Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004777.1 Hibiscus syriacus cultivar Beakdansim tig00010773_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: 89638
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2119 original size:20 final size:20
Alignment explanation
Indices: 2096--2133 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2086 CTTTCGGACT
2096 TTTGTAAAACCTTTGGGTAA
1 TTTGTAAAACCTTTGGGTAA
* *
2116 TTTGTAAATCTTTTGGGT
1 TTTGTAAAACCTTTGGGT
2134 CTCAGTTAGT
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:0.24, C:0.08, G:0.21, T:0.47
Consensus pattern (20 bp):
TTTGTAAAACCTTTGGGTAA
Found at i:2559 original size:51 final size:47
Alignment explanation
Indices: 2502--2617 Score: 135
Period size: 51 Copynumber: 2.4 Consensus size: 47
2492 TTTAGTTGTG
* * *
2502 TCACAGAAGAGTAATGAAACAGATTATGTT-CAAGTCATGCAAATTCAGCCT
1 TCACAGAAGAGTAGTGAAACAAATCAT-TTGCAAGTCAT-C--ATT-AGCCT
* *
2553 TCACAGAAGAGTAGTGAATCAAATCATTTGCAAGTCATCCTTAGCCT
1 TCACAGAAGAGTAGTGAAACAAATCATTTGCAAGTCATCATTAGCCT
2600 TCACAGAAGAGTAGTGAA
1 TCACAGAAGAGTAGTGAA
2618 GTATGACAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
47 23 0.39
48 2 0.03
50 3 0.05
51 31 0.53
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (47 bp):
TCACAGAAGAGTAGTGAAACAAATCATTTGCAAGTCATCATTAGCCT
Found at i:4013 original size:15 final size:15
Alignment explanation
Indices: 3986--4027 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
3976 TAAGGTAAAA
3986 TTATATATTTAGTCCT
1 TTATAT-TTTAGTCCT
**
4002 TTATATTTTAGTTGT
1 TTATATTTTAGTCCT
4017 TTATATTTTAG
1 TTATATTTTAG
4028 CCCCATTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.62
Consensus pattern (15 bp):
TTATATTTTAGTCCT
Found at i:4297 original size:22 final size:24
Alignment explanation
Indices: 4246--4298 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
4236 ATATTTATGT
*
4246 TTAATATTATTTAGTAATTATTTAAA
1 TTAA-ATTATTTAGTAA-TATTAAAA
4272 TTAAATTATTT-GTAA-ATTAAAA
1 TTAAATTATTTAGTAATATTAAAA
4294 TTAAA
1 TTAAA
4299 AGAGCAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 11 0.42
24 4 0.15
25 7 0.27
26 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TTAAATTATTTAGTAATATTAAAA
Found at i:10366 original size:37 final size:38
Alignment explanation
Indices: 10325--10399 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
10315 GGCAAATTGT
*
10325 CTCAAGTGAGAT-GAAATCTTGTTTAAAGA-GAAATAAC
1 CTCAAGTGAGATAAAAATCTTGTTTAAA-ATGAAATAAC
10362 CTCAAGTGAGATAAAAAATCTTGTTTAAAATGAAATAA
1 CTCAAGTGAGAT-AAAAATCTTGTTTAAAATGAAATAA
10400 ATTCAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
37 12 0.35
38 1 0.03
39 21 0.62
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (38 bp):
CTCAAGTGAGATAAAAATCTTGTTTAAAATGAAATAAC
Found at i:16890 original size:2 final size:2
Alignment explanation
Indices: 16883--16999 Score: 234
Period size: 2 Copynumber: 58.5 Consensus size: 2
16873 TATGCTTGTG
16883 TA TA TA TA TA 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 TA TA TA TA TA
16925 TA TA TA TA TA 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 TA TA TA TA TA
16967 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 T
17000 GCTTCATGAG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 115 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20229 original size:36 final size:36
Alignment explanation
Indices: 20141--20611 Score: 269
Period size: 37 Copynumber: 13.3 Consensus size: 36
20131 TATTTAGTAT
* * *
20141 ATATATTAAAATAGTATAGTTTTTCAAAACATTTTCAAAA
1 ATATA-TATAATA-TATAGTTTTT-GAAACATTTT-GAAA
20181 CATATATATAATATATAGTTTTTGAAACATTTTGAAA
1 -ATATATATAATATATAGTTTTTGAAACATTTTGAAA
* *
20218 ATATATATAATATATAGTTTTTTAAAACATTTTAAAAA
1 ATATATATAATATATAG-TTTTTGAAACATTTT-GAAA
*
20256 TATATATATAATATATAGTTTTTG--A-A-----AAC
1 -ATATATATAATATATAGTTTTTGAAACATTTTGAAA
*
20285 ATATATATAATATATATTTTTTGAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTTG-AAACATTTTGAAA
20322 ATATATATAATATATAGTTTTTGAAAACATTTTGAATA
1 ATATATATAATATATAGTTTTTG-AAACATTTTGAA-A
* * * **
20360 TATATATATATATATATA-TATAT-ATAGTTTTTGAAA
1 -ATATATATA-ATATATAGTTTTTGAAACATTTTGAAA
* * * *
20396 ACATATAT-ATATATAGCTTTTGAAAACAGTTTGAAT
1 ATATATATAATATATAGTTTTTG-AAACATTTTGAAA
* * * * * *
20432 ATATATAT-ATATATA-TATAT-ATATA-TAT--AT
1 ATATATATAATATATAGTTTTTGAAACATTTTGAAA
* * * * * *
20462 ATATATAT-ATATATA-TATAT-ATATA-TAT--AT
1 ATATATATAATATATAGTTTTTGAAACATTTTGAAA
*
20492 ATATATAT-ATATATAGTTTT-GAAAATATTTTGAAA
1 ATATATATAATATATAGTTTTTG-AAACATTTTGAAA
*
