Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003586.1 Hibiscus syriacus cultivar Beakdansim tig00007564_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: 75767
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:728 original size:105 final size:106
Alignment explanation
Indices: 292--1734 Score: 1849
Period size: 105 Copynumber: 14.0 Consensus size: 106
282 GCATTGTTCT
* * * **
292 GAGTCCAATATCCTCCGTCGTGAAGTTG-AATTGGCTCTGGAACCGAGAAATTGTTTGTTG---A
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * * * *
353 -CAGCCGTCCATTCGTTGTGAAGTTGAACTTGTGTTATCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
393 GAGTCCAATATCCTTCGCTGTGAAGTTGAAA-TGACTCTG-AA-T--GAAA-T-TTTGTTGA-GA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * * * * *
450 TCAGC-CTCTC-TCATCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * * * *
490 G-GTTCAAGATCATTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-TTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
553 CCAGCGGTCCCTTCG-CGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** * *
593 GAGTCCAATATCCTACACTGTGAAGTTGAAATTGGCTCTG-AATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
657 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
698 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
763 CCAGC-GTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
803 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
868 CCAG-GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
908 GAGTCC-ATATCCTTCATTGTGAAGTT-AAATTGGCTCTGAAATTGAGAATTTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
971 CCA---GTACCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1009 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
1074 CC--C---CCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1110 GAGTCC-A-ATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
1172 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCG-TGTCT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1211 --GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
1274 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1315 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGAC-A
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
1379 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
1420 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCAT-TGAAATTG-GAAAGTTGTTTATTGAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC-TCTGAAATTGAGAAA-TTGTTTGTTGAC
*
1483 AACCAGCGGTCCCTTCGTCGTGAAGTTGAAC-TGTGTTGTCTG
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1525 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
1590 CCAGCGGTCCCTTCG-CGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * ** *
1630 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCCGAAATCAAAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * * *
1694 CCAGCCGTCCCTTTGTTGTGAAGTTAAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1735 AGTGGCATAT
Statistics
Matches: 1199, Mismatches: 102, Indels: 78
0.87 0.07 0.06
Matches are distributed among these distances:
95 7 0.01
96 48 0.04
97 16 0.01
98 32 0.03
99 35 0.03
100 5 0.00
101 141 0.12
102 90 0.08
103 122 0.10
104 139 0.12
105 446 0.37
106 118 0.10
