATTATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
59 38 0.78
60 11 0.22
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (59 bp):
TAGTAAGTAACACCTTTTTTATGTGAACAATTTAAGTTATAAGTATGAAACCGTTAACG
Found at i:91729 original size:21 final size:22
Alignment explanation
Indices: 91690--91749 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
91680 TTCAATTTTT
91690 TAATATTTAAAACTATCGATAA
1 TAATATTTAAAACTATCGATAA
*
91712 TAATATATT-AAA-TATCGATATT
1 TAATAT-TTAAAACTATCGATA-A
* *
91734 TAAAATTTCAAACTAT
1 TAATATTTAAAACTAT
91750 TTTTTATGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 10 0.31
22 17 0.53
23 5 0.16
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (22 bp):
TAATATTTAAAACTATCGATAA
Found at i:91981 original size:146 final size:150
Alignment explanation
Indices: 91761--92137 Score: 389
Period size: 146 Copynumber: 2.5 Consensus size: 150
91751 TTTTATGCGT
* * *
91761 AACCTATTTTATTAATAAAAATATTAATATAACATTCTAGATCACAACATATTTCTTATTGAACC
1 AACCCATTTTATTAATAAAAA-A-T-AT-TAACATTCCAGATCACAACCTATTTCTTATTGAACC
* * * * *
91826 ATGATA-TTTTTGGATGAAACTTATTTTATTAATAGAAA-TATTAACATT-TTATATTGCAACCT
62 ATAACATTTTTTGG-CGAAACTAATTTTATTAATA-AAAGTATTAACATTCTT-GATTGCAACCT
*
91888 ATTTC-T-T-ATGACATTCTTGTG-TGC
124 ATTTCTTATAATGACATTCTTG-GACGC
* *
91912 AATCCCATTTTATTAAT-AAAAATATTAACATTCGAGATCAC-ACCTATTTCTTATTGAA-TAGT
1 AA-CCCATTTTATTAATAAAAAATATTAACATTCCAGATCACAACCTATTTCTTATTGAACCA-T
* *
91974 AACATTTTTTGGCGCAACTAATTTTATTAATAAAAGTATTAACATTCTTGATTGCAACTTATTTC
64 AACATTTTTTGGCGAAACTAATTTTATTAATAAAAGTATTAACATTCTTGATTGCAACCTATTTC
*
92039 TTAGTGAACCATGACATTCTTGGACGT
129 TTA-T--A--ATGACATTCTTGGACGC
* *
92066 AACCCATTTTATTAATAAAAAATATTAACATTCCAGATCGCAACCTACTTT-TTATTGAACCATG
1 AACCCATTTTATTAATAAAAAATATTAACATTCCAGATCACAACCTA-TTTCTTATTGAACCATA
92130 ACATTTTT
65 ACATTTTT
92138 AGGTATAACT
Statistics
Matches: 191, Mismatches: 17, Indels: 32
0.80 0.07 0.13
Matches are distributed among these distances:
145 4 0.02
146 60 0.31
147 25 0.13
148 2 0.01
149 2 0.01
150 1 0.01
151 6 0.03
152 13 0.07
153 15 0.08
154 37 0.19
155 22 0.12
156 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (150 bp):
AACCCATTTTATTAATAAAAAATATTAACATTCCAGATCACAACCTATTTCTTATTGAACCATAA
CATTTTTTGGCGAAACTAATTTTATTAATAAAAGTATTAACATTCTTGATTGCAACCTATTTCTT
ATAATGACATTCTTGGACGC
Found at i:92125 original size:78 final size:76
Alignment explanation
Indices: 91895--92134 Score: 261
Period size: 78 Copynumber: 3.1 Consensus size: 76
91885 CCTATTTCTT
* * *
91895 ATGACATTCTTGTGTGCAATCCCATTTTATTAATAAAAATATTAACATTCGAGATCAC-ACCTAT
1 ATGACATTCTTG-GCGCAA-CCCATTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTAT
*
91959 TTCTTATTGAA-T
64 TTCTTATTGAACC
* * ** * ** * *
91971 AGTAACATTTTTTGGCGCAACTAATTTTATTAATAAAAGTATTAACATTCTTGATTGCAACTTAT
1 A-TGACA-TTCTTGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTAT
*
92036 TTCTTAGTGAACC
64 TTCTTATTGAACC
*
92049 ATGACATTCTTGGACGTAACCCATTTTATTAATAAAAAATATTAACATTCCAGATCGCAACCTAC
1 ATGACATTCTTGG-CGCAACCCATTTTATTAAT-AAAAATATTAACATTCCAGATCGCAACCTA-
92114 TTT-TTATTGAACC
63 TTTCTTATTGAACC
92127 ATGACATT
1 ATGACATT
92135 TTTAGGTATA
Statistics
Matches: 133, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
76 38 0.29
77 44 0.33
78 48 0.36
79 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (76 bp):
ATGACATTCTTGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTATTT
CTTATTGAACC
Found at i:92587 original size:15 final size:15
Alignment explanation
Indices: 92561--92601 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
92551 TTAATTTGGT
92561 TAAAATTTAATTCAAA
1 TAAAA-TTAATTCAAA
*
92577 TAAAATTAATTTAAA
1 TAAAATTAATTCAAA
*
92592 TAAATTTAAT
1 TAAAATTAAT
92602 ATGAATTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAATTAATTCAAA
Found at i:93138 original size:22 final size:22
Alignment explanation
Indices: 93113--93154 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
93103 TAATAAATTA
93113 TTTAAAATAAATCAATCCATGT
1 TTTAAAATAAATCAATCCATGT
93135 TTTAAAATAAATCAATCCAT
1 TTTAAAATAAATCAATCCAT
93155 ACTAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATGT
Found at i:93164 original size:22 final size:22
Alignment explanation
Indices: 93115--93163 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
93105 ATAAATTATT
* **
93115 TAAAATAAATCAATCCATGTTT
1 TAAAATAAATCAATCCATCTAA
93137 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCAT-CTAA
93160 TAAA
1 TAAA
93164 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATCTAA
Found at i:93173 original size:32 final size:32
Alignment explanation
Indices: 93135--93252 Score: 227
Period size: 32 Copynumber: 3.7 Consensus size: 32
93125 CAATCCATGT
93135 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
93167 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
93199 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
93231 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
93253 AACTACAATA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 84 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:93177 original size:14 final size:14
