Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003999.1 Hibiscus syriacus cultivar Beakdansim tig00008715_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: 87707
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1113 original size:96 final size:96
Alignment explanation
Indices: 974--1225 Score: 318
Period size: 96 Copynumber: 2.7 Consensus size: 96
964 ATTATAATTA
* * * *
974 TATATATATACTATA-AAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAATGCCCCGGCTTTAT
1 TATA-ATATACAATATAAGCTTGAGTTGTCCCTCTAAAGAAATTGGTTAAAAGCCCCGGCTTTAT
1038 AGATAAGATTCAACTAGCCTGATAAAGGTGAT
65 AGATAAGATTCAACTAGCCTGATAAAGGTGAT
* * * *
1070 TATAATATACAATATAAGCTTGAGTTGTCCCTCTTAAGAAATTGGTTAAACGCCCCCGCTTTATG
1 TATAATATACAATATAAGCTTGAGTTGTCCCTCTAAAGAAATTGGTTAAAAGCCCCGGCTTTATA
* *
1135 GATAATATTCAGCTAGCCTGATAAAGGTGAT
66 GATAAGATTCAACTAGCCTGATAAAGGTGAT
* ** *
1166 TAT-A-ATACAACGAT-A--TTGAGTTGTCCCTCTGGAGTAATTGGTTAAAAGCCCCGGCTTTAT
1 TATAATATACAA-TATAAGCTTGAGTTGTCCCTCTAAAGAAATTGGTTAAAAGCCCCGGCTTTAT
1226 GGATCCAGCT
Statistics
Matches: 139, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
92 40 0.29
94 7 0.05
95 12 0.09
96 80 0.58
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (96 bp):
TATAATATACAATATAAGCTTGAGTTGTCCCTCTAAAGAAATTGGTTAAAAGCCCCGGCTTTATA
GATAAGATTCAACTAGCCTGATAAAGGTGAT
Found at i:2535 original size:21 final size:21
Alignment explanation
Indices: 2509--2576 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
2499 TCTTGAGACA
2509 GTTTCTCTTGAAACAAATTTT
1 GTTTCTCTTGAAACAAATTTT
*
2530 GTTTCTCTTGAGAC--A----
1 GTTTCTCTTGAAACAAATTTT
*
2545 GTTTCCCTTGAAACAAATTTT
1 GTTTCTCTTGAAACAAATTTT
*
2566 GTCTCTCTTGA
1 GTTTCTCTTGA
2577 GATAATTTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
15 12 0.33
17 1 0.03
19 1 0.03
21 22 0.61
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (21 bp):
GTTTCTCTTGAAACAAATTTT
Found at i:2537 original size:36 final size:36
Alignment explanation
Indices: 2481--2665 Score: 316
Period size: 36 Copynumber: 5.1 Consensus size: 36
2471 TAATTTACTC
*
2481 GAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 GAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTT
*
2518 GAAACAAATTTTGTTTCTCTTGAGACAGTTTCCCTT
1 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
* *
2554 GAAACAAATTTTGTCTCTCTTGAGATAATTTCCCTT
1 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
2590 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
*
2626 GAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTT
1 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
2662 GAAA
1 GAAA
2666 TAAAATCTTT
Statistics
Matches: 140, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 132 0.94
37 8 0.06
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
GAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
Found at i:2647 original size:21 final size:21
Alignment explanation
Indices: 2512--2648 Score: 60
Period size: 21 Copynumber: 7.4 Consensus size: 21
2502 TGAGACAGTT
2512 TCTCTTGAAACAAATTTTGTT-
1 TCTCTTGAAACAAATTTT-TTC
* *
2533 TCTCTTGAGAC--A--GTTTC
1 TCTCTTGAAACAAATTTTTTC
*
2550 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTTTC
* *
2569 TCTCTTGAGA-TAA---TTTC
1 TCTCTTGAAACAAATTTTTTC
*
2586 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTTTC
* *
2605 TCTCTTGAGAC--A--GTTTC
1 TCTCTTGAAACAAATTTTTTC
2622 -C-CTTGAAACAAATTTTTTC
1 TCTCTTGAAACAAATTTTTTC
2641 TCTCTTGA
1 TCTCTTGA
2649 GACAGTTTCC
Statistics
Matches: 81, Mismatches: 16, Indels: 38
0.60 0.12 0.28
Matches are distributed among these distances:
15 20 0.25
16 7 0.09
17 9 0.11
19 12 0.15
20 5 0.06
21 28 0.35
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTTTC
Found at i:2880 original size:33 final size:32
Alignment explanation
Indices: 2823--2911 Score: 142
Period size: 33 Copynumber: 2.8 Consensus size: 32
2813 CTAGAGACAT
*
2823 TTTCTCTTGAAACACAAAAACCTTTGAAATTG
1 TTTCTCTTGAAACACAAAAACCTTTGAAAATG
2855 TTTCTCTTGAAACACAAAAAACCTTTGAAAATG
1 TTTCTCTTGAAACAC-AAAAACCTTTGAAAATG
* *
2888 TTTCTCTTGAAACATAAAGACCTT
1 TTTCTCTTGAAACACAAAAACCTT
2912 CGAGTTCGAC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
32 23 0.43
33 30 0.57
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (32 bp):
TTTCTCTTGAAACACAAAAACCTTTGAAAATG
Found at i:3139 original size:80 final size:79
Alignment explanation
Indices: 2903--3184 Score: 248
Period size: 80 Copynumber: 3.5 Consensus size: 79
2893 CTTGAAACAT
* * *
2903 AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATTATTTGCAGCATAGA-TTAAGTCG
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAC---ATTTGCAGCATA-ACTTAAGTCG
* * *
2967 AGAATGGCTATTTG-C-C
62 AGAACGGTTATCTGCCAC
* * * * * * * * *
2983 AAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGAACATCATTTACATCATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAGG--CA-CATTTGCAGCATAACTTAAGTCG
