Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006433.1 Hibiscus syriacus cultivar Beakdansim tig00015530_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: 101256
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1598 original size:2 final size:2
Alignment explanation
Indices: 1591--1628 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1581 ATGCATATGC
1591 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
1629 TATGGGTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6486 original size:32 final size:32
Alignment explanation
Indices: 6443--6518 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
6433 GAGCATATGT
6443 ATATGTTGTTTGCTGGCAGGGTTATCCAATAC
1 ATATGTTGTTTGCTGGCAGGGTTATCCAATAC
*
6475 ATTTGTTGTTTGCTGGCAGGGTTATCCAATAC
1 ATATGTTGTTTGCTGGCAGGGTTATCCAATAC
6507 ATATGTTGTTTG
1 ATATGTTGTTTG
6519 GGTTGTGTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.20, C:0.13, G:0.25, T:0.42
Consensus pattern (32 bp):
ATATGTTGTTTGCTGGCAGGGTTATCCAATAC
Found at i:16108 original size:19 final size:19
Alignment explanation
Indices: 16080--16119 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
16070 ACTATTGAAT
*
16080 TTTAAGATTTTATATTCGA
1 TTTAAAATTTTATATTCGA
16099 TTTAAAATTTTATATTCGA
1 TTTAAAATTTTATATTCGA
16118 TT
1 TT
16120 AAATTATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (19 bp):
TTTAAAATTTTATATTCGA
Found at i:22273 original size:23 final size:21
Alignment explanation
Indices: 22228--22286 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 21
22218 CTCCTCGCTA
22228 TGTATCGATACACTATGAATG
1 TGTATCGATACACTATGAATG
22249 TGTATCGATACATTCCT-TGAATG
1 TGTATCGATACA---CTATGAATG
22272 TGTATCGATACACTA
1 TGTATCGATACACTA
22287 ACAAGTGTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.06
21 12 0.35
23 18 0.53
24 2 0.06
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (21 bp):
TGTATCGATACACTATGAATG
Found at i:22720 original size:20 final size:20
Alignment explanation
Indices: 22697--22739 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
22687 TTAAAAAATG
22697 TTTTTATTTTAAAT-TGTTGT
1 TTTTTA-TTTAAATATGTTGT
*
22717 TTTTTATTTAATTATGTTGT
1 TTTTTATTTAAATATGTTGT
22737 TTT
1 TTT
22740 CATGAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (20 bp):
TTTTTATTTAAATATGTTGT
Found at i:22793 original size:12 final size:13
Alignment explanation
Indices: 22764--22796 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
22754 GTATTATGAT
*
22764 TTTTCAAACATTG
1 TTTTCAAACATAG
22777 TTTTCAAA-ATAG
1 TTTTCAAACATAG
22789 TTTTCAAA
1 TTTTCAAA
22797 TTTTTCCCAT
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:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:24297 original size:17 final size:18
Alignment explanation
Indices: 24262--24298 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
24252 AATGGTTTGA
24262 ATATTTAATTTGAACTTC
1 ATATTTAATTTGAACTTC
24280 ATATTT-ATATTG-ACTTC
1 ATATTTAAT-TTGAACTTC
24297 AT
1 AT
24299 TAATTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.51
Consensus pattern (18 bp):
ATATTTAATTTGAACTTC
Found at i:24697 original size:17 final size:18
Alignment explanation
Indices: 24662--24698 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
24652 AATGGTTTGA
24662 ATATTTAATTTGAACTTC
1 ATATTTAATTTGAACTTC
24680 ATATTT-ATATTG-ACTTC
1 ATATTTAAT-TTGAACTTC
24697 AT
1 AT
24699 TAATTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.51
Consensus pattern (18 bp):
ATATTTAATTTGAACTTC
Found at i:24962 original size:400 final size:403
Alignment explanation
Indices: 24113--25347 Score: 2082
Period size: 415 Copynumber: 3.0 Consensus size: 403
24103 ATACGAGCAC
* *
24113 ATTTTCCTCCTCCCGATCCACCTATGTATAATTAGACCTTTTCTTGCTTAGTTTTCTTGGATTGA
1 ATTTTCCTCATCCCGATCCACCTATGGATAATTAGACCTTTTCTTGCTTAGTTTTCTTGGATTGA
* *
24178 ATTTGAACTTATTGTTAA-AACATTTTGAATGTTTTAGATTTGTGTGTTTTTGGATGTTTGGATA
66 ATTTAAACTTATTGTTAATAAC-------A--TTTTAGA----TATGTTTTTGGATGTTTGGATA
24242 TATTTGTTTGAATGGTTTGAATATTTAATTTGAACTTCATATTTATATTGACTTCATTAATTTTT
118 TATTTGTTTGAATGGTTTGAATATTTAATTTGAACTTCATATTTATATTGACTTCATTAATTTTT
24307 GCATCATCTGTATATTAGATTTTATATGACCAATTCCCAATTTACATATTGTTTATGAATATTGG
183 GCATCATCTGTATATTAGATTTTATATGACCAATTCCCAATTTACATATTGTTTATGAATATTGG
*
24372 TTATGTACTAATGACTAATCTTTCTCTTGATTGTGATCTTAGCAGCTACATCTATATCTATTTAT
248 TTATGGACTAATGACTAATCTTTCTCTTGATTGTGATCTTAGCAGCTACATCTATATCTATTTAT
24437 ATCAATTGGCTATTTTCTTAAAAATCTTCTTTAAACATTTTCTAGAGTCTTTTTGATTTAACAAA
313 ATCAATTGGCTATTTTCTTAAAAATCTTCTTTAAACATTTTCTAGAGTCTTTTTGATTTAACAAA