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2574 original size:22 final size:22
Alignment explanation
Indices: 2548--2624 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
2538 TTATGTTTGG
2548 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2570 TCAAAGGTTTGGCATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2592 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2614 TCAACGGTTTG
1 TCAAAGGTTTG
2625 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:3234 original size:16 final size:15
Alignment explanation
Indices: 3213--3282 Score: 54
Period size: 15 Copynumber: 4.4 Consensus size: 15
3203 TGCATGTGCT
3213 TTTTTGTCCTTTTTTC
1 TTTTTGT-CTTTTTTC
3229 TTTTTGAT-TTTTGTTC
1 TTTTTG-TCTTTT-TTC
*
3245 TTTTTTGTTCTTTTTGC
1 -TTTTTG-TCTTTTTTC
*
3262 TTCTTT-TCTTTTTTG
1 TT-TTTGTCTTTTTTC
3277 TTTTTG
1 TTTTTG
3283 CCCTTTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
14 3 0.07
15 13 0.30
16 11 0.25
17 13 0.30
18 4 0.09
ACGTcount: A:0.01, C:0.11, G:0.10, T:0.77
Consensus pattern (15 bp):
TTTTTGTCTTTTTTC
Found at i:3250 original size:25 final size:25
Alignment explanation
Indices: 3222--3278 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
3212 TTTTTTGTCC
*
3222 TTTT-TTCTTTTTGATTTTTGTTCTT
1 TTTTGTTCTTTTTGATTCTT-TTCTT
*
3247 TTTTGTTCTTTTTGCTTCTTTTCTT
1 TTTTGTTCTTTTTGATTCTTTTCTT
3272 TTTTGTT
1 TTTTGTT
3279 TTTGCCCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 16 0.55
26 13 0.45
ACGTcount: A:0.02, C:0.11, G:0.09, T:0.79
Consensus pattern (25 bp):
TTTTGTTCTTTTTGATTCTTTTCTT
Found at i:3251 original size:10 final size:10
Alignment explanation
Indices: 3236--3268 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3226 TTCTTTTTGA
3236 TTTTTGTTCT
1 TTTTTGTTCT
3246 TTTTTGTTC-
1 TTTTTGTTCT
3255 TTTTTGCTTCT
1 TTTTTG-TTCT
3266 TTT
1 TTT
3269 CTTTTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.29
10 12 0.57
11 3 0.14
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (10 bp):
TTTTTGTTCT
Found at i:3295 original size:25 final size:25
Alignment explanation
Indices: 3236--3295 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
3226 TTCTTTTTGA
***
3236 TTTTTGTTCTTTTTTGTTCTTTTTGC
1 TTTTT-TTCTTTTTTGTTCTTTGCCC
*
3262 TTCTTTTCTTTTTTGTT-TTTGCCC
1 TTTTTTTCTTTTTTGTTCTTTGCCC
3286 TTTTTATTCT
1 TTTTT-TTCT
3296 GATTGAATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 8 0.29
25 16 0.57
26 4 0.14
ACGTcount: A:0.02, C:0.15, G:0.08, T:0.75
Consensus pattern (25 bp):
TTTTTTTCTTTTTTGTTCTTTGCCC
Found at i:7849 original size:18 final size:20
Alignment explanation
Indices: 7803--7850 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 20
7793 GAAAACAAAT
7803 TAAGTAAAATGATAAAATGAAG
1 TAAGT-AAATGATAAAAT-AAG
*
7825 AAAGTAAA-GATAAAAT-AG
1 TAAGTAAATGATAAAATAAG
7843 TAAGTAAA
1 TAAGTAAA
7851 AAAAACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 9 0.38
20 8 0.33
21 3 0.12
22 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (20 bp):
TAAGTAAATGATAAAATAAG
Found at i:8332 original size:49 final size:47
Alignment explanation
Indices: 8267--8517 Score: 125
Period size: 49 Copynumber: 5.3 Consensus size: 47
8257 ATAAAAAAAG
8267 AAAATAAATATATATAATGATAATA-AAA-AATATAGAAAATTAATAGAAA
1 AAAATAAATATATATAAT-A-AATATAAATAATATA-AAAA-TAATAGAAA
* *
8316 AAAATATATATATATAATAAATATAAATAATATAAAAATAATA-CAA