*
3048 AGAAGGGTTATCTGCCAAC
62 AGAACGGTTATCTGCC-AC
*
3067 AAATACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATTTGCAGCATAACTTAAGTCGAGAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATTTGCAGCATAACTTAAGTCGAGAA
3132 CGGTTATCTGCCATCC
66 CGGTTATCTGCCA--C
* * * *
3148 AAAGACATTCGAG-TCAATTACATTCAGCTCAGAGGCA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
3185 AATAAAACTT
Statistics
Matches: 162, Mismatches: 30, Indels: 20
0.76 0.14 0.09
Matches are distributed among these distances:
79 1 0.01
80 80 0.49
81 45 0.28
82 1 0.01
83 7 0.04
84 28 0.17
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (79 bp):
AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATTTGCAGCATAACTTAAGTCGAGAA
CGGTTATCTGCCAC
Found at i:3242 original size:28 final size:28
Alignment explanation
Indices: 3173--3242 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
3163 AATTACATTC
* *
3173 AGCTCAGAGGCAAATAAAACTTACAGCAT
1 AGCTC-GAGGCAAGTAAAACTTACAACAT
3202 AGCTCGAGGCAAGTAAAACTTACAACAT
1 AGCTCGAGGCAAGTAAAACTTACAACAT
*
3230 AGCTCGAAGCAAG
1 AGCTCGAGGCAAG
3243 AAGGGCTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (28 bp):
AGCTCGAGGCAAGTAAAACTTACAACAT
Found at i:9072 original size:71 final size:71
Alignment explanation
Indices: 8991--9211 Score: 250
Period size: 74 Copynumber: 3.1 Consensus size: 71
8981 TAAAACATCT
* *
8991 TAAATCCTAATTAAAACACTTAAAA-ATATTTAAACTAAAATACCTAAAAAATAATATTTAAAAT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAAAATAATATTTAAAAT
9055 AATATTC
65 AATATTC
* **
9062 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATATCTAAAACAA-AGATAAAATATA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAA-AATA-AT-ATTTA-A
*
9126 AATAATATCC
62 AATAATATTC
* * * **
9136 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATTCAAAGATAAAAT-ATATTTAAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTA-A-AAAATAATATTTAAAA
*
9200 TATTATTC
64 TAATATTC
9208 TAAA
1 TAAA
9212 ACTTGAGTTT
Statistics
Matches: 126, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
70 5 0.04
71 41 0.33
72 17 0.13
73 6 0.05
74 52 0.41
75 3 0.02
76 2 0.02
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.32
Consensus pattern (71 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAATAATATTTAAAATA
ATATTC
Found at i:9089 original size:19 final size:19
Alignment explanation
Indices: 9061--9169 Score: 55
Period size: 19 Copynumber: 5.8 Consensus size: 19
9051 AAATAATATT
*
9061 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
* *
9080 CTAAAACCTATTTAAACTA
1 CTAAAACCTAATTAAAATA
* * *
9099 --AAATATCTAA-AACAAAGA
1 CTAAA-ACCTAATTA-AAATA
** * * *
9117 -TAAAATATAAATAATATC
1 CTAAAACCTAATTAAAATA
*
9135 CTAAAACTTAATTAAAATA
1 CTAAAACCTAATTAAAATA
*
9154 CTAAAACCTATTTAAA
1 CTAAAACCTAATTAAA
9170 CTAAAATTCA
Statistics
Matches: 65, Mismatches: 20, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
17 4 0.06
18 14 0.22
19 47 0.72
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.29
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:22900 original size:20 final size:20
Alignment explanation
Indices: 22875--22927 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
22865 GACCAACAAA
22875 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
22895 TTCGCAAC-CTAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
22915 TTCGCAACGCGAA
1 TTCGCAACGCGAA
22928 TATGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:23035 original size:20 final size:20
Alignment explanation
Indices: 22980--23063 Score: 96
Period size: 20 Copynumber: 4.2 Consensus size: 20
22970 TTGTAAATTA
*
22980 CAACACATAAGTCAAATTCG
1 CAACACAAAAGTCAAATTCG
* * * * *
23000 CAACGCGATAGCCAAATTTG
1 CAACACAAAAGTCAAATTCG
23020 CAACACAAAAGTCAAATTCG
1 CAACACAAAAGTCAAATTCG
* *
23040 TAACACAAAAATCAAATTCG
1 CAACACAAAAGTCAAATTCG
23060 CAAC
1 CAAC
23064 GCGAAACACA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.46, C:0.25, G:0.11, T:0.18
Consensus pattern (20 bp):
CAACACAAAAGTCAAATTCG
Found at i:23617 original size:20 final size:20
Alignment explanation
Indices: 23594--23638 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
23584 AAAATCGCAA
23594 TGCGATTTTCATTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
*
23614 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
23634 TGCGA
1 TGCGA
23639 ATTTAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.49
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:23649 original size:20 final size:20
Alignment explanation
Indices: 23606--23649 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
23596 CGATTTTCAT
* * *
23606 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
*
23626 TTTCGTGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
23646 TTTC
1 TTTC