24502 AAGGGGGAGAATAAAGTAAGGGAGTA
378 AAGGGGGAGAATAAAGTAAGGGAGTA
*
24528 ATTTTCCTCCTCCCGATCCACCTATGGATAATTAGACCTTTTCTTGCTTAGTTTTCTTGGATTGA
1 ATTTTCCTCATCCCGATCCACCTATGGATAATTAGACCTTTTCTTGCTTAGTTTTCTTGGATTGA
*
24593 ATTTGAACTTATTGTTAA-AACATTTT-GA-ATGTTTTTGGATGTTTGGATATATTTGTTTGAAT
66 ATTTAAACTTATTGTTAATAACATTTTAGATATGTTTTTGGATGTTTGGATATATTTGTTTGAAT
24655 GGTTTGAATATTTAATTTGAACTTCATATTTATATTGACTTCATTAATTTTTGCATCATCTGTAT
131 GGTTTGAATATTTAATTTGAACTTCATATTTATATTGACTTCATTAATTTTTGCATCATCTGTAT
*
24720 ATTAGATTTTATATGACCAATTTCCAATTTACATATTGTTTATGAATATTGGTTATGGACTAATG
196 ATTAGATTTTATATGACCAATTCCCAATTTACATATTGTTTATGAATATTGGTTATGGACTAATG
*
24785 ACTAATCTTTCTCTTGATTGTGATCTTAGCAGCTACATCTATATCTCTTTATATCAATTGGCTAT
261 ACTAATCTTTCTCTTGATTGTGATCTTAGCAGCTACATCTATATCTATTTATATCAATTGGCTAT
*
24850 TTTCTTAAAAATATTCTTTAAACATTTTCTAGAGTCTTTTTGATTTAACAAAAAGGGGGAGAATA
326 TTTCTTAAAAATCTTCTTTAAACATTTTCTAGAGTCTTTTTGATTTAACAAAAAGGGGGAGAATA
24915 AAGTAAGGGAGTA
391 AAGTAAGGGAGTA
24928 ATTTTCCTCATCCCGATCCACCTATGGATAATTAGACCTTTTCTTGCTTAGTTTTCTTGGATTGA
1 ATTTTCCTCATCCCGATCCACCTATGGATAATTAGACCTTTTCTTGCTTAGTTTTCTTGGATTGA
** *
24993 ATTTAAACTTATTGTTAATTTTTTTTGAATGTTTTAGATTTGTGTGTTTTTGGATGTTTGGATAT
66 ATTTAAACTTATTGTTAA-------T-AACATTTTAGA----TATGTTTTTGGATGTTTGGATAT
25058 ATTTGTTTGAATGGTTTGAATATTTAATTTGAACTTCATATTTATATTGACTTCATTAATTTTTG
119 ATTTGTTTGAATGGTTTGAATATTTAATTTGAACTTCATATTTATATTGACTTCATTAATTTTTG
*
25123 CATCATCTGTATATTAGATTTCATATGACCAATTCCCAATTTACATATTGTTTATGAATATTGGT
184 CATCATCTGTATATTAGATTTTATATGACCAATTCCCAATTTACATATTGTTTATGAATATTGGT
25188 TATGGACTAATGACTAATCTTTCTCTTGATTGTGATCTTAGCAGCTACATCTATATCTATTTATA
249 TATGGACTAATGACTAATCTTTCTCTTGATTGTGATCTTAGCAGCTACATCTATATCTATTTATA
*
25253 ACAATTGGCTATTTTCTTAAAAATCTTCTTTAAACATTTTCTAGAGTCTTTTTGATTTAACAAAA
314 TCAATTGGCTATTTTCTTAAAAATCTTCTTTAAACATTTTCTAGAGTCTTTTTGATTTAACAAAA
25318 AGGGGGAGAATAAAGTAAGGGAGTA
379 AGGGGGAGAATAAAGTAAGGGAGTA
25343 ATTTT
1 ATTTT
25348 TCAAAATTGA
Statistics
Matches: 789, Mismatches: 16, Indels: 30
0.94 0.02 0.04
Matches are distributed among these distances:
400 383 0.49
405 2 0.00
406 4 0.01
408 1 0.00
409 6 0.01
410 2 0.00
415 391 0.50
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.45
Consensus pattern (403 bp):
ATTTTCCTCATCCCGATCCACCTATGGATAATTAGACCTTTTCTTGCTTAGTTTTCTTGGATTGA
ATTTAAACTTATTGTTAATAACATTTTAGATATGTTTTTGGATGTTTGGATATATTTGTTTGAAT
GGTTTGAATATTTAATTTGAACTTCATATTTATATTGACTTCATTAATTTTTGCATCATCTGTAT
ATTAGATTTTATATGACCAATTCCCAATTTACATATTGTTTATGAATATTGGTTATGGACTAATG
ACTAATCTTTCTCTTGATTGTGATCTTAGCAGCTACATCTATATCTATTTATATCAATTGGCTAT
TTTCTTAAAAATCTTCTTTAAACATTTTCTAGAGTCTTTTTGATTTAACAAAAAGGGGGAGAATA
AAGTAAGGGAGTA
Found at i:25112 original size:17 final size:18
Alignment explanation
Indices: 25077--25113 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
25067 AATGGTTTGA
25077 ATATTTAATTTGAACTTC
1 ATATTTAATTTGAACTTC
25095 ATATTT-ATATTG-ACTTC
1 ATATTTAAT-TTGAACTTC
25112 AT
1 AT
25114 TAATTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.51
Consensus pattern (18 bp):
ATATTTAATTTGAACTTC
Found at i:25687 original size:20 final size:20
Alignment explanation
Indices: 25658--25711 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
25648 TTATAAAGGG
*
25658 ATGTATCGATACACTCATGT
1 ATGTACCGATACACTCATGT
*
25678 ATGTACCGATACACTCTTGT
1 ATGTACCGATACACTCATGT
*
25698 ATGTACTGATACAC
1 ATGTACCGATACAC
25712 CCATATTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTACCGATACACTCATGT
Found at i:33460 original size:141 final size:141
Alignment explanation
Indices: 33205--33464 Score: 367
Period size: 141 Copynumber: 1.8 Consensus size: 141
33195 ACTAAACCTA
* * * * * *
33205 AAAATGGAGGGTTTAATATTAATCATAATTTATTTTAACCTATTATTGAGTCGAGTAATCAAAAT
1 AAAATGGAGGCTCTAATATCAATCATAATTTATTTTAACCAATTATTGAATCGAATAATCAAAAT
*
33270 AGATCCTCATGCATTTAAATGCGGGAGCCAAATCAAATTATTCCCTAAATTAAGGGACTAAAATG
66 AGATCCTCATGCATTTAAATGCGAGAGCCAAATCAAATTATTCCCTAAATTAAGGGACTAAAATG
33335 AAAATGAATCT
131 AAAATGAATCT
* * *
33346 AAAATGGAGGCTCTAATATCAATCCTAATTTATTTTATCCAATTATTGAATTGAATAATCAAAAT
1 AAAATGGAGGCTCTAATATCAATCATAATTTATTTTAACCAATTATTGAATCGAATAATCAAAAT
* * * * ** *
33411 GGATCCTCGTGCATTTTAATGCGAGAGTCAAATTGAATTATTCCTTAAATTAAG
66 AGATCCTCATGCATTTAAATGCGAGAGCCAAATCAAATTATTCCCTAAATTAAG
33465 ATGTTCATAG
Statistics
Matches: 102, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
141 102 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (141 bp):