20527 ATATATATAGTATATAGTTTTTGAAAACATTTTTG--A
1 ATATATATAATATATAGTTTTTG-AAACA-TTTTGAAA
* * *
20563 ACATACATAATATATTG-TTTTGAAAGCATTTTTCGAAA
1 ATATATATAATATATAGTTTTTGAAA-CA-TTTT-GAAA
20601 ATATATATAAT
1 ATATATATAAT
20612 GTCATTTTTT
Statistics
Matches: 355, Mismatches: 44, Indels: 65
0.77 0.09 0.14
Matches are distributed among these distances:
28 22 0.06
29 2 0.01
30 47 0.13
31 3 0.01
32 7 0.02
33 12 0.03
34 5 0.01
35 31 0.09
36 67 0.19
37 69 0.19
38 33 0.09
39 39 0.11
40 13 0.04
41 5 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTGAAACATTTTGAAA
Found at i:20278 original size:28 final size:28
Alignment explanation
Indices: 20247--20423 Score: 117
Period size: 28 Copynumber: 6.4 Consensus size: 28
20237 TTTTAAAACA
* *
20247 TTTTAAAAATATATATATAATATATAGT
1 TTTTGAAAACATATATATAATATATAGT
*
20275 TTTTGAAAACATATATATAATATATATT
1 TTTTGAAAACATATATATAATATATAGT
20303 TTTTGAAAACATTTTGAAAATATATATAATATATAGT
1 TTTTGAAAAC---------ATATATATAATATATAGT
20340 TTTTGAAAACAT-T-T-TGAATATATA--
1 TTTTGAAAACATATATAT-AATATATAGT
* * *
20364 -TAT--ATATATATATAT-ATATATAGT
1 TTTTGAAAACATATATATAATATATAGT
*
20388 TTTTGAAAAC--ATATAT-ATATATAGC
1 TTTTGAAAACATATATATAATATATAGT
20413 TTTTGAAAACA
1 TTTTGAAAACA
20424 GTTTGAATAT
Statistics
Matches: 119, Mismatches: 11, Indels: 40
0.70 0.06 0.24
Matches are distributed among these distances:
21 4 0.03
22 8 0.07
23 3 0.03
24 1 0.01
25 27 0.23
26 9 0.08
27 3 0.03
28 37 0.31
37 27 0.23
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (28 bp):
TTTTGAAAACATATATATAATATATAGT
Found at i:20290 original size:65 final size:63
Alignment explanation
Indices: 20210--20364 Score: 215
Period size: 65 Copynumber: 2.4 Consensus size: 63
20200 TTTTGAAACA
*
20210 TTTTGAAAATATATATAATATATAGTTTTTT-AAAACATTTTAAAAATATATATATAATATATAG
1 TTTTGAAAACATATATAATATATA-TTTTTTGAAAACATTTT-AAAA-ATATATATAATATATAG
20274 T
63 T
*
20275 TTTTGAAAACATATATATAATATATATTTTTTGAAAACATTTTGAAAATATATATAATATATAGT
1 TTTTGAAAAC--ATATATAATATATATTTTTTGAAAACATTTTAAAAATATATATAATATATAGT
*
20340 TTTTGAAAACAT-TTTGAATATATAT
1 TTTTGAAAACATATAT-AATATATAT
20365 ATATATATAT
Statistics
Matches: 83, Mismatches: 3, Indels: 10
0.86 0.03 0.10
Matches are distributed among these distances:
62 2 0.02
63 11 0.13
65 37 0.45
66 9 0.11
67 24 0.29
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (63 bp):
TTTTGAAAACATATATAATATATATTTTTTGAAAACATTTTAAAAATATATATAATATATAGT
Found at i:20355 original size:48 final size:48
Alignment explanation
Indices: 20303--20399 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 48
20293 AATATATATT
*
20303 TTTTGAAAACAT-TTTGAAA-ATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAACATATAT-AAATATATATAT-ATATATAGTTTTTGAAAACA
* * *
20351 TTTTGAATATATATATATATATATATATATATATAGTTTTTGAAAACA
1 TTTTGAAAACATATATAAATATATATATATATATAGTTTTTGAAAACA
20399 T
1 T
20400 ATATATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 33 0.77
49 10 0.23
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (48 bp):
TTTTGAAAACATATATAAATATATATATATATATAGTTTTTGAAAACA
Found at i:20405 original size:2 final size:2
Alignment explanation
Indices: 20357--20385 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20347 AACATTTTGA
20357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20386 GTTTTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20421 original size:73 final size:74
Alignment explanation
Indices: 20314--20458 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 74
20304 TTTGAAAACA
* * *
20314 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAATATATATATATATATATATAT
1 TTTTGAAAACATATATAATATATAGCTTTTGAAAACAGTTTGAATATATATATATATATATATAT
20379 ATATATAGT
66 ATATATAGT
20388 TTTTGAAAACATATAT-ATATATAGCTTTTGAAAACAGTTTGAATATATATATATATATATATAT
1 TTTTGAAAACATATATAATATATAGCTTTTGAAAACAGTTTGAATATATATATATATATATATAT
20452 ATATATA
66 ATATATA
20459 TATATATATA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
73 53 0.78
74 15 0.22
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (74 bp):
TTTTGAAAACATATATAATATATAGCTTTTGAAAACAGTTTGAATATATATATATATATATATAT
ATATATAGT
Found at i:20436 original size:26 final size:25
Alignment explanation
Indices: 20373--20423 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
20363 ATATATATAT
*
20373 ATATATATATATAGTTTTTGAAAAC
1 ATATATATATATAGCTTTTGAAAAC
20398 ATATATATATATAGCTTTTGAAAAC
1 ATATATATATATAGCTTTTGAAAAC
20423 A
1 A
20424 GTTTGAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (25 bp):
ATATATATATATAGCTTTTGAAAAC