23650 AAAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:25393 original size:4 final size:4
Alignment explanation
Indices: 25384--25433 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
25374 TTTTTCGGCA
* * * *
25384 TTAT TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
25432 TT
1 TT
25434 TCAGCGGCCC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:25596 original size:21 final size:20
Alignment explanation
Indices: 25570--25625 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
25560 GAAGCCCGAT
25570 GCACCTATCATCATTCAAGAG
1 GCACCT-TCATCATTCAAGAG
* *
25591 GCACCTCCTATCGTTCAAGAG
1 GCACCTTC-ATCATTCAAGAG
*
25612 GCCCCTCTCATCAT
1 GCACCT-TCATCAT
25626 CGAAGAAGCC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (20 bp):
GCACCTTCATCATTCAAGAG
Found at i:25624 original size:42 final size:42
Alignment explanation
Indices: 25577--25675 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
25567 GATGCACCTA
* *
25577 TCATCATTCAAGAGGCACCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCACCTCCCACCGTTCAAGAGGCCCCTC
* * * *
25619 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCTCTG
1 TCATCATTC-AAGAGGCACCTCCCACCGTTCAAGAGGCCCCTC
**
25661 TCATTGTTCAAGAGG
1 TCATCATTCAAGAGG
25676 TCTCGCCCAC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
41 2 0.04
42 42 0.91
43 2 0.04
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAGGCACCTCCCACCGTTCAAGAGGCCCCTC
Found at i:25652 original size:21 final size:21
Alignment explanation
Indices: 25578--25675 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 21
25568 ATGCACCTAT
* *
25578 CATCATTCAAGAGGCACCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
25599 TATCGTTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
* *
25620 CATC-ATCGAAGAAGCCCCTCC
1 CATCGTTC-AAGAGGCCCCTCC
* * **
25641 CACCGTTCAAGAGGCCTCTGT
1 CATCGTTCAAGAGGCCCCTCC
*
25662 CATTGTTCAAGAGG
1 CATCGTTCAAGAGG
25676 TCTCGCCCAC
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 2 0.03
21 55 0.93
22 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.22
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:27099 original size:69 final size:67
Alignment explanation
Indices: 27023--27191 Score: 231
Period size: 66 Copynumber: 2.5 Consensus size: 67
27013 GTACACTTTG
27023 TTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAA
1 TTTGCTTGTTTAATTGAATTTGT--A---AAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAA
27086 TTA-TTT
61 TTATTTT
* *
27092 TTTGCTTGTTTAATTG-ATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATT
1 TTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATTATT
27156 TT
66 TT
*
27158 TTTGCTTGTTTAATTG-ATTTGTAAAAGTTTATTT
1 TTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTT
27192 TTTTGTTTTA
Statistics
Matches: 94, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
64 17 0.18
65 19 0.20
66 36 0.38
67 1 0.01
68 4 0.04
69 17 0.18
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (67 bp):
TTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATTATT
TT
Found at i:27154 original size:65 final size:65
Alignment explanation
Indices: 27051--27191 Score: 239
Period size: 66 Copynumber: 2.2 Consensus size: 65
27041 TTTTACATTG
27051 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTA
* *
27115 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
27180 A
65 A
*
27181 AAAGTTTATTT
1 AAAGTTGATTT
27192 TTTTGTTTTA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
64 17 0.24
65 19 0.26
66 36 0.50
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.51
Consensus pattern (65 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTA
Found at i:27274 original size:20 final size:20
Alignment explanation
Indices: 27249--27306 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
27239 GTTGAAGGTA
*
27249 TAAATTCGTAACGCGAAAGG
1 TAAATTCGCAACGCGAAAGG
*
27269 TAAATTCGCAACGTGAAAGG
1 TAAATTCGCAACGCGAAAGG
27289 TAAATTCGCAACGCGAAA
1 TAAATTCGCAACGCGAAA
27307 TAAGCGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.19
Consensus pattern (20 bp):
TAAATTCGCAACGCGAAAGG
Found at i:27959 original size:16 final size:16
Alignment explanation
Indices: 27938--27968 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27928 AAACCATTGA
27938 AAAATTATATAAAAAT
1 AAAATTATATAAAAAT
*
27954 AAAATTATGTAAAAA
1 AAAATTATATAAAAA
27969 AATGCCTTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAATTATATAAAAAT
Found at i:29076 original size:25 final size:25
Alignment explanation
Indices: 29048--29097 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
29038 CATTATTTTC
* *
29048 CAAATAATGTACCCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
29073 CAAATAATATACCCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
29098 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:29200 original size:20 final size:20