AAAATGGAGGCTCTAATATCAATCATAATTTATTTTAACCAATTATTGAATCGAATAATCAAAAT
AGATCCTCATGCATTTAAATGCGAGAGCCAAATCAAATTATTCCCTAAATTAAGGGACTAAAATG
AAAATGAATCT
Found at i:33588 original size:107 final size:107
Alignment explanation
Indices: 33415--33628 Score: 410
Period size: 107 Copynumber: 2.0 Consensus size: 107
33405 CAAAATGGAT
*
33415 CCTCGTGCATTTTAATGCGAGAGTCAAATTGAATTATTCCTTAAATTAAGATGTTCATAGATTGA
1 CCTCGTGCATTTTAATGCGAGAGTCAAATTGAATTATTCCTTAAATTAAGATGTTCATAGACTGA
*
33480 AGTGTGAAAAATCTAACGTCAAATAATTTAATCTAATATAAA
66 AGTGTGAAAAATCTAACGTCAAATAATTTAATCTAACATAAA
33522 CCTCGTGCATTTTAATGCGAGAGTCAAATTGAATTATTCCTTAAATTAAGATGTTCATAGACTGA
1 CCTCGTGCATTTTAATGCGAGAGTCAAATTGAATTATTCCTTAAATTAAGATGTTCATAGACTGA
33587 AGTGTGAAAAATCTAACGTCAAATAATTTAATCTAACATAAA
66 AGTGTGAAAAATCTAACGTCAAATAATTTAATCTAACATAAA
33629 ATTAAATGAA
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (107 bp):
CCTCGTGCATTTTAATGCGAGAGTCAAATTGAATTATTCCTTAAATTAAGATGTTCATAGACTGA
AGTGTGAAAAATCTAACGTCAAATAATTTAATCTAACATAAA
Found at i:34103 original size:2 final size:2
Alignment explanation
Indices: 33996--34093 Score: 178
Period size: 2 Copynumber: 49.0 Consensus size: 2
33986 TATATAGAAC
* *
33996 AT AT AT TT AC 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
34038 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
34080 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
34094 TGAATATATA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35596 original size:36 final size:35
Alignment explanation
Indices: 35521--35835 Score: 209
Period size: 37 Copynumber: 8.8 Consensus size: 35
35511 ATAAGTTTTT
* * *
35521 AAACATATATTATATAGTTTTGAAAACACATTTTTGA
1 AAACGTATAATATATAGTTTT-AAAA-ATATTTTTGA
35558 AAACGTATAATATATAGTTTTAAAAATGATTTTTGA
1 AAACGTATAATATATAGTTTTAAAAAT-ATTTTTGA
* * * *
35594 AAACGTATAATATAAACTTTTTGAAAACA-TTTTG-
1 AAACGTATAATATATA-GTTTTAAAAATATTTTTGA
35628 AAA--TAT-ATATATAGTTTTTAAAAATCTATTTTTGA
1 AAACGTATAATATATAG-TTTTAAAAA--TATTTTTGA
** * * * *
35663 AAATATATAGTGTATAGTTTTTAAAATAGTTTTTAA
1 AAACGTATAATATATAGTTTTAAAAATA-TTTTTGA
*
35699 AAATGTATAATATATAGTTTTTAAAAA-AGGTTTTTGA
1 AAACGTATAATATATAG-TTTTAAAAATA--TTTTTGA
* * * *
35736 AAACATATAGTATATAGTTTTGAAAATA-TTTTAA
1 AAACGTATAATATATAGTTTTAAAAATATTTTTGA
* *
35770 AAACGTAT-ATAATATAATTTTCTAAAAACATATTTTTGG
1 AAACGTATAAT-ATAT-AGTTT-T-AAAA-ATATTTTTGA
* * *
35809 AAAC--ATAATATATGGTTTCAGAAATAT
1 AAACGTATAATATATAGTTTTAAAAATAT
35836 ATTATATAGA
Statistics
Matches: 222, Mismatches: 35, Indels: 46
0.73 0.12 0.15
Matches are distributed among these distances:
31 14 0.06
32 3 0.01
33 6 0.03
34 27 0.12
35 15 0.07
36 61 0.27
37 77 0.35
38 11 0.05
39 8 0.04
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (35 bp):
AAACGTATAATATATAGTTTTAAAAATATTTTTGA
Found at i:35702 original size:13 final size:12
Alignment explanation
Indices: 35676--35700 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35666 TATATAGTGT
35676 ATAGTTTTTAAA
1 ATAGTTTTTAAA
35688 ATAGTTTTTAAA
1 ATAGTTTTTAAA
35700 A
1 A
35701 ATGTATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAGTTTTTAAA
Found at i:35720 original size:105 final size:105
Alignment explanation
Indices: 35525--35761 Score: 257
Period size: 105 Copynumber: 2.2 Consensus size: 105
35515 GTTTTTAAAC
*
35525 ATATATTATATAGTTTTGAAAACACATTTTTGAAAACGTATAATATATAGTTTTAAAAATGATTT
1 ATATATTATATAGTTTTGAAAACACATTTTTGAAAACATATAATATATAGTTTTAAAAATGATTT
* *
35590 TTGAAAACGTATAATATAAACTTTTTGAAAACATTTTGAA
66 TTAAAAACGTATAATATAAACTTTTTAAAAACATTTTGAA
* * * * *
35630 ATATA-TATATAGTTTTTAAAA-ATCTATTTTTGAAAATATATAGTGTATAGTTTTTAAAAT-AG
1 ATATATTATATAGTTTTGAAAACA-C-ATTTTTGAAAACATATAATATATAGTTTTAAAAATGA-
* * *
35692 TTTTTAAAAATGTATAATATATAGTTTTTAAAAA-AGGTTTTTGAAAA
63 TTTTTAAAAACGTATAATATAAACTTTTTAAAAACA---TTTTG--AA
*
35739 CATATAGTATATAGTTTTGAAAA
1 -ATATATTATATAGTTTTGAAAA
35762 TATTTTAAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
103 1 0.01
104 18 0.16
105 64 0.58
107 5 0.05
109 2 0.02
110 5 0.05
111 15 0.14
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (105 bp):
ATATATTATATAGTTTTGAAAACACATTTTTGAAAACATATAATATATAGTTTTAAAAATGATTT
TTAAAAACGTATAATATAAACTTTTTAAAAACATTTTGAA
Found at i:35744 original size:73 final size:71
Alignment explanation
Indices: 35521--35815 Score: 271
Period size: 73 Copynumber: 4.1 Consensus size: 71
35511 ATAAGTTTTT
* *
35521 AAACATATATTATATAGTTTTGAAAACACATTTTTGAAAACGTATAATATATAG-TTTTAAAAA-
1 AAACATATAGTATATAGTTTTG-AAA-ACA-TTTTAAAAACGTAT-ATATATAGTTTTTAAAAAC
*
35584 TGATTTTTGA