1 AAAATAAATATATATAATAAATATAAATAATATAAAAATAATAGAAA
** * * * *
8362 GTAAT-AATATAAGAATAATAAA-AGAAAGAGA-AGTAAAAAT-ATA-ATA
1 AAAATAAATAT-A-TATAATAAATATAAATA-ATA-TAAAAATAATAGAAA
* * *
8408 ATAATAAA-ATATA-AA-AAATATACAT-ATATATAAATAAGTAGAATA
1 AAAATAAATATATATAATAAATATAAATAATATAAAAATAA-TAGAA-A
* *
8453 AAAGA-AAAAAAATAATAATAAATATAATAGTAATAATAAAAATCAA-AGAAA
1 AAA-ATAAATATAT-ATAATAAATATAA-A-TAAT-ATAAAAAT-AATAGAAA
*
8504 ATAAATATATATAT
1 A-AAATAAATATAT
8518 GGGTAATAAC
Statistics
Matches: 153, Mismatches: 24, Indels: 47
0.68 0.11 0.21
Matches are distributed among these distances:
41 7 0.05
42 5 0.03
43 7 0.05
44 2 0.01
45 11 0.07
46 26 0.17
47 28 0.18
48 10 0.07
49 30 0.20
50 1 0.01
51 4 0.03
52 13 0.08
53 7 0.05
54 2 0.01
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.26
Consensus pattern (47 bp):
AAAATAAATATATATAATAAATATAAATAATATAAAAATAATAGAAA
Found at i:8333 original size:23 final size:22
Alignment explanation
Indices: 8265--8355 Score: 71
Period size: 23 Copynumber: 4.0 Consensus size: 22
8255 CAATAAAAAA
*
8265 AGAAAATAAATATATATAATGAT
1 AGAAAA-AAATATATATAATAAT
* *
8288 A-ATAAAAAATATAGAAAATTAAT
1 AGA-AAAAAATATATATAA-TAAT
8311 AGAAAAAAATATATATATATAAT
1 AGAAAAAAATATATATA-ATAAT
* *
8334 A-AATATAAATA-ATATAAAAAT
1 AGAA-AAAAATATATATAATAAT
8355 A
1 A
8356 ATACAAGTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
21 5 0.09
22 18 0.32
23 31 0.55
24 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (22 bp):
AGAAAAAAATATATATAATAAT
Found at i:8334 original size:13 final size:13
Alignment explanation
Indices: 8318--8358 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
8308 AATAGAAAAA
*
8318 AATATATATATAT
1 AATATATATAAAT
*
8331 AATAAATATAAAT
1 AATATATATAAAT
8344 AATATA-A-AAAT
1 AATATATATAAAT
8355 AATA
1 AATA
8359 CAAGTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 8 0.32
12 1 0.04
13 16 0.64
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AATATATATAAAT
Found at i:8339 original size:17 final size:17
Alignment explanation
Indices: 8315--8355 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
8305 ATTAATAGAA
*
8315 AAAAATATATAT-ATAT
1 AAAAATATAAATAATAT
8331 AATAAATATAAATAATAT
1 AA-AAATATAAATAATAT
8349 AAAAATA
1 AAAAATA
8356 ATACAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 14 0.64
18 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAATATAAATAATAT
Found at i:8358 original size:20 final size:20
Alignment explanation
Indices: 8272--8381 Score: 52
Period size: 23 Copynumber: 5.4 Consensus size: 20
8262 AAAAGAAAAT
8272 AAATATATATAATGATAATA-AA
1 AAATA-ATATAA--ATAATATAA
* *
8294 AAAT-ATAGAAAATTAATAGAA
1 AAATAATA-TAAA-TAATATAA
*
8315 AAA-AATATATAT-ATAT-A
1 AAATAATATAAATAATATAA
*
8332 ATA-AATATAAATAATATAA
1 AAATAATATAAATAATATAA
*
8351 AAATAATACAAGTAATAATATAA
1 AAATAATA-TA--AATAATATAA
*
8374 GAATAATA
1 AAATAATA
8382 AAAGAAAGAG
Statistics
Matches: 69, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
17 11 0.16
18 7 0.10
19 5 0.07
20 14 0.20
21 11 0.16
22 4 0.06
23 17 0.25
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (20 bp):
AAATAATATAAATAATATAA
Found at i:8386 original size:11 final size:11
Alignment explanation
Indices: 8341--8387 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
8331 AATAAATATA