Alignment explanation
Indices: 29168--29284 Score: 95
Period size: 20 Copynumber: 6.2 Consensus size: 20
29158 AAGGTAAACT
*
29168 TTCGTAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
29188 TTCGCAACACGAAAAGT-AAA
1 TTCGCAACGCG-AAAGTCAAA
29208 TTCGCAACGCGAAA-T--AA
1 TTCGCAACGCGAAAGTCAAA
*** *
29225 ---GCGTTGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
29242 TTCGCAATGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
* *
29262 TTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
29282 TTC
1 TTC
29285 ACGTTGCGAT
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
14 7 0.09
15 1 0.01
17 4 0.05
18 1 0.01
19 3 0.04
20 56 0.73
21 5 0.06
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:31934 original size:24 final size:24
Alignment explanation
Indices: 31907--31953 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
31897 CAAAATCTGA
31907 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
31931 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
31954 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:31962 original size:24 final size:24
Alignment explanation
Indices: 31911--31962 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
31901 ATCTGAGTAT
** *
31911 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
31935 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
31959 TGAC
1 TGAC
31963 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:32095 original size:12 final size:12
Alignment explanation
Indices: 32074--32107 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
32064 GGTTGTGGGT
*
32074 TTTGAGATTGTG
1 TTTGATATTGTG
32086 TTTGATATTGTG
1 TTTGATATTGTG
*
32098 TTTGGTATTG
1 TTTGATATTG
32108 GAAATGTGGT
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:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:32738 original size:14 final size:15
Alignment explanation
Indices: 32702--32739 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
32692 GAAATCATTG
32702 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
32717 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
32732 AAAAATTA
1 AAAAATTA
32740 GAGATAGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:32927 original size:19 final size:20
Alignment explanation
Indices: 32899--32948 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
32889 ACTAAAACCT
*
32899 GTTGCAAATTCAAAATTCA-
1 GTTGCGAATTCAAAATTCAC
**
32918 GTTGCGAATTTGAAATTCAGC
1 GTTGCGAATTCAAAATTCA-C
32939 GTTGCGAATT
1 GTTGCGAATT
32949 TGACTTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
21 10 0.38
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTCAAAATTCAC
Found at i:32964 original size:20 final size:20
Alignment explanation
Indices: 32939--33065 Score: 173
Period size: 20 Copynumber: 6.3 Consensus size: 20
32929 GAAATTCAGC
32939 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * *
32959 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
* *
32979 GTTGCGAATTTGACTTCTAT
1 GTTGCGAATTTGACTTTTGT
32999 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * *
33019 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
33039 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
33059 GTTGCGA
1 GTTGCGA
33066 TTTATAAATT
Statistics
Matches: 90, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:32981 original size:40 final size:40
Alignment explanation
Indices: 32918--33053 Score: 166
Period size: 40 Copynumber: 3.4 Consensus size: 40
32908 TCAAAATTCA
*
32918 GTTGCGAATTTGA-AATTCAGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTA-TC-GCGTTGCGAATTTGACTTTTGT
* *
32959 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTAT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* * * * * *
32999 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
33039 GTTGCGAATTTGACT
1 GTTGCGAATTTGACT
33054 TATGTGTTGC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
40 67 0.81
41 15 0.18
42 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
Found at i:33005 original size:60 final size:60
Alignment explanation
Indices: 32939--33065 Score: 236
Period size: 60 Copynumber: 2.1 Consensus size: 60
32929 GAAATTCAGC
*
32939 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTAT
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATAT
*
32999 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATAT
33059 GTTGCGA
1 GTTGCGA
33066 TTTATAAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (60 bp):
GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATAT
Found at i:33082 original size:40 final size:39
Alignment explanation
Indices: 32939--33088 Score: 160
Period size: 40 Copynumber: 3.8 Consensus size: 39
32929 GAAATTCAGC
* * *
32939 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGAC-TATCGC
1 GTTGCGAATTTGACTTCT-CGTTGCGAATTTGACTTAT-GT