62 AGATTTTTGA
* * * * * *
35594 AAACGTATAATATAAACTTTTTGAAAACATTTT-GAAA--TATATATATAGTTTTTAAAAATC-T
1 AAACATATAGTATATA-GTTTTGAAAACATTTTAAAAACGTATATATATAGTTTTTAAAAA-CAG
35655 ATTTTTGA
64 ATTTTTGA
* * * * *
35663 AAATATATAGTGTATAGTTTTTAAAATAGTTTTTAAAAATGTATAATATATAGTTTTTAAAAA-A
1 AAACATATAGTATATAGTTTTGAAAACA--TTTTAAAAACGTAT-ATATATAGTTTTTAAAAACA
*
35727 GGTTTTTGA
63 GATTTTTGA
* * *
35736 AAACATATAGTATATAGTTTTGAAAATATTTTAAAAACGTATATAATATAATTTTCTAAAAACAT
1 AAACATATAGTATATAGTTTTGAAAACATTTTAAAAACGTATAT-ATATAGTTTT-TAAAAACAG
*
35801 ATTTTTGG
64 ATTTTTGA
35809 AAACATA
1 AAACATA
35816 ATATATGGTT
Statistics
Matches: 183, Mismatches: 25, Indels: 28
0.78 0.11 0.12
Matches are distributed among these distances:
67 8 0.04
68 21 0.11
69 19 0.10
70 9 0.05
71 29 0.16
72 9 0.05
73 65 0.36
74 23 0.13
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (71 bp):
AAACATATAGTATATAGTTTTGAAAACATTTTAAAAACGTATATATATAGTTTTTAAAAACAGAT
TTTTGA
Found at i:35881 original size:10 final size:10
Alignment explanation
Indices: 35868--35898 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
35858 TTTATTATCA
35868 TTTGTTTTTT
1 TTTGTTTTTT
35878 TTTGTTTTTTT
1 TTTG-TTTTTT
35889 TTTGTTTTTT
1 TTTGTTTTTT
35899 CATTTCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (10 bp):
TTTGTTTTTT
Found at i:35888 original size:11 final size:11
Alignment explanation
Indices: 35868--35898 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
35858 TTTATTATCA
35868 TTTG-TTTTTT
1 TTTGTTTTTTT
35878 TTTGTTTTTTT
1 TTTGTTTTTTT
35889 TTTGTTTTTT
1 TTTGTTTTTT
35899 CATTTCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTGTTTTTTT
Found at i:37221 original size:20 final size:20
Alignment explanation
Indices: 37198--37247 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
37188 TTCAACATTT
*
37198 TTTTAATTTATTCGTT-TTTA
1 TTTTAATTTATTC-TTAATTA
*
37218 TTTTGATATT-TTCTTAATTA
1 TTTTAAT-TTATTCTTAATTA
37238 TTTTAATTTA
1 TTTTAATTTA
37248 ATTTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
19 4 0.17
20 18 0.75
21 2 0.08
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.68
Consensus pattern (20 bp):
TTTTAATTTATTCTTAATTA
Found at i:37310 original size:15 final size:15
Alignment explanation
Indices: 37285--37320 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
37275 AATATTGTTC
*
37285 TATTCAACTTTTTTA
1 TATTTAACTTTTTTA
*
37300 TTTTTAACTTTTTTA
1 TATTTAACTTTTTTA
37315 TATTTA
1 TATTTA
37321 TTTCACAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTAACTTTTTTA
Found at i:37412 original size:6 final size:6
Alignment explanation
Indices: 37403--37432 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
37393 TGAATCTTTA
37403 AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
37433 CGCAATTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:42399 original size:26 final size:26
Alignment explanation
Indices: 42363--42422 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
42353 AATTCAAAAC
*
42363 CAAATCGCATGGATCTTGATAATTGT
1 CAAATGGCATGGATCTTGATAATTGT
42389 CAAATGGCATGGATCTTGATAATTGT
1 CAAATGGCATGGATCTTGATAATTGT
42415 CAAATGGC
1 CAAATGGC
42423 TATAACCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (26 bp):
CAAATGGCATGGATCTTGATAATTGT
Found at i:43817 original size:22 final size:23
Alignment explanation
Indices: 43771--43819 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
43761 TAGAATCAAC
*
43771 TTCAAATCGGGTTTGAGAGCCAA
1 TTCAAATCGGGTTTGAGAGACAA
*
43794 TTCAAA-CGGGTTTGAGAGATAA
1 TTCAAATCGGGTTTGAGAGACAA
43816 TTCA
1 TTCA
43820 GAAAAGATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (23 bp):
TTCAAATCGGGTTTGAGAGACAA
Found at i:44926 original size:36 final size:36
Alignment explanation
Indices: 44886--45034 Score: 129
Period size: 36 Copynumber: 4.3 Consensus size: 36
44876 TAATAAAATC
*
44886 GTTTTTGAAAATACGTTTTT-AAACATATACTATATA
1 GTTTTTGAAAA-ACGTTTTTAAAACATATAATATATA
* *
44922 G-TTTTGAAAACACATTTTTGAAAACGTATAATATATA
1 GTTTTTGAAAA-ACGTTTTT-AAAACATATAATATATA
* *
44959 G-TTTT-AAAAATGATTTTTGAAAACGTATAATATATA
1 GTTTTTGAAAAACG-TTTTT-AAAACATATAATATATA
*
44995 GTTTTTG-AAAAC-ATTTT-AAA-A-AT-ATATATA
1 GTTTTTGAAAAACGTTTTTAAAACATATAATATATA
45025 GTTTTTGAAA
1 GTTTTTGAAA
45035 CGTATATAGT
Statistics
Matches: 98, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
30 14 0.14
31 4 0.04
33 3 0.03
35 21 0.21
36 29 0.30
37 27 0.28
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (36 bp):
GTTTTTGAAAAACGTTTTTAAAACATATAATATATA
Found at i:45115 original size:73 final size:71