Found at i:20437 original size:2 final size:2
Alignment explanation
Indices: 20430--20506 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
20420 AACAGTTTGA
20430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20507 GTTTTGAAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22279 original size:6 final size:6
Alignment explanation
Indices: 22270--22299 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
22260 TGAGTCTTTA
*
22270 AATTTT AATTTT AATTTT AATTTA AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
22300 CACAATTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:22287 original size:12 final size:12
Alignment explanation
Indices: 22266--22299 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
22256 GAATTGAGTC
22266 TTTAAATTTTAA
1 TTTAAATTTTAA
*
22278 TTTTAATTTTAA
1 TTTAAATTTTAA
22290 TTTAAATTTT
1 TTTAAATTTT
22300 CACAATTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAAATTTTAA
Found at i:22484 original size:16 final size:18
Alignment explanation
Indices: 22463--22496 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
22453 TTAAAATTAG
22463 CATGCA-GGGT-AGAATT
1 CATGCATGGGTAAGAATT
22479 CATGCATGGGTAAGAATT
1 CATGCATGGGTAAGAATT
22497 AAAGCATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (18 bp):
CATGCATGGGTAAGAATT
Found at i:24276 original size:24 final size:24
Alignment explanation
Indices: 24244--24292 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
24234 ATTCTGTCTG
*
24244 ATTCAACCATTTAGTGGTACAACC
1 ATTCAACCATTCAGTGGTACAACC
24268 ATTCAACCATTCAGTGGTACAACC
1 ATTCAACCATTCAGTGGTACAACC
24292 A
1 A
24293 GCTGAACCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (24 bp):
ATTCAACCATTCAGTGGTACAACC
Found at i:28958 original size:37 final size:37
Alignment explanation
Indices: 28891--29198 Score: 412
Period size: 39 Copynumber: 8.2 Consensus size: 37
28881 TTAATATAGC
28891 ATAGTTTTTGAAAACATTTTGAAAACATATATATAATAT
1 ATAGTTTTTGAAAACATTTTG-AAA-ATATATATAATAT
*
28930 ATAGTTTTTGAAAACATTTTGAATATATATATAATAT
1 ATAGTTTTTGAAAACATTTTGAAAATATATATAATAT
28967 ATAGTTTTTGAAAACATTTTGAAAAAATATATATAATAT
1 ATAGTTTTTGAAAACATTTTG--AAAATATATATAATAT
*
29006 ATAATTTTTGAAAACATTTTGAAAACATATATATAATAT
1 ATAGTTTTTGAAAACATTTTG-AAA-ATATATATAATAT
* *
29045 ATAGTTTTTGAAATCAGTTTG--AATATATATAATAT
1 ATAGTTTTTGAAAACATTTTGAAAATATATATAATAT
29080 ATAG-TTTTGAAAACATTTTGAAAATATATATAATAT
1 ATAGTTTTTGAAAACATTTTGAAAATATATATAATAT
* *
29116 ATAGTTTTTGAAAACATTTTTGAACATATATATAATTT
1 ATAGTTTTTGAAAACA-TTTTGAAAATATATATAATAT
* **
29154 AT-GGTTTTGAAAGGATTTTTCGAAAATATATATAATAT
1 ATAGTTTTTGAAAACA-TTTT-GAAAATATATATAATAT
29192 -TA-TTTTT
1 ATAGTTTTT
29199 AAATCATATA
Statistics
Matches: 244, Mismatches: 16, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
34 14 0.06
35 17 0.07
36 19 0.08
37 65 0.27
38 42 0.17
39 87 0.36
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (37 bp):
ATAGTTTTTGAAAACATTTTGAAAATATATATAATAT
Found at i:29002 original size:76 final size:74
Alignment explanation
Indices: 28891--29198 Score: 412
Period size: 76 Copynumber: 4.1 Consensus size: 74
28881 TTAATATAGC
*
28891 ATAGTTTTTGAAAACATTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAATAT
1 ATAGTTTTTGAAAACATTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACATTTTGAAAAT
28956 ATATATAATAT
64 ATATATAATAT
*
28967 ATAGTTTTTGAAAACATTTTGAAAAAATATATATAATATATAATTTTTGAAAACATTTTGAAAAC
1 ATAGTTTTTGAAAACATTTTG--AAAATATATATAATATATAGTTTTTGAAAACATTTTG-AAA-
29032 ATATATATAATAT
62 ATATATATAATAT
* *
29045 ATAGTTTTTGAAATCAGTTTG--AATATATATAATATATAG-TTTTGAAAACATTTTGAAAATAT
1 ATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
29107 ATATAATAT
66 ATATAATAT
* * * **
29116 ATAGTTTTTGAAAACATTTTTGAACATATATATAATTTAT-GGTTTTGAAAGGATTTTTCGAAAA
1 ATAGTTTTTGAAAACA-TTTTGAAAATATATATAATATATAGTTTTTGAAAACA-TTTT-GAAAA
29180 TATATATAATAT
63 TATATATAATAT
29192 -TA-TTTTT
1 ATAGTTTTT
29199 AAATCATATA
Statistics
Matches: 212, Mismatches: 11, Indels: 20
0.87 0.05 0.08
Matches are distributed among these distances:
71 28 0.13
72 7 0.03
73 17 0.08
74 45 0.21
75 6 0.03
76 71 0.33
77 6 0.03
78 32 0.15
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (74 bp):
ATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
ATATAATAT
Found at i:29264 original size:16 final size:16
Alignment explanation
Indices: 29220--29256 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
29210 ATAATGCCAT
29220 TTTATTTATTTCATTTCA
1 TTTATTTATTT-A-TTCA
29238 TTTATTTATTTATTCA
1 TTTATTTATTTATTCA
29254 TTT
1 TTT