* *
32979 GTTGCGAATTTGACTTCTATGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCT-CGTTGCGAATTTGACTTATGT
*
33019 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACT-TCTCGTTGCGAATTTGACTTATGT
* * *
33059 GTTGCGATTTATAAATTCTCGTTGC-AATTT
1 GTTGCGAATT-TGACTTCTCGTTGCGAATTT
33089 ACAGATTTGC
Statistics
Matches: 96, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
39 5 0.05
40 84 0.88
41 7 0.07
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.44
Consensus pattern (39 bp):
GTTGCGAATTTGACTTCTCGTTGCGAATTTGACTTATGT
Found at i:33083 original size:60 final size:60
Alignment explanation
Indices: 32939--33088 Score: 178
Period size: 60 Copynumber: 2.5 Consensus size: 60
32929 GAAATTCAGC
* * * * *
32939 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTAT
1 GTTGCGAATTTAAATTCTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATAT
* * * * *
32999 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGT
1 GTTGCGAATTTAAATTCTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATAT
*
33059 GTTGCGATTTATAAATTCT-CGTTGC-AATTT
1 GTTGCGAATT-TAAATTCTGCGTTGCGAATTT
33089 ACAGATTTGC
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
59 5 0.06
60 72 0.88
61 5 0.06
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.44
Consensus pattern (60 bp):
GTTGCGAATTTAAATTCTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATAT
Found at i:33142 original size:20 final size:20
Alignment explanation
Indices: 33093--33146 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
33083 CAATTTACAG
33093 ATTTGCGTTGCGAAATTGGA
1 ATTTGCGTTGCGAAATTGGA
* *
33113 AATTGGGTTGCGAAATT-GA
1 ATTTGCGTTGCGAAATTGGA
33132 AGTTTGCGTTGCGAA
1 A-TTTGCGTTGCGAA
33147 TTTATTGGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.26, C:0.09, G:0.31, T:0.33
Consensus pattern (20 bp):
ATTTGCGTTGCGAAATTGGA
Found at i:33967 original size:4 final size:4
Alignment explanation
Indices: 33958--34545 Score: 847
Period size: 4 Copynumber: 147.2 Consensus size: 4
33948 AATATATGAT
* * * *
33958 TATG TATG TATG TATG CATG CATG TATG TATG CATG CATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * * * *
34006 CATG CATA TATG TATG TATG CATG CATG CATG CATG TATG TATA TATC
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
34054 TATA TATG --TG TGTG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
34100 TATG TATG TATG TATG TATG TATG TATA TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
34148 TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
34196 CATG CATG CATG TATG CATG TATG CATG TATG TATG CATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
34244 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
34292 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
34340 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
34388 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
34436 TATG TATG AATG TATG TAATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG T-ATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * *
34485 CATG CATG TATG TATG CATG CATG CATG TATG TATG CATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
34533 TATG GATG TATG T
1 TATG TATG TATG T
34546 GTGTGTGTGT
Statistics
Matches: 544, Mismatches: 37, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
2 2 0.00
4 538 0.99
5 4 0.01
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:34550 original size:4 final size:4
Alignment explanation
Indices: 34543--34747 Score: 203
Period size: 4 Copynumber: 51.2 Consensus size: 4
34533 TATGGATGTA
34543 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
* * * * * *
34591 TGTG TGTG TGTG TGTG TGTG TGTG CGTG TGCG TGTG CGTG CGCG TGCG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
* * * * * * * * * *
34639 CGTG CGCG TGCG CGTG CGCG CGCG CGTG TGTG TGTG TGTG TGTG TGTG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
* * * * * * *
34687 TGTG TGTG TGTG TGTG TGTG TGTG TGCG TGCG TGCG CGTG CGCG TGCG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
34735 TGTG TGTG TGTG T
1 TGTG TGTG TGTG T
34748 ATGTATATAT
Statistics
Matches: 179, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 179 1.00
ACGTcount: A:0.00, C:0.11, G:0.50, T:0.39
Consensus pattern (4 bp):
TGTG
Found at i:34554 original size:6 final size:6
Alignment explanation
Indices: 34543--34747 Score: 203
Period size: 6 Copynumber: 34.2 Consensus size: 6
34533 TATGGATGTA
34543 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * *
34591 TGTGTG TGTGTG TGTGTG TGTGTG CGTGTG CGTGTG CGTGCG CGTGCG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * * * * * *
34639 CGTGCG CGTGCG CGTGCG CGCGCG CGTGTG TGTGTG TGTGTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * * *
34687 TGTGTG TGTGTG TGTGTG TGTGTG TGCGTG CGTGCG CGTGCG CGTGCG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