Alignment explanation
Indices: 45038--45218 Score: 184
Period size: 73 Copynumber: 2.5 Consensus size: 71
45028 TTTGAAACGT
* * * **
45038 ATATAGTTTTTTAAAAAATGGTTTTTGAAAATATATAGTATATAGTTTTTAATTTTTTTTAAAAA
1 ATATA-TTTTTTAAAAAA-GGTTTTTGAAAACATATAGTATATAGTTTTAAAATAATTTTAAAAA
*
45103 AATGTATA
64 AATATATA
* *
45111 ATATATAATTTTTAAAGAAGGTTTTTGTAAACATATAGTATATAGTTTTAAAATAATTTTAAAAA
1 ATATAT--TTTTTAAAAAAGGTTTTTGAAAACATATAGTATATAGTTTTAAAATAATTTTAAAAA
**
45176 CGTATATA
64 AATATATA
* *
45184 ATATAATTTTCT-AAAAAGGTATTTTTGGAAACATA
1 ATAT-ATTTTTTAAAAAAGG--TTTTTGAAAACATA
45219 ATATATGGTT
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
71 6 0.07
72 5 0.06
73 67 0.74
74 12 0.13
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (71 bp):
ATATATTTTTTAAAAAAGGTTTTTGAAAACATATAGTATATAGTTTTAAAATAATTTTAAAAAAA
TATATA
Found at i:46226 original size:19 final size:20
Alignment explanation
Indices: 46197--46241 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
46187 TATGTTTTAG
*
46197 TATTTTATTAACGCTTTTTC
1 TATTTTATTAACACTTTTTC
* *
46217 T-TTTTCTTAACATTTTTTC
1 TATTTTATTAACACTTTTTC
46236 TATTTT
1 TATTTT
46242 TTATTTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.18, C:0.13, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTTTATTAACACTTTTTC
Found at i:48103 original size:44 final size:44
Alignment explanation
Indices: 48037--48361 Score: 220
Period size: 44 Copynumber: 7.5 Consensus size: 44
48027 TTTCAACTCA
* ** * * *
48037 TTATGTGATAGAAAAGAACAAAATGGTGATGCTAATCCAATTTC
1 TTATGTGATGGAATCGAGCAAAATGGTGATGCTGATCCAACTTC
* * * *
48081 TTATGTGATGGAATCTAGCAAAAAGGTCGACG-TTACTCCAAC-TC
1 TTATGTGATGGAATCGAGCAAAATGGT-GATGCTGA-TCCAACTTC
* * * * *
48125 TTAAGTGATTGAAACAAG-AGAAATGATGATG-TCGATCCAAC-TC
1 TTATGTGATGGAATCGAGCA-AAATGGTGATGCT-GATCCAACTTC
* *
48168 --CT-T-ATGGAATCGAGCGAAAATGGTGATGCTGATCCAACTCC
1 TTATGTGATGGAATCGAGC-AAAATGGTGATGCTGATCCAACTTC
* * * * * *
48209 TTATATGATGGAACCGAGCTAGATGGAGATGCTGATCCAACTCC
1 TTATGTGATGGAATCGAGCAAAATGGTGATGCTGATCCAACTTC
* ** *
48253 TTATGCGATGGAATCGAGGGAAATGGTGATGTTGATCCAACTTC
1 TTATGTGATGGAATCGAGCAAAATGGTGATGCTGATCCAACTTC
* * * * *
48297 TTATGTGATGAAATTGAGCAATAAAGGAG-TGTTGATCCAACTTC
1 TTATGTGATGGAATCGAGCAA-AATGGTGATGCTGATCCAACTTC
* *
48341 TTATGTGATGAAATTGAGCAA
1 TTATGTGATGGAATCGAGCAA
48362 TAAAGGAATA
Statistics
Matches: 223, Mismatches: 45, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
39 8 0.04
40 19 0.09
41 3 0.01
43 14 0.06
44 155 0.70
45 24 0.11
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (44 bp):
TTATGTGATGGAATCGAGCAAAATGGTGATGCTGATCCAACTTC
Found at i:48362 original size:44 final size:44
Alignment explanation
Indices: 48281--48379 Score: 180
Period size: 44 Copynumber: 2.2 Consensus size: 44
48271 GGAAATGGTG
48281 ATGTTGATCCAACTTCTTATGTGATGAAATTGAGCAATAAAGGA
1 ATGTTGATCCAACTTCTTATGTGATGAAATTGAGCAATAAAGGA
*
48325 GTGTTGATCCAACTTCTTATGTGATGAAATTGAGCAATAAAGGA
1 ATGTTGATCCAACTTCTTATGTGATGAAATTGAGCAATAAAGGA
*
48369 ATATTGATCCA
1 ATGTTGATCCA
48380 CCTCCTTCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (44 bp):
ATGTTGATCCAACTTCTTATGTGATGAAATTGAGCAATAAAGGA
Found at i:50480 original size:30 final size:29
Alignment explanation
Indices: 50423--50480 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
50413 GATTTATTTA
* *
50423 GTGACCAAATTATAATTTGGTAAAGTTTG
1 GTGACCAAAGTATAATTTGGAAAAGTTTG
50452 GTGACCAAAGTATAAACTTT-GAAAAGTTT
1 GTGACCAAAGTAT-AA-TTTGGAAAAGTTT
50481 AAGGACCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 10 0.40
31 3 0.12
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (29 bp):
GTGACCAAAGTATAATTTGGAAAAGTTTG
Found at i:51716 original size:24 final size:24
Alignment explanation
Indices: 51684--51731 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
51674 GCATGATATG
51684 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
51708 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
51732 CTGGAAGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:57544 original size:17 final size:18
Alignment explanation
Indices: 57522--57556 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
57512 CGTCAAAAAA
57522 CATAAAATATGA-TTTTT
1 CATAAAATATGACTTTTT
*
57539 CATAAAATTTGACTTTTT
1 CATAAAATATGACTTTTT
57557 AGTCAAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (18 bp):
CATAAAATATGACTTTTT
Found at i:60361 original size:11 final size:12
Alignment explanation
Indices: 60336--60360 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60326 CCCTTAATCC