8341 AATAATATAAA-
1 AATAATA-AAAG
*
8352 AATAATACAAG
1 AATAATAAAAG
*
8363 TAATAATATAAG
1 -AATAATAAAAG
8375 AATAATAAAAG
1 AATAATAAAAG
8386 AA
1 AA
8388 AGAGAAGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 2 0.06
11 19 0.61
12 10 0.32
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.23
Consensus pattern (11 bp):
AATAATAAAAG
Found at i:8443 original size:25 final size:25
Alignment explanation
Indices: 8314--8429 Score: 69
Period size: 26 Copynumber: 4.4 Consensus size: 25
8304 AATTAATAGA
8314 AAAAAATATATATATATAAT-AAATAT
1 AAAAAATATA-ATA-ATAATAAAATAT
* * *
8340 AAATAATATAAAAATAATACAAGTAAT
1 AAAAAATATAATAATAATA-AAAT-AT
* *
8367 AATATAAGA-ATAATAA-AAGAAAGAGA-
1 AA-A-AA-ATATAATAATAATAAA-ATAT
8393 AGTAAAAATATAATAATAATAAAATAT
1 A--AAAAATATAATAATAATAAAATAT
8420 AAAAAATATA
1 AAAAAATATA
8430 CATATATATA
Statistics
Matches: 68, Mismatches: 10, Indels: 25
0.66 0.10 0.24
Matches are distributed among these distances:
24 5 0.07
25 12 0.18
26 24 0.35
27 14 0.21
28 5 0.07
29 7 0.10
30 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (25 bp):
AAAAAATATAATAATAATAAAATAT
Found at i:8480 original size:71 final size:73
Alignment explanation
Indices: 8329--8494 Score: 165
Period size: 71 Copynumber: 2.4 Consensus size: 73
8319 ATATATATAT
*
8329 ATAATAAATAT-A-AAT--AATAT-AAAAATAATACAAGTAATAATATAAGAATAATAAAAGAAA
1 ATAATAAATATAATAATAAAATATAAAAAATAATACAAGTAATAATATAAGAAGAATAAAAGAAA
* *
8389 GAGAAGTA
66 GAAAAATA
* * *
8397 AAAATATA-ATAATAATAAAATATAAAAAAT-ATACATA-TATATAA-ATAAGTAGAATAAAAGA
1 ATAATAAATATAATAATAAAATATAAAAAATAATACA-AGTA-ATAATATAAGAAGAATAAAAGA
8458 AA-AAAAATA
64 AAGAAAAATA
* *
8467 ATAATAAATATAATAGTAATA-ATAAAAA
1 ATAATAAATATAATAATAAAATATAAAAA
8495 TCAAAGAAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
67 2 0.03
68 7 0.09
69 3 0.04
70 18 0.22
71 39 0.49
72 11 0.14
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (73 bp):
ATAATAAATATAATAATAAAATATAAAAAATAATACAAGTAATAATATAAGAAGAATAAAAGAAA
GAAAAATA
Found at i:9081 original size:37 final size:37
Alignment explanation
Indices: 9040--9144 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
9030 GTGCTTGTGG
* * *
9040 ATCCTATCTTTAGCAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* *
9077 ATCCTATTTTTAGGAGTTTAAATCCTA-TCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGT-AGAACTCT
* *
9114 AACCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
9145 GACGAAAAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
36 1 0.02
37 56 0.97
38 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:9781 original size:21 final size:21
Alignment explanation
Indices: 9747--9786 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9737 AGTCATATCT
*
9747 AGCCGTTGGGGAT-GTTTTGG
1 AGCCGTTGGAGATGGTTTTGG
9767 AGCCGTTTGGAGATGGTTTT
1 AGCCG-TTGGAGATGGTTTT
9787 TCTGCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (21 bp):
AGCCGTTGGAGATGGTTTTGG
Found at i:13048 original size:21 final size:21
Alignment explanation
Indices: 13022--13069 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
13012 CGGTTTCTGA
*
13022 ATCATCTG-GATTATAATCATT
1 ATCATC-GAGATTATAATCATC
13043 ATCATCGAGATTATAATCATC
1 ATCATCGAGATTATAATCATC
13064 ATCATC
1 ATCATC
13070 ATCAGAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (21 bp):