34735 TGTGTG TGTGTG T
1 TGTGTG TGTGTG T
34748 ATGTATATAT
Statistics
Matches: 187, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 187 1.00
ACGTcount: A:0.00, C:0.11, G:0.50, T:0.39
Consensus pattern (6 bp):
TGTGTG
Found at i:34752 original size:4 final size:4
Alignment explanation
Indices: 34745--34896 Score: 163
Period size: 4 Copynumber: 39.5 Consensus size: 4
34735 TGTGTGTGTG
*
34745 TGTA TGTA TATA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * *
34793 TGTA TGTA TGTA TATA TGTA TGCA TGCA TGTA TATA TCTA TGTA TG--
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * *
34839 TGTG TGTA TGTA TGCA TGTA TG-- TGTG TGTA TGTA TGTA --TA TGTG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
34883 TGTG TGTA TGTA TG
1 TGTA TGTA TGTA TG
34897 AAACTAACCC
Statistics
Matches: 127, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
2 6 0.05
4 121 0.95
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:44156 original size:2 final size:2
Alignment explanation
Indices: 44149--44199 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
44139 TAAATGAGCT
44149 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
44191 TA TA TA TA T
1 TA TA TA TA T
44200 GCAAAACGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46908 original size:525 final size:525
Alignment explanation
Indices: 45909--46964 Score: 1941
Period size: 525 Copynumber: 2.0 Consensus size: 525
45899 CATCAGTTTG
* * *
45909 ACGGAAAGACGCTATGTCATTTTTGAGTTGAGTGTGCATGTTCAGTGGATTATACCGTAGCAAAA
1 ACGGAAAGACGCAATGTCATTTTTGAGTTGAGTGTGCATCTTCAGTGGATTATACCATAGCAAAA
*
45974 AACTTTTGCATAGATCAACCCATGATTACATCGAGCTGGATGGAATTCTACTCAACCAAACCCTT
66 AACTTTTGCATAGATCAACCCATGATTACATCGAGCTGGATGGAATTCTACTCAACCAAACCCTC
46039 GCCCAGTCACATAAAGAATATGGAAATAATTTAAGCTTCAACACATCTTCATGCACTCATTCTTG
131 GCCCAGTCACATAAAGAATATGGAAATAATTTAAGCTTCAACACATCTTCATGCACTCATTCTTG
* *
46104 CCTAAATGAGCCATATACTTCCAAGAAAGTATGAATGTGTTGCCTTGCATCTTCATGTGGCATGC
196 CCTAAATGAACCATATACTTCCAAGAAACTATGAATGTGTTGCCTTGCATCTTCATGTGGCATGC
46169 CACCAAATTACCCGATCGAGTTTAACATGTTAAACATGATTGATTTAAGCTCAAAGTATGCTGCC
261 CACCAAATTACCCGATCGAGTTTAACATGTTAAACATGATTGATTTAAGCTCAAAGTATGCTGCC
46234 TGAATCTCAGGAGCTACAATTCCAGGATTGAGATAATCCAAAATAGGAGTTAAGTGATCTCGAAT
326 TGAATCTCAGGAGCTACAATTCCAGGATTGAGATAATCCAAAATAGGAGTTAAGTGATCTCGAAT
* *
46299 AGCTTTAGGCCGGGGTATAATTCCAGCATTCCAATTTGCAGCAACATTTGGATCTGCTGGAACTT
391 AGCTTTAGGCCAGGGTATAATTCCAACATTCCAATTTGCAGCAACATTTGGATCTGCTGGAACTT
* *
46364 GTACTTGCGGAGTTCATTGGTTCTGAATGTTGTACATGGCTCTATTAGCACGTTGAGCACGACGT
456 GTACTTGCGGAGCTCATTGGTTCTAAATGTTGTACATGGCTCTATTAGCACGTTGAGCACGACGT
46429 TTTCT
521 TTTCT
*
46434 ATGGAAAGACGCAATGTCATTTTTGAGTTGAGTGTGCATCTTCAGTGGATTATACCATAGCAAAA
1 ACGGAAAGACGCAATGTCATTTTTGAGTTGAGTGTGCATCTTCAGTGGATTATACCATAGCAAAA
*
46499 AACTTTTGCATAGATCAACCCATGATTACATCGAGCTGGATGGAATTCTACTCAACCAAGCCCTC
66 AACTTTTGCATAGATCAACCCATGATTACATCGAGCTGGATGGAATTCTACTCAACCAAACCCTC
*
46564 GCTCAGTCACATAAAGAATATGGAAATAATTTAAGCTTCAACACATCTTCATGCACTCATTCTTG
131 GCCCAGTCACATAAAGAATATGGAAATAATTTAAGCTTCAACACATCTTCATGCACTCATTCTTG
46629 CCTAAATGAACCATATACTTCCAAGAAACTATGAATGTGTTGCCTTGCATCTTCATGTGGCATGC
196 CCTAAATGAACCATATACTTCCAAGAAACTATGAATGTGTTGCCTTGCATCTTCATGTGGCATGC
*
46694 CACCAAATTACCCGATCGAGTTTAACATGTTAAACATGATTGATTTAAGCTCAAAGTATGTTGCC
261 CACCAAATTACCCGATCGAGTTTAACATGTTAAACATGATTGATTTAAGCTCAAAGTATGCTGCC
* * *
46759 TGTATCTTAGGAGCTACAATTCCAGGATTGAGATAATCTAAAATAGGAGTTAAGTGATCTCGAAT
326 TGAATCTCAGGAGCTACAATTCCAGGATTGAGATAATCCAAAATAGGAGTTAAGTGATCTCGAAT
* *
46824 AGCTTTAGGCCATGGTATAATTCCAACATTCCAATTTGCCGCAACATTTGGATCTGCTGGAACTT
391 AGCTTTAGGCCAGGGTATAATTCCAACATTCCAATTTGCAGCAACATTTGGATCTGCTGGAACTT
46889 GTACTTGCGGAGCTCATTGGTTCTAAATGTTGTACATGGCTCTATTAGCACGTTGAGCACGACGT
456 GTACTTGCGGAGCTCATTGGTTCTAAATGTTGTACATGGCTCTATTAGCACGTTGAGCACGACGT
46954 TTTCT
521 TTTCT
46959 ACGGAA
1 ACGGAA
46965 TAAGTGTCCA
Statistics
Matches: 511, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
525 511 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (525 bp):
ACGGAAAGACGCAATGTCATTTTTGAGTTGAGTGTGCATCTTCAGTGGATTATACCATAGCAAAA
AACTTTTGCATAGATCAACCCATGATTACATCGAGCTGGATGGAATTCTACTCAACCAAACCCTC
GCCCAGTCACATAAAGAATATGGAAATAATTTAAGCTTCAACACATCTTCATGCACTCATTCTTG
CCTAAATGAACCATATACTTCCAAGAAACTATGAATGTGTTGCCTTGCATCTTCATGTGGCATGC
CACCAAATTACCCGATCGAGTTTAACATGTTAAACATGATTGATTTAAGCTCAAAGTATGCTGCC
TGAATCTCAGGAGCTACAATTCCAGGATTGAGATAATCCAAAATAGGAGTTAAGTGATCTCGAAT
AGCTTTAGGCCAGGGTATAATTCCAACATTCCAATTTGCAGCAACATTTGGATCTGCTGGAACTT
GTACTTGCGGAGCTCATTGGTTCTAAATGTTGTACATGGCTCTATTAGCACGTTGAGCACGACGT
TTTCT
Found at i:47853 original size:18 final size:17
Alignment explanation
Indices: 47830--47865 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
47820 GTAGAATTTG
*
47830 TCCCGAATGACCACTATA