29257 TGTTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTTATTTATTCA
Found at i:30566 original size:21 final size:21
Alignment explanation
Indices: 30542--30610 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
30532 AACACTATTT
*
30542 TTTTATTTTGTTTTATTTTTA
1 TTTTATATTGTTTTATTTTTA
*** *
30563 TTTTCCCGCTTCTTT-ATT-TTA
1 TTTT--ATATTGTTTTATTTTTA
30584 TTTTATATTGTTTTATTTTTA
1 TTTTATATTGTTTTATTTTTA
30605 TTTTAT
1 TTTTAT
30611 CTTTTAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 5 0.14
20 3 0.08
21 20 0.56
22 3 0.08
23 5 0.14
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTATATTGTTTTATTTTTA
Found at i:30604 original size:26 final size:26
Alignment explanation
Indices: 30580--30640 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
30570 GCTTCTTTAT
* *
30580 TTTATTTT-ATATTGTTTTATTTTTAT
1 TTTATTTTAACATT-TTTTATATTTAT
30606 TTTATCTTTTAACATTTTTTATATTT-T
1 TTTA--TTTTAACATTTTTTATATTTAT
30633 TTTATTTT
1 TTTATTTT
30641 TCTTTTCTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
27 5 0.17
28 13 0.43
29 4 0.13
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTATTTTAACATTTTTTATATTTAT
Found at i:32829 original size:25 final size:25
Alignment explanation
Indices: 32786--32855 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 25
32776 TGGTTGCTAG
32786 AATTATTTTGTTAATTAT-ATATCTTAAA
1 AATTA-TTT-TTAATTATAAT-TC-TAAA
*
32814 TATTATTTTTAA-TATAATTCTAAA
1 AATTATTTTTAATTATAATTCTAAA
*
32838 AATTATTTTAAATT-TAAT
1 AATTATTTTTAATTATAAT
32856 GTTAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 18 0.49
25 6 0.16
26 6 0.16
27 3 0.08
28 4 0.11
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (25 bp):
AATTATTTTTAATTATAATTCTAAA
Found at i:32861 original size:24 final size:23
Alignment explanation
Indices: 32809--32862 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
32799 ATTATATATC
* *
32809 TTAAATATTATTTTTAATATAAT
1 TTAAAAATTATTTTAAATATAAT
*
32832 TCTAAAAATTATTTTAAATTTAAT
1 T-TAAAAATTATTTTAAATATAAT
32856 GTTAAAA
1 -TTAAAA
32863 TAATCTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAAAAATTATTTTAAATATAAT
Found at i:38200 original size:21 final size:21
Alignment explanation
Indices: 38174--38226 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
38164 GTTTCCATAT
38174 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
* *
38195 TCGCAACACGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
38216 TCGCAATGCGA
1 TCGCAACGCGA
38227 TTTTCCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:38246 original size:19 final size:19
Alignment explanation
Indices: 38230--38417 Score: 160
Period size: 19 Copynumber: 9.3 Consensus size: 19
38220 AATGCGATTT
*
38230 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
38249 TCCAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
38270 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* * *
38289 TCTAAGTTCGCATTGCGGTTTAT
1 TCCAAGTTCG--TTGC-G-ATAG
* * *
38312 TCCAAATTCGCTGTGATAG
1 TCCAAGTTCGTTGCGATAG
38331 TCCAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
*
38352 TCCAAGTTCGTTGTGATAG
1 TCCAAGTTCGTTGCGATAG
* * *
38371 TCAAAGTTCGCGTTGTGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
38394 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
38413 TCCAA
1 TCCAA
38418 AATCGCAACG
Statistics
Matches: 137, Mismatches: 20, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
19 60 0.44
20 1 0.01
21 57 0.42
22 1 0.01
23 18 0.13
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:38264 original size:21 final size:21
Alignment explanation
Indices: 38238--38417 Score: 169
Period size: 21 Copynumber: 8.8 Consensus size: 21
38228 TTTCCAAATT
38238 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
38259 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
*
38278 CGTTGCGATAGTCTAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * * *
38299 CATTGCGGTTTATTCCAAATTCG
1 CGTTGC-G-ATAGTCCAAGTTCG
*
38322 C--TGTGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
38341 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
* *
38360 CGTTGTGATAGTCAAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * *
38381 CGTTGTGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
38402 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
38418 AATCGCAACG
Statistics
Matches: 131, Mismatches: 18, Indels: 22
0.77 0.11 0.13
Matches are distributed among these distances:
19 54 0.41
20 1 0.01
21 56 0.43
22 1 0.01
23 19 0.15
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:38280 original size:40 final size:40