ATCATCGAGATTATAATCATC
Found at i:14870 original size:48 final size:48
Alignment explanation
Indices: 14788--15501 Score: 960
Period size: 48 Copynumber: 15.0 Consensus size: 48
14778 ACTCTAAAGG
* * * * *
14788 ATCAACAAAAGAACTTTTATTGATCTGAAAAACATT-TTGTGATTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTT-TGCTTCTTC
* * *
14836 ATCAACATGAGAACTTTTACTGGTCTGGATAACATTATTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
*
14884 ATCAACAAGAGAACTTTTACTGGTTTGAATAACATTGTTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
*
14932 AT---CAAGAGAACTTTTACTGGTCTGAATAATATTGTTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* * *
14977 ATCAACAGGAGAACTTTTACTGGTTTGAATAACATTGTTTGCTGCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
*
15025 ATCAACAAGAGAAC-TTTACTGGTATGAATAACATTGTTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* ** *
15072 ATCAACAAGAGAATTTTTACTAATTTGAATAACATTGTTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* *
15120 ATCAACAAGAGAACTTTTACTGGTCTGAATAATATAGTTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* *
15168 ATCAAC---AGAACTTTTACTGGTTTGAATAACATTGTTTGCTGCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* * * *
15213 ATCAACAGGAGAACTTTTACTAGTTTGAATAACATTGTTTGCTTTTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
** **
15261 ATCAACAAGAGAACTTTTACCAGTCTGAATAACATTGCCTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* * * *
15309 ATCAACAGGAGAATTTTTACTGCTCTGAATAACGTTGTTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* * *
15357 ATCAACAAGAGAACTTTTACCGGTCTGAATAACATTGTTTCCTTCTTT
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* * * *
15405 ATCAACAAGAGGAA-TTTTACTGGTTTGAATAGCATTGCTTGTTTCTTC
1 ATCAACAAGA-GAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
* *
15453 ATCAATAGGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
15501 A
1 A
15502 GAAGGTAACT
Statistics
Matches: 585, Mismatches: 71, Indels: 20
0.87 0.11 0.03
Matches are distributed among these distances:
45 84 0.14
47 47 0.08
48 449 0.77
49 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (48 bp):
ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTC
Found at i:15247 original size:141 final size:142
Alignment explanation
Indices: 14788--15501 Score: 913
Period size: 141 Copynumber: 5.0 Consensus size: 142
14778 ACTCTAAAGG
* * * * *
14788 ATCAACAAAAGAACTTTTA-TTGATCTGAAAAACATT-TTGTGATTCTTCATCAACATGAGAACT
1 ATCAACAAGAGAACTTTTACTAG-TCTGAATAACATTGTT-TGCTTCTTCATCAACAAGAGAACT
* * *
14851 TTTACTGGTCTGGATAACATTATTTGCTTCTTCATCAACAAGAGAACTTTTACTGGTTTGAATAA
64 TTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAAC-A-AGAACTTTTACTGGTCTGAATAA
14916 CATTGTTTGCTTCTTC
127 CATTGTTTGCTTCTTC
* * *
14932 AT---CAAGAGAACTTTTACTGGTCTGAATAATATTGTTTGCTTCTTCATCAACAGGAGAACTTT
1 ATCAACAAGAGAACTTTTACTAGTCTGAATAACATTGTTTGCTTCTTCATCAACAAGAGAACTTT
* * *
14994 TACTGGTTTGAATAACATTGTTTGCTGCTTCATCAACAAGAGAAC-TTTACTGGTATGAATAACA
66 TACTGGTCTGAATAACATTGTTTGCTTCTTCATCAAC-A-AGAACTTTTACTGGTCTGAATAACA
15058 TTGTTTGCTTCTTC
129 TTGTTTGCTTCTTC
* * *
15072 ATCAACAAGAGAATTTTTACTAATTTGAATAACATTGTTTGCTTCTTCATCAACAAGAGAACTTT
1 ATCAACAAGAGAACTTTTACTAGTCTGAATAACATTGTTTGCTTCTTCATCAACAAGAGAACTTT
* * *
15137 TACTGGTCTGAATAATATAGTTTGCTTCTTCATCAAC-AGAACTTTTACTGGTTTGAATAACATT