60336 TTAAAAGATTTT
1 TTAAAAGATTTT
60348 TTAAAAGATTTT
1 TTAAAAGATTTT
60360 T
1 T
60361 AGGGGGAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TTAAAAGATTTT
Found at i:63012 original size:3 final size:3
Alignment explanation
Indices: 63004--63100 Score: 167
Period size: 3 Copynumber: 31.7 Consensus size: 3
62994 TCGAAAACAA
63004 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
63052 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT CAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA-T TAT
63099 TA
1 TA
63101 CATATATTTT
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
3 84 0.93
4 6 0.07
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:65305 original size:26 final size:25
Alignment explanation
Indices: 65276--65326 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
65266 CAAATTGTGG
*
65276 TTTTCAAATAAAAGTTATAATTGTTT
1 TTTTAAAATAAAA-TTATAATTGTTT
* *
65302 TTTTAAAATAATATTTTAATTGTTT
1 TTTTAAAATAAAATTATAATTGTTT
65327 CGAAAAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (25 bp):
TTTTAAAATAAAATTATAATTGTTT
Found at i:69179 original size:35 final size:35
Alignment explanation
Indices: 69133--69230 Score: 97
Period size: 36 Copynumber: 2.7 Consensus size: 35
69123 GTTTTTCTCG
* *
69133 AAACAAAATTTTGTCTTGCTAGAGACAGTTATGTAA
1 AAAC-AAATTTTGTCTCGCTAGAGACAGTTATCTAA
* * * * *
69169 AAACAAATTTTATCTCGCTTGAGACAATTTCTCTCA
1 AAACAAATTTTGTCTCGCTAGAGAC-AGTTATCTAA
* *
69205 AAACAAATTTCGTCTCACTAGAGACA
1 AAACAAATTTTGTCTCGCTAGAGACA
69231 ATTTTTCTCT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
35 19 0.38
36 31 0.62
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (35 bp):
AAACAAATTTTGTCTCGCTAGAGACAGTTATCTAA
Found at i:69208 original size:36 final size:36
Alignment explanation
Indices: 69168--69239 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
69158 CAGTTATGTA
* * *
69168 AAAACAAATTTTATCTCGCTTGAGACAATTTCTCTC
1 AAAACAAATTTCATCTCACTAGAGACAATTTCTCTC
* *
69204 AAAACAAATTTCGTCTCACTAGAGACAATTTTTCTC
1 AAAACAAATTTCATCTCACTAGAGACAATTTCTCTC
69240 TGAGATACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (36 bp):
AAAACAAATTTCATCTCACTAGAGACAATTTCTCTC
Found at i:69368 original size:21 final size:21
Alignment explanation
Indices: 69335--69413 Score: 55
Period size: 21 Copynumber: 4.1 Consensus size: 21
69325 CACCATTAAG
* *
69335 TTTGTTTCCCTTGAAACAAGT
1 TTTGTCTCTCTTGAAACAAGT
* *
69356 TTTGTCTCTCTTGAGA-TAG-
1 TTTGTCTCTCTTGAAACAAGT
69375 -TT-TC-C-CTTGAAACAAGT
1 TTTGTCTCTCTTGAAACAAGT
* *
69392 TTTGTCTCTATTGAGAC-AGT
1 TTTGTCTCTCTTGAAACAAGT
69412 TT
1 TT
69414 CCCTTGAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
15 6 0.14
16 3 0.07
17 2 0.05
18 4 0.09
19 2 0.05
20 8 0.18
21 19 0.43
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (21 bp):
TTTGTCTCTCTTGAAACAAGT
Found at i:69384 original size:36 final size:36
Alignment explanation
Indices: 69338--69424 Score: 156
Period size: 36 Copynumber: 2.4 Consensus size: 36
69328 CATTAAGTTT
* *
69338 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAACAAGTTTTGTCTCTATTGAGACA
69374 GTTTCCCTTGAAACAAGTTTTGTCTCTATTGAGACA
1 GTTTCCCTTGAAACAAGTTTTGTCTCTATTGAGACA
69410 GTTTCCCTTGAAACA
1 GTTTCCCTTGAAACA
69425 CCCATCTTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAGTTTTGTCTCTATTGAGACA
Found at i:69478 original size:65 final size:64
Alignment explanation
Indices: 69374--69589 Score: 270
Period size: 65 Copynumber: 3.3 Consensus size: 64
69364 TCTTGAGATA
* * * **
69374 GTTTCCCTTGAAACAAGTTTTGTCTCTATTGAGACAGTTTCCCTTGAAACACCCATCTTTGAGTC
1 GTTTCCCTTGAAATAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGTC
* * *
69439 GTTTCCCTTGAAATGAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACAATCATCTTTGATTC
1 GTTTCCCTTGAAAT-AATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGTC
* * *
69504 TATTTCCTTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAG
1 -GTTTCCCTTG-AA-ATAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAG
*
69569 TAT
63 T-C
69572 GTTTCCCTTGAAATAATT
1 GTTTCCCTTGAAATAATT
69590 CCCTAAAGAT
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
65 59 0.46
66 12 0.09
67 56 0.44
68 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (64 bp):
GTTTCCCTTGAAATAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGTC
Found at i:69548 original size:67 final size:65
Alignment explanation
Indices: 69375--69584 Score: 269
Period size: 67 Copynumber: 3.2 Consensus size: 65
69365 CTTGAGATAG
* * * ** *