Alignment explanation
Indices: 38230--38417 Score: 232
Period size: 40 Copynumber: 4.6 Consensus size: 40
38220 AATGCGATTT
38230 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
* * * * *
38270 TCCAAGTTCGTTGCGATAGTCTAAGTTCGCATTGCGGTTTAT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGC-G-ATAG
* *
38312 TCCAAATTCGCTGTGATAGTCCAAGTTCGCGTTGCGATAG
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
* * * * *
38352 TCCAAGTTCGTTGTGATAGTCAAAGTTCGCGTTGTGATTTAT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAG
38394 TCCAAATTCGTTGCGATAGTCCAA
1 TCCAAATTCGTTGCGATAGTCCAA
38418 AATCGCAACG
Statistics
Matches: 124, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
40 67 0.54
41 2 0.02
42 55 0.44
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (40 bp):
TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
Found at i:38334 original size:82 final size:82
Alignment explanation
Indices: 38216--38417 Score: 318
Period size: 82 Copynumber: 2.5 Consensus size: 82
38206 ACTTCGACTA
*
38216 TCGCAATGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
*
38279 GTTGCGATAGTCTAAGT
66 GTTGCGATAGTCAAAGT
* * *
38296 TCGCATTGCGGTTTATTCCAAATTCGCTGTGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
*
38361 GTTGTGATAGTCAAAGT
66 GTTGCGATAGTCAAAGT
* *
38378 TCGCGTTGTGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
38418 AATCGCAACG
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 9 0.08
81 2 0.02
82 98 0.90
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (82 bp):
TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
GTTGCGATAGTCAAAGT
Found at i:38518 original size:6 final size:6
Alignment explanation
Indices: 38507--38538 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
38497 GACACGTATT
38507 ACCACG ACCACG ACCACG ACCACG A-CACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
38539 CGAGACGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:39197 original size:6 final size:6
Alignment explanation
Indices: 39182--39214 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
39172 TCTCGTCTCG
*
39182 GGTCGA GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
39215 AATACGTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.03, C:0.15, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:40770 original size:5 final size:5
Alignment explanation
Indices: 40748--41065 Score: 125
Period size: 5 Copynumber: 63.0 Consensus size: 5
40738 TGAAAATTTC
* * *
40748 ATATT ATA-T ATATAT ATATT ATATT ATTATT GT-TG AGATTT AGTATT
1 ATATT ATATT ATAT-T ATATT ATATT A-TATT ATATT ATA-TT A-TATT
* * * *
40795 ACATAT ATACT ATATA ATGTTT ATATT ATA-T ATTATT -T-TT A-ATAT
1 ATAT-T ATATT ATATT AT-ATT ATATT ATATT A-TATT ATATT ATAT-T
* * *
40840 ATAGT ATATT AT-GT ATTATT ATATT ATATA ATACTT ATATT -T-TT ATA-T
1 ATATT ATATT ATATT A-TATT ATATT ATATT ATA-TT ATATT ATATT ATATT
* *
40888 ACTATAT ATATT ATATT ACATT ATATT A-A-T ATTTT ATATT ATATT ATATAGT
1 A-TAT-T ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT--T
* *
40940 ATATT ATTATT ATA-T AGTATTT ATATT TTA-T AGTGTT ATATT ATATT
1 ATATT A-TATT ATATT A-TA-TT ATATT ATATT A-TATT ATATT ATATT
* ** *
40987 ATA-T ATAATAT ATATT ATAGT ATA-- ATATT A-ATAT ATATT GCATA
1 ATATT AT-AT-T ATATT ATATT ATATT ATATT ATAT-T ATATT ATATT
* *
41031 ATA-T ATATT ATATT ATATTT TTATT ATATT TTATT
1 ATATT ATATT ATATT ATA-TT ATATT ATATT ATATT
41066 CTTATTATTA
Statistics
Matches: 234, Mismatches: 38, Indels: 82
0.66 0.11 0.23
Matches are distributed among these distances:
3 9 0.04
4 27 0.12
5 137 0.59
6 48 0.21
7 13 0.06
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:40770 original size:7 final size:7
Alignment explanation
Indices: 40748--41043 Score: 103
Period size: 7 Copynumber: 40.3 Consensus size: 7
40738 TGAAAATTTC
40748 ATATTAT
1 ATATTAT
40755 ATATATAT
1 ATAT-TAT
40763 ATATTAT
1 ATATTAT
40770 ATTATTAT
1 A-TATTAT
* *
40778 -TGTTGAG
1 ATATT-AT
40785 AT-TTAGT
1 ATATTA-T
*
40792 ATTACATAT
1 A-TA-TTAT
*
40801 ATACTAT
1 ATATTAT
*
40808 ATAATGTTT
1 AT-AT-TAT
40817 ATATTAT
1 ATATTAT
40824 ATATTAT
1 ATATTAT
*
40831 -TTTTA-
1 ATATTAT
40836 ATATATAGT
1 ATAT-TA-T
40845 ATATTAT
1 ATATTAT
*
40852 GTATTATT
1 ATATTA-T
40860 ATATTAT
1 ATATTAT
40867 ATA--AT
1 ATATTAT
*
40872 A-CTTAT
1 ATATTAT
*
40878 ATTTTTAT
1 A-TATTAT
40886 ATACTATAT
1 ATA-T-TAT
40895 ATATTAT
1 ATATTAT
*
40902 AT-TACATT
1 ATAT-TA-T
40910 ATATTA-
1 ATATTAT
*
40916 ATATTTT
1 ATATTAT
40923 ATATTAT
1 ATATTAT
40930 ATTATATAGT