66 TACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACAAGAACTTTTACTGGTCTGAATAACATT
*
15201 GTTTGCTGCTTC
131 GTTTGCTTCTTC
* * *
15213 ATCAACAGGAGAACTTTTACTAGTTTGAATAACATTGTTTGCTTTTTCATCAACAAGAGAACTTT
1 ATCAACAAGAGAACTTTTACTAGTCTGAATAACATTGTTTGCTTCTTCATCAACAAGAGAACTTT
** ** * * *
15278 TACCAGTCTGAATAACATTGCCTGCTTCTTCATCAACAGGAGAATTTTTACTGCTCTGAATAACG
66 TACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA--AGAACTTTTACTGGTCTGAATAACA
15343 TTGTTTGCTTCTTC
129 TTGTTTGCTTCTTC
** * *
15357 ATCAACAAGAGAACTTTTACCGGTCTGAATAACATTGTTTCCTTCTTTATCAACAAGAGGAA-TT
1 ATCAACAAGAGAACTTTTACTAGTCTGAATAACATTGTTTGCTTCTTCATCAACAAGA-GAACTT
* * * * *
15421 TTACTGGTTTGAATAGCATTGCTTGTTTCTTCATCAATAGGAGAACTTTTACTGGTCTGAATAAC
65 TTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA--AGAACTTTTACTGGTCTGAATAAC
15486 ATTGTTTGCTTCTTC
128 ATTGTTTGCTTCTTC
15501 A
1 A
15502 GAAGGTAACT
Statistics
Matches: 505, Mismatches: 55, Indels: 20
0.87 0.09 0.03
Matches are distributed among these distances:
140 39 0.08
141 212 0.42
142 4 0.01
143 87 0.17
144 160 0.32
145 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (142 bp):
ATCAACAAGAGAACTTTTACTAGTCTGAATAACATTGTTTGCTTCTTCATCAACAAGAGAACTTT
TACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACAAGAACTTTTACTGGTCTGAATAACATT
GTTTGCTTCTTC
Found at i:17294 original size:22 final size:22
Alignment explanation
Indices: 17268--17309 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
17258 CTTGTTATAT
*
17268 ATTTTTGGGTAAATTATAAATG
1 ATTTTTGGGTAAAGTATAAATG
*
17290 ATTTTTGGGTCAAGTATAAA
1 ATTTTTGGGTAAAGTATAAA
17310 GATGGTCCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (22 bp):
ATTTTTGGGTAAAGTATAAATG
Found at i:17428 original size:60 final size:60
Alignment explanation
Indices: 17324--17436 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
17314 GTCCCCCGGT
* * *
17324 TATATGGTATTTCTTTGTTAAGTCCTCTGACTATAAAAAATTACAAAATGATCTCTCAAC
1 TATAGGGTATTTCTTTGTTAAGTCCCCGGACTATAAAAAATTACAAAATGATCTCTCAAC
* * * *
17384 TATAGGGTATTTCTTTTTTGAGTCCCCGGACTATTAAAAGTTACAAAATGATC
1 TATAGGGTATTTCTTTGTTAAGTCCCCGGACTATAAAAAATTACAAAATGATC
17437 ACACGACTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (60 bp):
TATAGGGTATTTCTTTGTTAAGTCCCCGGACTATAAAAAATTACAAAATGATCTCTCAAC
Found at i:21996 original size:34 final size:34
Alignment explanation
Indices: 21936--22001 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
21926 CTATGCATTT
* *
21936 TCTTAAAGATGTTTTATCATTGATTTTCTATACG
1 TCTTAAACATGTTTTATCATTGATTTTATATACG
21970 TCTTAAACATGTTTTATCATAT-ATTTTATATA
1 TCTTAAACATGTTTTATCAT-TGATTTTATATA
22002 TTTTCTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.97
35 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.52
Consensus pattern (34 bp):
TCTTAAACATGTTTTATCATTGATTTTATATACG
Found at i:32546 original size:52 final size:52
Alignment explanation
Indices: 32468--32594 Score: 236
Period size: 52 Copynumber: 2.4 Consensus size: 52
32458 TAAAGAGGCG
32468 ATTTTAGCATCGGGGAATATTTTATAGGGTAAAGTACTCTCGTCGATCCATA
1 ATTTTAGCATCGGGGAATATTTTATAGGGTAAAGTACTCTCGTCGATCCATA
32520 ATTTTAGCATCGGGGAATATTTTATAGGGTAAAGTACTCTCGTCGATCCATA
1 ATTTTAGCATCGGGGAATATTTTATAGGGTAAAGTACTCTCGTCGATCCATA
* *
32572 GTTCTAGCATCGGGGAATATTTT
1 ATTTTAGCATCGGGGAATATTTT