69375 TTTCCCTTGAAACAAGTTTTGTCTCTATTGAGACAGTTTCCCTTGAAACACCCATCTTTGAGTCG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGTCA
** * * *
69440 TTTCCCTTGAAATGAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACAATCATCTTTGATTCT
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGTC-
69505 A
65 A
*
69506 TTTCCTTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGT-
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGTC
69570 A
65 A
69571 TGTTTCCCTTGAAA
1 --TTTCCCTTGAAA
69585 TAATTCCCTA
Statistics
Matches: 123, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
65 55 0.45
66 11 0.09
67 57 0.46
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (65 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGTCA
Found at i:69827 original size:131 final size:131
Alignment explanation
Indices: 69589--69946 Score: 405
Period size: 131 Copynumber: 2.7 Consensus size: 131
69579 TTGAAATAAT
* * * * *
69589 TCCCTAAAGATGGCATGTCATCTTCATCACGTAGGAACCGTGTCATCCACCGATCATACCTCATT
1 TCCCTAAAGATGGTATGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGA-CAGACCTCCTC
* * * * *
69654 ATCACATAGGAGTCGTGTCACCCCTAGATAACCAGTCTTCCTCATCATGTAGGAATCGTGTTATC
65 ATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGACGTCCTCATCATGTAGGAACCATGTTATC
69719 A-
130 AC
* ** * *
69720 TCCCTAAAGATGATATACCATCCTCATCACATAAGAACCGTGTCATCCACCGACAAGACCTCCTC
1 TCCCTAAAGATGGTATGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGAC-AGACCTCCTC
* *
69785 ATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGACGTCCTCGTCGTGTAGGAACCATGTTATC
65 ATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGACGTCCTCATCATGTAGGAACCATGTTATC
69850 ACCC
130 A--C
* * * * * * * * *
69854 TCCCTAAAGATGGTTTGTCGTCCACAGCATGTAGGAACTGTGTCATCCATCGGCCAGATCTCCTC
1 TCCCTAAAGATGGTATGTCATCCTCATCACGTAGGAACCGTGTCATCCA-CCGACAGACCTCCTC
*
69919 ATCACGTAGGAG-CTGTGTCACCCTTAGA
65 ATCACGTAGGAGTC-GTGTCACCCCTAGA
69947 CGACCAGAAC
Statistics
Matches: 189, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
130 1 0.01
131 112 0.59
133 1 0.01
134 72 0.38
135 3 0.02
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (131 bp):
TCCCTAAAGATGGTATGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGACAGACCTCCTCA
TCACGTAGGAGTCGTGTCACCCCTAGATAACCAGACGTCCTCATCATGTAGGAACCATGTTATCA
C
Found at i:70137 original size:3 final size:3
Alignment explanation
Indices: 70131--70180 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
70121 CTCGAAAAAA
70131 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
70177 ATT A
1 ATT A
70181 CATATCTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:71632 original size:3 final size:3
Alignment explanation
Indices: 71624--71700 Score: 145
Period size: 3 Copynumber: 25.3 Consensus size: 3
71614 GTCTCAAAAA
71624 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
71672 ATT ATT ATT ATT ATT ATT ATT ATAT ATT A
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT A
71701 CATATTTTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 70 0.96
4 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:73401 original size:5 final size:5
Alignment explanation
Indices: 73384--73413 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
73374 CTCTTTTCAC
73384 TTTTA TTTT- TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
73414 CTTTGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:74194 original size:19 final size:17
Alignment explanation
Indices: 74160--74193 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
74150 CTAAAATCAG
74160 ATTTTTTTTAATAAAAT
1 ATTTTTTTTAATAAAAT
*
74177 ATTTTTATTTTATAAAA
1 ATTTTT-TTTAATAAAA
74194 ACTACCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTTTTTAATAAAAT
Found at i:75529 original size:44 final size:44
Alignment explanation
Indices: 75466--75563 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 44
75456 GCAATCCAAC
* * *
75466 AGTATCAATACTGGCCAGGGAGTATCGATACTACTTTGTAGTA-T
1 AGTATCGATACTGGCCAGGGAGTATCGATACTACTATGTA-AAGT
*
75510 AGTATCGATACTGTCCAGGGAGTATCGATACTACTATGTAAAGT
1 AGTATCGATACTGGCCAGGGAGTATCGATACTACTATGTAAAGT
75554 AGTATCGATA
1 AGTATCGATA
75564 TCGATCATGG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 1 0.02
44 48 0.98
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (44 bp):
AGTATCGATACTGGCCAGGGAGTATCGATACTACTATGTAAAGT
Found at i:75953 original size:18 final size:18
Alignment explanation
Indices: 75914--75954 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
75904 ATTTGAATAA
* * *
75914 TTAAATCGAATATAATTT
1 TTAAATCAAATATAAATC