1 A-TAT-TA-T
40940 ATATTAT
1 ATATTAT
40947 -TATTAT
1 ATATTAT
*
40953 ATAGTATTT
1 ATA-T-TAT
*
40962 ATATTTT
1 ATATTAT
40969 ATAGTGT-T
1 ATA-T-TAT
40977 ATATTAT
1 ATATTAT
40984 AT-TATAT
1 ATAT-TAT
*
40991 ATAATAT
1 ATATTAT
40998 ATATTAT
1 ATATTAT
*
41005 AGTATAAT
1 A-TATTAT
*
41013 ATTAATAT
1 A-TATTAT
**
41021 ATATTGC
1 ATATTAT
*
41028 ATAATAT
1 ATATTAT
41035 ATATTAT
1 ATATTAT
41042 AT
1 AT
41044 TATATTTTTA
Statistics
Matches: 219, Mismatches: 33, Indels: 74
0.67 0.10 0.23
Matches are distributed among these distances:
5 3 0.01
6 27 0.12
7 95 0.43
8 62 0.28
9 28 0.13
10 4 0.02
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (7 bp):
ATATTAT
Found at i:40810 original size:2 final size:2
Alignment explanation
Indices: 40797--41048 Score: 68
Period size: 2 Copynumber: 139.0 Consensus size: 2
40787 TTAGTATTAC
* * * *
40797 AT AT AT ACT AT AT A- AT GT TT AT AT -T AT AT AT -T AT TT TT A-
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
40836 AT AT AT AGT AT AT -T AT GT AT -T AT -T AT AT -T AT AT A- AT ACT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
40875 -T AT AT TT TT AT AT ACT AT AT AT AT -T AT AT -T AC AT -T AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
40914 -T A- AT AT -T TT AT AT -T AT AT -T AT AT AGT AT AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
40950 -T AT AT AGT AT TT AT AT -T TT AT AGT GT -T AT AT -T AT AT -T AT
1 AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
40989 AT AT A- AT AT AT AT -T AT AGT AT A- AT AT -T A- AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
**
41026 GC AT A- AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
41049 TTTTATTATA
Statistics
Matches: 189, Mismatches: 19, Indels: 84
0.65 0.07 0.29
Matches are distributed among these distances:
1 34 0.18
2 141 0.75
3 14 0.07
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (2 bp):
AT
Found at i:40920 original size:40 final size:39
Alignment explanation
Indices: 40844--41065 Score: 153
Period size: 40 Copynumber: 5.7 Consensus size: 39
40834 TAATATATAG
* *
40844 TATATTAT-GTAT-TATTATATTATATAATACTTATATTT
1 TATATTATATTATATATTATATTATATTATA-TTATATTT
*
40882 T-TA-TATACTATATATATTATATTACATTATATTAATATTT
1 TATATTATA-T-TATATATTATATTATATTATATT-ATATTT
*
40922 TATATTATATTATATAGTATATTATTATTATA-TAGTA-TT
1 TATATTATATTATATATTATATTA-TATTATATTA-TATTT
* * *
40961 TATA-T-T-TTATAGTGTTATATTATATTATA-TATAATA
1 TATATTATATTATA-TATTATATTATATTATATTATATTT
* * *
40997 TATATTATAGTATAATATTA-ATATATATTGCATAATATATAT
1 TATATTATATTAT-ATATTATAT-TATATT--ATATTATATTT
* *
41039 TATATTATATT-TTTATTATATTTTATT
1 TATATTATATTATATATTATATTATATT
41066 CTTATTATTA
Statistics
Matches: 148, Mismatches: 16, Indels: 38
0.73 0.08 0.19
Matches are distributed among these distances:
35 2 0.01
36 22 0.15
37 12 0.08
38 5 0.03
39 25 0.17
40 49 0.33
41 15 0.10
42 18 0.12
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (39 bp):
TATATTATATTATATATTATATTATATTATATTATATTT
Found at i:40968 original size:46 final size:43
Alignment explanation
Indices: 40751--41060 Score: 170
Period size: 44 Copynumber: 7.3 Consensus size: 43
40741 AAATTTCATA
*
40751 TTATATATA-TATATATTATATTATTATTGT-TGAG-ATTTAGTATT
1 TTATATATATTATATA-TATATTA-TATTATAT-AGTATTTA-TATT
** * * * * *
40795 ACATATATACTATATA-ATGTTTATATTATATATTATTTTTAAT
1 TTATATATATTATATATAT-ATTATATTATATAGTATTTATATT
* * * *
40838 ATATAGTATATTATGTAT-TATTATATTATATAATACTTATATT
1 TTATA-TATATTATATATATATTATATTATATAGTATTTATATT
* * *
40881 TT-TATATA--CTATATATATTATATTACATTA-TATTAATATT
1 TTATATATATTATATATATATTATATTATA-TAGTATTTATATT
40921 TTATATTATATTATATAGTATATTATTATTATATAGTATTTATATT
1 TTATA-TATATTATATA-TATATTA-TATTATATAGTATTTATATT
* *
40967 TTATA-GTGTTATAT-TATATTATA-TATA-A-TA--TATATT
1 TTATATATATTATATATATATTATATTATATAGTATTTATATT
* * *
41003 ATAGTATAATATTA-ATATATATTGCATAATATATATTATATTATATT
1 TTA-TAT-ATATTATATATATATT--ATATTATATAGTAT-TTATATT
41050 TT-TATTATATT
1 TTATA-TATATT
41061 TTATTCTTAT
Statistics
Matches: 208, Mismatches: 30, Indels: 55
0.71 0.10 0.19
Matches are distributed among these distances:
36 8 0.04
37 2 0.01
38 4 0.02
39 15 0.07
40 25 0.12
41 13 0.06
42 17 0.08
43 36 0.17
44 38 0.18
45 22 0.11
46 21 0.10
47 7 0.03
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (43 bp):
TTATATATATTATATATATATTATATTATATAGTATTTATATT
Found at i:40972 original size:34 final size:34
Alignment explanation
Indices: 40839--41059 Score: 137
Period size: 34 Copynumber: 6.6 Consensus size: 34
40829 ATTTTTAATA