32595 TTTTAAATAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (52 bp):
ATTTTAGCATCGGGGAATATTTTATAGGGTAAAGTACTCTCGTCGATCCATA
Found at i:36886 original size:3 final size:3
Alignment explanation
Indices: 36878--36923 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
36868 ATTCCTAGAC
*
36878 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
36924 GTGATAAGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:36930 original size:9 final size:9
Alignment explanation
Indices: 36880--36930 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
36870 TCCTAGACAA
*
36880 TAATAATAA
1 TAATAATAG
*
36889 TAATAATAA
1 TAATAATAG
*
36898 TAATAATAA
1 TAATAATAG
36907 TAATAATAG
1 TAATAATAG
36916 TAATAATAG
1 TAATAATAG
*
36925 TGATAA
1 TAATAA
36931 GGAGTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (9 bp):
TAATAATAG
Found at i:48573 original size:15 final size:15
Alignment explanation
Indices: 48553--48628 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
48543 ATTATCGATG
48553 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
48568 AATTTTTATCTAAAT
1 AATTTTTATATAAAT
* *
48583 -A-TATTATCGAT-GAT
1 AATTTTTAT--ATAAAT
*
48597 --TTTTTACATAAAT
1 AATTTTTATATAAAT
*
48610 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
48625 AATT
1 AATT
48629 AGAATTTCAC
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
12 2 0.04
13 7 0.15
14 7 0.15
15 30 0.65
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.53
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:48587 original size:42 final size:42
Alignment explanation
Indices: 48538--48629 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
48528 ATAATAAAAT
*
48538 AATATATTATCGATGAATTTTTATATAAATAATTTTTATCTA
1 AATATATTATCGATGAATTTTTACATAAATAATTTTTATCTA
* *
48580 AATATATTATCGATGATTTTTTACATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTACATAAATAATTTTTATCTA
48622 AATA-ATTA
1 AATATATTA
48630 GAATTTCACT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (42 bp):
AATATATTATCGATGAATTTTTACATAAATAATTTTTATCTA
Found at i:48945 original size:25 final size:25
Alignment explanation
Indices: 48911--48970 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
48901 ACCCACCCCT
*
48911 TTCTTCTTCTCCAAGTTATTTTTTC
1 TTCTTCTTCTCCAAGTTATTTCTTC
* *
48936 TTCTTATTCTCCATGTTATTTCTTC
1 TTCTTCTTCTCCAAGTTATTTCTTC
48961 TTCTTCTTCT
1 TTCTTCTTCT
48971 TCTAAAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.10, C:0.25, G:0.03, T:0.62
Consensus pattern (25 bp):
TTCTTCTTCTCCAAGTTATTTCTTC
Found at i:49991 original size:25 final size:25
Alignment explanation
Indices: 49957--50013 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
49947 ATGTCGTTTT
49957 AGAAGAAGAAGAAAA-AACATGGAGA
1 AGAAGAAGAA-AAAATAACATGGAGA
*
49982 AGAAGAAGAAAAAATAACTTGGAGA
1 AGAAGAAGAAAAAATAACATGGAGA
50007 AGAAGAA
1 AGAAGAA
50014 AGGGGTGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.63, C:0.04, G:0.26, T:0.07
Consensus pattern (25 bp):
AGAAGAAGAAAAAATAACATGGAGA
Found at i:59043 original size:16 final size:16
Alignment explanation
Indices: 59022--59059 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
59012 TAGTGTCAGA
59022 GTATGGATTATACAAG
1 GTATGGATTATACAAG
59038 GTATGGATTATACAAG
1 GTATGGATTATACAAG
*
59054 GCATGG
1 GTATGG