1 TCCCGAAGGACCAC-ATA
47848 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
47865 T
1 T
47866 AACACATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.19
Consensus pattern (17 bp):
TCCCGAAGGACCACATA
Found at i:49061 original size:23 final size:23
Alignment explanation
Indices: 49035--49112 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
49025 CACCACAGCT
49035 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
49058 CATATAATTGCACCGGAGTTCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
49081 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
49104 TATAATAAT
1 CAT-ATAAT
49113 GTCCATAAGG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 39 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:49290 original size:103 final size:103
Alignment explanation
Indices: 49119--49332 Score: 374
Period size: 103 Copynumber: 2.1 Consensus size: 103
49109 TAATGTCCAT
* *
49119 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
49184 GACTTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
49222 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGCTCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
49287 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
49325 CAGGACCA
1 AAGGACCA
49333 TATAGACCCT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:50194 original size:64 final size:64
Alignment explanation
Indices: 50122--50278 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 64
50112 TTCCCTATCG
* * * ** *
50122 GTGCATCGATGCACTACCTGTGCATCGGTGCATAAAATACATTCGATGTTTGTT-TATT-ACTGG
1 GTGCATCGATGCACTACCTGTGCATCGATGCACAAAATACATTCGATGTTT-TTAGATTAAAAGA
* * * * **
50185 GATGCATCGATGCA-TGCCTTATGCATCGATGCACCAATTGTATTCGATGTTTTTAGATTAAAAG
1 G-TGCATCGATGCACTACC-TGTGCATCGATGCACAAAATACATTCGATGTTTTTAGATTAAAAG
50249 A
64 A
50250 GTGCATCGATGCACTACCTGTGCATCGAT
1 GTGCATCGATGCACTACCTGTGCATCGAT
50279 ACACCTTCAA
Statistics
Matches: 75, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
63 6 0.08
64 63 0.84
65 6 0.08
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTGTGCATCGATGCACAAAATACATTCGATGTTTTTAGATTAAAAGA
Found at i:55143 original size:103 final size:103
Alignment explanation
Indices: 54964--55181 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
54954 TAATGCCCAT
* *
54964 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
55029 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
55067 AAGGACCACATATCATTCCTTTAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
55132 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
55170 AAGGACCACATA
1 AAGGACCACATA
55182 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:55992 original size:64 final size:64
Alignment explanation
Indices: 55920--56076 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
55910 TTCCCTATCG
* * * **
55920 GTGCATCGATGCACTACCTGTGCATCGGTGCATAAAATACATTCGATGTTTGTT-TATT-ACTGA
1 GTGCATCGATGCACTACCTGTGCATCGATGCACAAAATACATTCGATGTTT-TTAGATTAAAAGA
* * * * *
55983 GATGCATCGATGCA-TGCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTTAGATTAAAAG
1 G-TGCATCGATGCACTACC-TGTGCATCGATGCACAAAATACATTCGATGTTTTTAGATTAAAAG
56047 A
64 A
56048 GTGCATCGATGCACTACCTGTGCATCGAT
1 GTGCATCGATGCACTACCTGTGCATCGAT
56077 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
63 6 0.08
64 64 0.83
65 7 0.09
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTGTGCATCGATGCACAAAATACATTCGATGTTTTTAGATTAAAAGA
Found at i:60680 original size:6 final size:6
Alignment explanation
Indices: 60665--60712 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
60655 ATTTATCAAA
* * *
60665 ACATAA ACACAT ACACAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
60713 CATTTCATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (6 bp):
ACATAT
Found at i:60758 original size:12 final size:12
Alignment explanation
Indices: 60717--60749 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
60707 ACATATCATT
60717 TCATTATTCTTA
1 TCATTATTCTTA
*
60729 TTATTATTCTTA
1 TCATTATTCTTA
60741 TCATTATTC
1 TCATTATTC
60750 ATATGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (12 bp):
TCATTATTCTTA
Found at i:61099 original size:18 final size:18
Alignment explanation
Indices: 61078--61119 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
61068 TGTCCTGAAT
61078 GACCACTATG-TCTCAAAG
1 GACCACTATGTTC-CAAAG
*
61096 GACCACTATGTTCCGAAG
1 GACCACTATGTTCCAAAG
61114 GACCAC
1 GACCAC
61120 ATATAACACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (18 bp):
GACCACTATGTTCCAAAG
Found at i:65735 original size:6 final size:6
Alignment explanation
Indices: 65724--65752 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
65714 AAACGTATTT
65724 ATGTAA ATGTAA ATGTAA ATGTAA ATGTA
1 ATGTAA ATGTAA ATGTAA ATGTAA ATGTA
65753 TAGTAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