Alignment explanation
Indices: 93158--93242 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 14
93148 AATCCATACT
93158 AATAAATTATTTAA
1 AATAAATTATTTAA
* * *
93172 AATAAATCAATCCATACT
1 AATAAAT-TAT--TTA-A
93190 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
93204 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
93222 AATAAATTATTTAA
1 AATAAATTATTTAA
93236 AATAAAT
1 AATAAAT
93243 CAATCCATAC
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
14 21 0.40
15 9 0.17
17 9 0.17
18 14 0.26
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:93225 original size:18 final size:18
Alignment explanation
Indices: 93140--93228 Score: 68
Period size: 18 Copynumber: 5.4 Consensus size: 18
93130 CATGTTTTAA
*
93140 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
* *
93158 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
*
93172 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
* *
93190 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
93204 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
93222 AATAAAT
1 AATAAAT
93229 TATTTAAAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
14 14 0.27
15 9 0.17
17 8 0.15
18 21 0.40
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:93287 original size:22 final size:22
Alignment explanation
Indices: 93262--93317 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
93252 CAACTACAAT
93262 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
93284 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
*
93306 AATAAATTAATC
1 AATAAATCAATC
93318 TATACTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:93352 original size:166 final size:161
Alignment explanation
Indices: 93081--93390 Score: 457
Period size: 166 Copynumber: 1.9 Consensus size: 161
93071 TACTGAAATT
*
93081 TAAATAATCCATACAACTACAATAATAAATTATTTAAAATAAATCAATCCATGTTTTAAAATAAA
1 TAAATAATCCATACAACTACAATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
93146 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-CT-AA-TAAATTA-TTTAAAAT
66 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATCTAAACTAAATTATTTTAAAAT
*
93207 AAATCAATTCATACTAATAAATTATTTAAAA
131 AAATCAATCCATACTAATAAATTATTTAAAA
93238 TAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTT
1 TAAAT-AATCCATACAACTACAATAAT--A--AAT---TA-TTTAAAATAAATCAATCCATATTT
* * *
93303 TAAAATAAATTAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAACTAAATT
57 TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-TCTAAACTAAATT
93368 ATTTTAAAATAAATCAATCCATA
121 ATTTTAAAATAAATCAATCCATA
93391 TTTTATAATA
Statistics
Matches: 134, Mismatches: 5, Indels: 14
0.88 0.03 0.09
Matches are distributed among these distances:
157 5 0.04
158 21 0.16
160 1 0.01
162 3 0.02
165 2 0.01
166 72 0.54
168 1 0.01
169 2 0.01
170 7 0.05
171 20 0.15
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (161 bp):
TAAATAATCCATACAACTACAATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATCTAAACTAAATTATTTTAAAAT
AAATCAATCCATACTAATAAATTATTTAAAA
Found at i:93358 original size:22 final size:22
Alignment explanation
Indices: 93333--93401 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
93323 TAATAAATTA
93333 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
93355 TTTAAACT--A--AAT---TAT
1 TTTAAAATAAATCAATCCATAT
93370 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
93392 TTTATAATAA
1 TTTAAAATAA
93402 TTTATTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
15 10 0.27
17 1 0.03
18 3 0.08
19 3 0.08
20 1 0.03
22 19 0.51
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:93379 original size:37 final size:36
Alignment explanation
Indices: 93298--93418 Score: 160
Period size: 37 Copynumber: 3.4 Consensus size: 36
93288 AATCAATCCA
* **
93298 TATTTTAAAATAAATTAAT-C-TATACT-AATAAAT
1 TATTTTAAAATAAATCAATCCATATTTTAAATAAAT
93331 TA-TTTAAAATAAATCAATCCATATTTTAAACTAAAT
1 TATTTTAAAATAAATCAATCCATATTTTAAA-TAAAT
*
93367 TATTTTAAAATAAATCAATCCATATTTTATAATAATT
1 TATTTTAAAATAAATCAATCCATATTTTA-AATAAAT
93404 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
93419 TATTTTATAA
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
32 15 0.19
33 3 0.04
34 4 0.05
35 2 0.03
36 7 0.09
37 45 0.58
38 2 0.03
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (36 bp):
TATTTTAAAATAAATCAATCCATATTTTAAATAAAT
Found at i:93409 original size:15 final size:15
Alignment explanation
Indices: 93389--93493 Score: 167
Period size: 15 Copynumber: 7.0 Consensus size: 15
93379 AATCAATCCA
*
93389 TATTTTATAATAATT
1 TATTTTATAATAAAT
*
93404 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
93419 TATTTTATAATAAAT
1 TATTTTATAATAAAT
93434 TATTTTATAATAAAT
1 TATTTTATAATAAAT
93449 TATTTTATAATAAAT
1 TATTTTATAATAAAT
*
93464 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
93479 TATTTT-TAAATAAAT
1 TATTTTAT-AATAAAT
93494 AACCTTATTA
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
15 84 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTATAATAAAT
Done.