59060 TTCGTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (16 bp):
GTATGGATTATACAAG
Found at i:59300 original size:93 final size:93
Alignment explanation
Indices: 59141--59321 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
59131 ACGCATAGTT
* * * * **
59141 TTTTTTAGCAACTTGTAGTGTCAGTGTATGGATTATATAGGACATGGTTCGATATAGTTGTATCT
1 TTTTTTAGCAACTTGTAGTGTCAGGGTATGGATTATAAAAGACATGGCTCGATATAACTGTATCT
*
59206 AATGAGCAGGCTACTTAATATAGATAAC
66 AATGAGCAGGCTACGTAATATAGATAAC
*
59234 TTTTTTAGCAACTTGTAGTGTCAGGGTATGGATTATACAAAG-CATGGCTCGTTATAACTGTATC
1 TTTTTTAGCAACTTGTAGTGTCAGGGTATGGATTATA-AAAGACATGGCTCGATATAACTGTATC
*
59298 TAATGAGCAGGTTACGTAATATAG
65 TAATGAGCAGGCTACGTAATATAG
59322 CTATGCATGG
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
93 76 0.97
94 2 0.03
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (93 bp):
TTTTTTAGCAACTTGTAGTGTCAGGGTATGGATTATAAAAGACATGGCTCGATATAACTGTATCT
AATGAGCAGGCTACGTAATATAGATAAC
Found at i:63654 original size:26 final size:26
Alignment explanation
Indices: 63584--63647 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
63574 CTCGACGAGC
* *
63584 ATCGCTGAGCACCGCTAATGATAAGT
1 ATCGTTGAGCACCACTAATGATAAGT
63610 ATCGTTGAGCACCACTAATGATAAGT
1 ATCGTTGAGCACCACTAATGATAAGT
63636 ATCGTTGAGCAC
1 ATCGTTGAGCAC
63648 TATTAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (26 bp):
ATCGTTGAGCACCACTAATGATAAGT
Found at i:69836 original size:16 final size:16
Alignment explanation
Indices: 69815--69846 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
69805 AAAGTATTTC
*
69815 ATATATTGTTAGGATT
1 ATATATTGCTAGGATT
69831 ATATATTGCTAGGATT
1 ATATATTGCTAGGATT
69847 GAAAAGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (16 bp):
ATATATTGCTAGGATT
Found at i:72393 original size:106 final size:103
Alignment explanation
Indices: 72133--72381 Score: 309
Period size: 103 Copynumber: 2.4 Consensus size: 103
72123 TTCTTAGTGG
* * * * *
72133 CAAACAAATTTATCACAATTTCTATTGATAATAGCGTTGAACACTTGGTCACTAAAAAATATTTA
1 CAAACAAATTCATCACAATTTCTATTGATAATAGTGTCGAACACTTGGTCATTAAAAAATACTTA
*
72198 GTGTGACAACATTGATGGTCACAAAATATCTTCAATGT
66 GAGTGACAACATTGATGGTCACAAAATATCTTCAATGT
* * * * * *
72236 CAAACAAATTCATCAAAATTTCCATTGAAAATTGTGTCGAACATTTGGTCATTAAATATATACTT
1 CAAACAAATTCATCACAATTTCTATTGATAATAGTGTCGAACACTTGGTCATTAAA-AAATACTT
* *
72301 AGAGTGACAACATTGATGGTCACAAAATATGTTTTCAGTGT
65 AGAGTGACAACATTGATGGTCACAAAATA--TCTTCAATGT
* * * *
72342 CGAATAAGTTCATCACAATTTATATTGATAATAGTGTCGA
1 CAAACAAATTCATCACAATTTCTATTGATAATAGTGTCGA
72382 CTAGATGGTC
Statistics
Matches: 121, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
103 47 0.39
104 34 0.28
106 40 0.33
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (103 bp):
CAAACAAATTCATCACAATTTCTATTGATAATAGTGTCGAACACTTGGTCATTAAAAAATACTTA
GAGTGACAACATTGATGGTCACAAAATATCTTCAATGT
Found at i:73539 original size:19 final size:19
Alignment explanation
Indices: 73503--73544 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
73493 ATGGCTCAAA
73503 GATCGATCCCTTAGGAAAAG
1 GATCGATCCCTTA-GAAAAG
73523 GATCGATCCCCTT-GAAAAG
1 GATCGAT-CCCTTAGAAAAG
73542 GAT
1 GAT
73545 ATATCCCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 7 0.33
21 5 0.24
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (19 bp):
GATCGATCCCTTAGAAAAG
Done.