40839 TATAGTATATTATGTATTAT-TA-TAT-TATATA-
1 TATAGTATATTAT-TATTATATAGTATATATATAT
* *
40870 -ATACTTATATTTTTA-TATACTA-TATATATTATAT
1 TATA-GTATATTATTATTATA-TAGTATATA-TATAT
* * * *
40904 TACATTATATTAATATTTTATA-T-TATAT-TA-
1 TATAGTATATTATTATTATATAGTATATATATAT
* *
40934 TATAGTATATTATTATTATATAGTATTTATATTT
1 TATAGTATATTATTATTATATAGTATATATATAT
40968 TATAGTGTTATATTA-TATTATATA-TA-ATATATAT
1 TATA--G-TATATTATTATTATATAGTATATATATAT
* * *
41002 TATAGTATAATATTAATATATATTGCATAATATATAT
1 TATAGTATATTATT-AT-TATATAGTAT-ATATATAT
* *
41039 TATATTATATTTTTATTATAT
1 TATAGTATATTATTATTATAT
41060 TTTATTCTTA
Statistics
Matches: 149, Mismatches: 20, Indels: 38
0.72 0.10 0.18
Matches are distributed among these distances:
29 3 0.02
30 23 0.15
31 21 0.14
32 9 0.06
33 11 0.07
34 31 0.21
35 13 0.09
36 12 0.08
37 26 0.17
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (34 bp):
TATAGTATATTATTATTATATAGTATATATATAT
Found at i:41055 original size:16 final size:16
Alignment explanation
Indices: 41036--41073 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
41026 GCATAATATA
*
41036 TATTATATTATATTTT
1 TATTATATTATATTCT
*
41052 TATTATATTTTATTCT
1 TATTATATTATATTCT
41068 TATTAT
1 TATTAT
41074 TAGTTTGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTATATTATATTCT
Found at i:43907 original size:21 final size:21
Alignment explanation
Indices: 43877--43928 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
43867 GGTCCCATCT
43877 GAATTGGAAGTAGCA-AAGAAA
1 GAATTGGAAGTAG-AGAAGAAA
* *
43898 GAATTTGAAGTAGAGAAGAAG
1 GAATTGGAAGTAGAGAAGAAA
43919 GAATTGGAAG
1 GAATTGGAAG
43929 AAAAACTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.48, C:0.02, G:0.33, T:0.17
Consensus pattern (21 bp):
GAATTGGAAGTAGAGAAGAAA
Found at i:58950 original size:28 final size:29
Alignment explanation
Indices: 58893--58951 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
58883 ACTGGATCTA
* *
58893 TGTTAAAAAAGAGAGAAAATTTTTCGATC
1 TGTTAAAAAAGAGAGAAAATTTTCCAATC
58922 TGTTAAAAAA-AGAGAAAATTTTCCAATC
1 TGTTAAAAAAGAGAGAAAATTTTCCAATC
58950 TG
1 TG
58952 GTAGAGGTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (29 bp):
TGTTAAAAAAGAGAGAAAATTTTCCAATC
Found at i:61156 original size:12 final size:12
Alignment explanation
Indices: 61139--61169 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
61129 AACATAATAC
61139 ACATAATGCAAA
1 ACATAATGCAAA
61151 ACATAATGCAAA
1 ACATAATGCAAA
61163 ACA-AATG
1 ACATAATG
61170 ACATGCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.58, C:0.16, G:0.10, T:0.16
Consensus pattern (12 bp):
ACATAATGCAAA
Found at i:63515 original size:59 final size:59
Alignment explanation
Indices: 63443--63640 Score: 306
Period size: 59 Copynumber: 3.4 Consensus size: 59
63433 TTTAAAAAGT
*
63443 AATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGGC
1 AATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGGA
* **
63502 AATCATACTAAGTGTATGAATTTCCAGATAGGTCACTTTGTGTGCTAAAATGATAATTA
1 AATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGGA
* * * *
63561 AATCATACTAAGTGTATGGACTTCCAGATAGGGCACTTCGTGTGCTAAAATAATAAGGA
1 AATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGGA
* *
63620 AAACATACTACGTGTATGAAT
1 AATCATACTAAGTGTATGAAT
63641 ATTTGTGGGG
Statistics
Matches: 124, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 124 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (59 bp):
AATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGGA
Found at i:64170 original size:45 final size:46
Alignment explanation
Indices: 64121--64213 Score: 127
Period size: 45 Copynumber: 2.0 Consensus size: 46
64111 TAAGCAGAAC
*
64121 ATAAAAGGCATGAAAGAACGCCATAAAT-GAAA-GGTATAATAGTGT
1 ATAAAAGGAATGAAAGAACGCCAT-AATGGAAATGGTATAATAGTGT
* * *
64166 ATAAAAGGAATGAAAGGATGCCATAATGGAAATGGTATAATGGTGT
1 ATAAAAGGAATGAAAGAACGCCATAATGGAAATGGTATAATAGTGT
64212 AT
1 AT
64214 TATAAGCATG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
44 3 0.07
45 25 0.60
46 14 0.33
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.23
Consensus pattern (46 bp):
ATAAAAGGAATGAAAGAACGCCATAATGGAAATGGTATAATAGTGT
Found at i:70316 original size:34 final size:34
Alignment explanation
Indices: 70272--70421 Score: 113
Period size: 34 Copynumber: 4.1 Consensus size: 34
70262 GCATCTGTTC
*
70272 ATGCCAATAATGCACCCATATGCATTATTCTTTT
1 ATGCTAATAATGCACCCATATGCATTATTCTTTT
* *
70306 ATGCTGATAATGCACCCATATTCATTTCAGTTATGGCATCATTT
1 ATGCTAATAATGCACCCATATGCA-TT-A--T-T--C-T--TTT
* * * *
70350 CATGCCAGTAATGCACCTATATGCATTACTCTTTT