75932 TTAAATCAAATATAAATC
1 TTAAATCAAATATAAATC
75950 TTAAA
1 TTAAA
75955 ATTCATTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (18 bp):
TTAAATCAAATATAAATC
Found at i:76239 original size:13 final size:13
Alignment explanation
Indices: 76221--76245 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76211 CATTAGTCGA
76221 CATAATCAATATT
1 CATAATCAATATT
76234 CATAATCAATAT
1 CATAATCAATAT
76246 GCAATAGGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAATCAATATT
Found at i:76379 original size:16 final size:16
Alignment explanation
Indices: 76360--76396 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
76350 CCAAAACACT
76360 CAAATATACAAACAAC
1 CAAATATACAAACAAC
* *
76376 CAAATATTCAAATAAC
1 CAAATATACAAACAAC
76392 CAAAT
1 CAAAT
76397 CTATCAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (16 bp):
CAAATATACAAACAAC
Found at i:77878 original size:17 final size:18
Alignment explanation
Indices: 77856--77892 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
77846 AGAAACAATG
77856 TAATTAAAT-AAAAAAAA
1 TAATTAAATCAAAAAAAA
*
77873 TAATTAAATCAAAAACAA
1 TAATTAAATCAAAAAAAA
77891 TA
1 TA
77893 TTTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
TAATTAAATCAAAAAAAA
Found at i:79648 original size:26 final size:26
Alignment explanation
Indices: 79612--79666 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
79602 CCCCCATCAT
79612 GCTCATCTCAAATTTACCTTGCGTTA
1 GCTCATCTCAAATTTACCTTGCGTTA
79638 GCTCATCTCAAATTTACCTTGCGTTA
1 GCTCATCTCAAATTTACCTTGCGTTA
79664 GCT
1 GCT
79667 TTGAAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (26 bp):
GCTCATCTCAAATTTACCTTGCGTTA
Found at i:84242 original size:44 final size:44
Alignment explanation
Indices: 84177--84273 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
84167 CAATCCAACG
* * * * **
84177 GTATCGATACTGGCCATGGAGTATCGATACTACTTTTTAGTGTA
1 GTATCGATACCGGCCAGGGAGTATCGATACTACTATATAAAGTA
*
84221 GTATCGATACCGTCCAGGGAGTATCGATACTACTATATAAAGTA
1 GTATCGATACCGGCCAGGGAGTATCGATACTACTATATAAAGTA
84265 GTATCGATA
1 GTATCGATA
84274 TCGATCATGG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (44 bp):
GTATCGATACCGGCCAGGGAGTATCGATACTACTATATAAAGTA
Found at i:87782 original size:3 final size:3
Alignment explanation
Indices: 87689--87765 Score: 136
Period size: 3 Copynumber: 25.3 Consensus size: 3
87679 TACCCATATC
*
87689 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
87737 ATT ATT ATT ATT ATT ATT ATAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT A
87766 ATATATAAAT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:89254 original size:20 final size:21
Alignment explanation
Indices: 89217--89257 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
89207 GATATTTTTA
**
89217 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
89238 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
89258 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:90009 original size:13 final size:15
Alignment explanation
Indices: 89978--90014 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
89968 TTATATGTTT
89978 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
89993 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
90006 TA-TTTATTT
1 TATTTTATTT
90015 TTCTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:100574 original size:13 final size:12
Alignment explanation
Indices: 100558--100604 Score: 69
Period size: 12 Copynumber: 3.8 Consensus size: 12
100548 GCTTGAAGAG
100558 AAAAGAAAAAAA
1 AAAAGAAAAAAA
100570 GAAAA-AAAAAAA
1 -AAAAGAAAAAAA
100582 AAAAGAAAAAAA
1 AAAAGAAAAAAA
100594 AAGAAGAAAAA
1 AA-AAGAAAAA
100605 GAAAGGGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 4 0.12
12 16 0.50
13 12 0.38
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:100582 original size:16 final size:16
Alignment explanation
Indices: 100558--100595 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
100548 GCTTGAAGAG
*
100558 AAAAGAAAAAAAGAAA
1 AAAAAAAAAAAAGAAA
100574 AAAAAAAAAAAAGAAA
1 AAAAAAAAAAAAGAAA
100590 AAAAAA
1 AAAAAA
100596 GAAGAAAAAG
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAGAAA
Found at i:100955 original size:15 final size:16
Alignment explanation
Indices: 100922--100960 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
100912 ATACAATTCT
*
100922 ATTTATTTCAAGTTCA
1 ATTTATTTCAAGATCA
100938 ATTTATTT-AAGATCA
1 ATTTATTTCAAGATCA
100953 ATTTATTT
1 ATTTATTT
100961 TTGGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (16 bp):
ATTTATTTCAAGATCA
Done.