ATGTAA
Found at i:65840 original size:21 final size:21
Alignment explanation
Indices: 65814--65853 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
65804 CTGTAGCAGT
*
65814 ACTGTAGCATTGCATCGATAC
1 ACTGTAGCAGTGCATCGATAC
65835 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
65854 GCACAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Found at i:67353 original size:19 final size:19
Alignment explanation
Indices: 67331--67367 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
67321 AATAGATATA
67331 CATAAAAACTCAAATCATT
1 CATAAAAACTCAAATCATT
*
67350 CATAAAAACTCACATCAT
1 CATAAAAACTCAAATCAT
67368 ATAAGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (19 bp):
CATAAAAACTCAAATCATT
Found at i:69686 original size:20 final size:20
Alignment explanation
Indices: 69661--69711 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
69651 CCCAGCCCTA
*
69661 GAGTATCGATACTCAATTAG
1 GAGTATCGATACTCAATCAG
*
69681 GAGTATCAATACTCAATCAG
1 GAGTATCGATACTCAATCAG
69701 GAGTATCGATA
1 GAGTATCGATA
69712 TTGCCTCTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (20 bp):
GAGTATCGATACTCAATCAG
Found at i:69805 original size:19 final size:20
Alignment explanation
Indices: 69763--69805 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
69753 AAAAGATGAG
*
69763 TATCGATACTAAGGGTTCAA
1 TATCGATACTAAGGGGTCAA
69783 TATCGATA-TGAAGGGGT-AA
1 TATCGATACT-AAGGGGTCAA
69802 TATC
1 TATC
69806 AGTACCAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (20 bp):
TATCGATACTAAGGGGTCAA
Found at i:70601 original size:16 final size:15
Alignment explanation
Indices: 70538--70619 Score: 78
Period size: 15 Copynumber: 5.3 Consensus size: 15
70528 GAAAAGATAA
70538 AATAAAATAAAAAAT
1 AATAAAATAAAAAAT
*
70553 TATAATTTAA-AAAAAAT
1 AATAA---AATAAAAAAT
*
70570 AATAAAATAAATAAT
1 AATAAAATAAAAAAT
70585 AATAAAA-AAGGAAAAT
1 AATAAAATAA--AAAAT
*
70601 AATAAAATAATAAAT
1 AATAAAATAAAAAAT
70616 AATA
1 AATA
70620 TTAGTAAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
14 4 0.07
15 25 0.45
16 11 0.20
17 13 0.24
18 2 0.04
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AATAAAATAAAAAAT
Found at i:70680 original size:18 final size:18
Alignment explanation
Indices: 70659--70701 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
70649 GTTGTTTTTA
*
70659 AAATAAAATATAAGAATT
1 AAATAAAATAAAAGAATT
*
70677 AAATAAAATAAAATAATT
1 AAATAAAATAAAAGAATT
70695 AAATAAA
1 AAATAAA
70702 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAAATAAAAGAATT
Found at i:81364 original size:22 final size:21
Alignment explanation
Indices: 81339--81392 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
81329 TCAGGAGTTA
* *
81339 CAGGAGTTATTTGATTTAATT
1 CAGGAGTTATATGATATAATT
* *
81360 CCAGGGGTTACATGATATAATT
1 -CAGGAGTTATATGATATAATT
81382 CAGGAGTTATA
1 CAGGAGTTATA
81393 ACAGCTGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.37
Consensus pattern (21 bp):
CAGGAGTTATATGATATAATT
Found at i:81544 original size:20 final size:19
Alignment explanation
Indices: 81501--81544 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
81491 GAGGGCTATA
*
81501 TTCAACTTCTCAACTCACT
1 TTCAACTTCACAACTCACT
* *
81520 CTCAACATTCACAATTCACT
1 TTCAAC-TTCACAACTCACT
81540 TTCAA
1 TTCAA
81545 AGTGTTTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (19 bp):
TTCAACTTCACAACTCACT
Found at i:84453 original size:31 final size:29
Alignment explanation
Indices: 84400--84498 Score: 119
Period size: 31 Copynumber: 3.4 Consensus size: 29
84390 CTTTTTCATT
* *
84400 TAAGTATCTAAAATA-TTTTTGGTCAAAA
1 TAAGTACCTAAAGTATTTTTTGGTCAAAA
*
84428 TAAGTATCTAAAGTTATCTTTTTGGTCAAAA
1 TAAGTACCTAAAG-TAT-TTTTTGGTCAAAA
* *
84459 TGAGTACCTAAAGTATTTTTTGATCAAAA
1 TAAGTACCTAAAGTATTTTTTGGTCAAAA
*
84488 TAGGTACCTAA
1 TAAGTACCTAA
84499 TTTTTTCATC
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
28 12 0.19
29 23 0.37
30 3 0.05
31 24 0.39
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (29 bp):
TAAGTACCTAAAGTATTTTTTGGTCAAAA
Found at i:84640 original size:16 final size:18
Alignment explanation
Indices: 84619--84652 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
84609 CTTAGGTACT
84619 TATTTT-GA-ATAAAAAA
1 TATTTTAGATATAAAAAA
84635 TATTTTAGATATAAAAAA
1 TATTTTAGATATAAAAAA
84653 AAAGTATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TATTTTAGATATAAAAAA
Found at i:85675 original size:20 final size:18
Alignment explanation
Indices: 85632--85678 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
85622 CTGAAATAAT
85632 AAAAAATATTATTTTTCA
1 AAAAAATATTATTTTTCA
85650 ATAAAAATAGTTATTTAATT-A
1 A-AAAAATA-TTATTT--TTCA
85671 AAAAAATA
1 AAAAAATA
85679 ATATATAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.04
19 7 0.28
20 13 0.52
21 2 0.08
22 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAAAATATTATTTTTCA
Done.