1 -ATGCTAATAATGCACCCATATGCATTATTCTTTT
* *
70385 CTGCTAATAATGCACCCATATTCATTATTC-TTT
1 ATGCTAATAATGCACCCATATGCATTATTCTTTT
70418 ATGC
1 ATGC
70422 AATCATTTTA
Statistics
Matches: 89, Mismatches: 16, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
33 6 0.07
34 45 0.51
35 5 0.06
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
44 5 0.06
45 19 0.21
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (34 bp):
ATGCTAATAATGCACCCATATGCATTATTCTTTT
Found at i:70318 original size:79 final size:79
Alignment explanation
Indices: 70222--70410 Score: 281
Period size: 79 Copynumber: 2.4 Consensus size: 79
70212 TTGTGGTATA
* * *
70222 CTTTTATGCCGATAATGCACCCATATGCATTTCGGCTATGGCATC-TGTTCATGCCAATAATGCA
1 CTTTTATGCTGATAATGCACCCATATTCATTTCAGCTATGGCATCAT-TTCATGCCAATAATGCA
*
70286 CCCATATGCATTATT
65 CCCATATGCATTACT
* *
70301 CTTTTATGCTGATAATGCACCCATATTCATTTCAGTTATGGCATCATTTCATGCCAGTAATGCAC
1 CTTTTATGCTGATAATGCACCCATATTCATTTCAGCTATGGCATCATTTCATGCCAATAATGCAC
*
70366 CTATATGCATTACT
66 CCATATGCATTACT
* *
70380 CTTTTCTGCTAATAATGCACCCATATTCATT
1 CTTTTATGCTGATAATGCACCCATATTCATT
70411 ATTCTTTATG
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 99 0.99
80 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (79 bp):
CTTTTATGCTGATAATGCACCCATATTCATTTCAGCTATGGCATCATTTCATGCCAATAATGCAC
CCATATGCATTACT
Found at i:72112 original size:57 final size:59
Alignment explanation
Indices: 71955--72121 Score: 187
Period size: 57 Copynumber: 2.9 Consensus size: 59
71945 TATACGCACC
* *
71955 ATAGTGCTAA-CCCGAGTAGGACACATAAGGTCGTGCCCACCATCTGCACTAGTTATACT
1 ATAGTGC-AATCCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACT
* * ** * * * * *
72014 TTAGTGCAGTCATGAATATGACACATAAGGGCGTTCCCACCATATGCACTTG-TA-CCT
1 ATAGTGCAATCCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACT
**
72071 ATAGTGCAATCCCGAGTATGACACATAAGGTCGTGGTCACCATATGCACTA
1 ATAGTGCAATCCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTA
72122 ATATTTTAGT
Statistics
Matches: 86, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
57 43 0.50
58 3 0.03
59 40 0.47
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (59 bp):
ATAGTGCAATCCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACT
Found at i:76094 original size:23 final size:24
Alignment explanation
Indices: 76036--76098 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
76026 GACTGCGAAA
*
76036 AATTT-TTCCTGAAGGACCACGTAG
1 AATTTGTTCC-GAAGGACCACATAG
* *
76060 AATATGTTCCGAATGACCACATAG
1 AATTTGTTCCGAAGGACCACATAG
76084 -ATTTGTTCCGAAGGA
1 AATTTGTTCCGAAGGA
76099 TCGCGTAGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 13 0.39
24 16 0.48
25 4 0.12
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (24 bp):
AATTTGTTCCGAAGGACCACATAG
Found at i:76107 original size:23 final size:23
Alignment explanation
Indices: 76037--76107 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
76027 ACTGCGAAAA
76037 ATTT-TTCCTGAAGGACCACGTAG
1 ATTTGTTCC-GAAGGACCACGTAG
* * *
76060 AATATGTTCCGAATGACCACATAG
1 -ATTTGTTCCGAAGGACCACGTAG
* *
76084 ATTTGTTCCGAAGGATCGCGTAG
1 ATTTGTTCCGAAGGACCACGTAG
76107 A
1 A
76108 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
23 19 0.50
24 15 0.39
25 4 0.11
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (23 bp):
ATTTGTTCCGAAGGACCACGTAG
Found at i:83141 original size:18 final size:18
Alignment explanation
Indices: 83115--83158 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
83105 TTTGTTTTAT
* *
83115 TATTATTATTATTATATA
1 TATTTTTATTATTATAAA
83133 TATTTTTATTATTATAAA
1 TATTTTTATTATTATAAA
*
83151 TGTTTTTA
1 TATTTTTA
83159 AATAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TATTTTTATTATTATAAA
Found at i:83219 original size:14 final size:14
Alignment explanation
Indices: 83200--83228 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
83190 GGAAGCCTAT
83200 CATACTGGCCCAAA
1 CATACTGGCCCAAA
83214 CATACTGGCCCAAA
1 CATACTGGCCCAAA
83228 C
1 C
83229 CCAATAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.38, G:0.14, T:0.14
Consensus pattern (14 bp):
CATACTGGCCCAAA
Found at i:85383 original size:27 final size:29
Alignment explanation
Indices: 85339--85396 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 29
85329 ATTTATATAC
**
85339 TTATTATTATTATTTTTTATTT-TTGTTT
1 TTATTATTATTAAATTTTATTTATTGTTT
*
85367 TTATT-TTATTAAATTTTATTTATTTTTT
1 TTATTATTATTAAATTTTATTTATTGTTT
85395 TT
1 TT
85397 GTTAGAGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.78
Consensus pattern (29 bp):
TTATTATTATTAAATTTTATTTATTGTTT
Done.