Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000376.1 Hibiscus syriacus cultivar Beakdansim tig00000687_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: 59228
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:998 original size:13 final size:13
Alignment explanation
Indices: 980--1026 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
970 CATTGTCAAA
980 AAAATAATA-AAAG
1 AAAATAA-AGAAAG
993 AAAATAAAGAAAG
1 AAAATAAAGAAAG
* *
1006 AAAAGATGAGAAAG
1 AAAATA-AAGAAAG
1020 AAAATAA
1 AAAATAA
1027 GAACTTCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 1 0.04
13 16 0.57
14 11 0.39
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (13 bp):
AAAATAAAGAAAG
Found at i:2950 original size:26 final size:25
Alignment explanation
Indices: 2921--2970 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
2911 TGGTGTACCT
* *
2921 AAAAATATAAACAAGAATAAATAAAC
1 AAAAAAATAAACAAAAAT-AATAAAC
*
2947 AAAAAAATAAATAAAAATAATAAA
1 AAAAAAATAAACAAAAATAATAAA
2971 ATTGATTGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (25 bp):
AAAAAAATAAACAAAAATAATAAAC
Found at i:2954 original size:12 final size:12
Alignment explanation
Indices: 2921--2970 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
2911 TGGTGTACCT
*
2921 AAAAATATAAAC
1 AAAAAAATAAAC
2933 AAGAATAAATAAAC
1 AA-AA-AAATAAAC
*
2947 AAAAAAATAAAT
1 AAAAAAATAAAC
2959 AAAAATAATAAA
1 AAAAA-AATAAA
2971 ATTGATTGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 14 0.42
13 10 0.30
14 9 0.27
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAATAAAC
Found at i:9495 original size:19 final size:18
Alignment explanation
Indices: 9467--9502 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9457 TACCGAGATA
*
9467 TCTAAGTAAATAACTAATT
1 TCTAAATAAATAA-TAATT
9486 TCTAAATAAATAATAAT
1 TCTAAATAAATAATAAT
9503 AATAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (18 bp):
TCTAAATAAATAATAATT
Found at i:9502 original size:3 final size:3
Alignment explanation
Indices: 9494--9522 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
9484 TTTCTAAATA
9494 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9523 CAAACTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19996 original size:14 final size:13
Alignment explanation
Indices: 19969--20030 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 13
19959 TAAAATAGAT
*
19969 AATAATAAATAAA
1 AATAATAAAGAAA
*
19982 TA-AATAAAGAAA
1 AATAATAAAGAAA
19994 AATAATAAAAGAAAA
1 AATAAT-AAAG-AAA
* *
20009 AAGAAAAAAGAAA
1 AATAATAAAGAAA
20022 AATAATAAA
1 AATAATAAA
20031 TTAATAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
12 10 0.26
13 14 0.36
14 8 0.21
15 7 0.18
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
AATAATAAAGAAA
Found at i:19998 original size:28 final size:27
Alignment explanation
Indices: 19967--20041 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 27
19957 AATAAAATAG
19967 ATAATAATAAATAAATAAATAAAGAAAA
1 ATAATAATAAATAAATAAA-AAAGAAAA
* * *
19995 ATAATAAAAGAAAAAAGAAAAAAGAAAA
1 ATAATAATA-AATAAATAAAAAAGAAAA
*
20023 ATAATAAATTAATAAATAA
1 ATAAT-AATAAATAAATAA
20042 TAGTAGTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 28 0.74
29 10 0.26
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (27 bp):
ATAATAATAAATAAATAAAAAAGAAAA
Found at i:20002 original size:21 final size:21
Alignment explanation
Indices: 19951--20016 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
19941 TGAAAAGATT
* *
19951 TAATAAAATAAAATAGATAATAA
1 TAATAAAAGAAAAAAGA-AA-AA
*
19974 TAAATAAATA-AATAAAGAAAAA
1 T-AATAAA-AGAAAAAAGAAAAA
19996 TAATAAAAGAAAAAAGAAAAA
1 TAATAAAAGAAAAAAGAAAAA
20017 AGAAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.03
21 17 0.46
22 3 0.08
23 3 0.08
24 12 0.32
25 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (21 bp):
TAATAAAAGAAAAAAGAAAAA
Found at i:20756 original size:12 final size:12
Alignment explanation
Indices: 20739--20766 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20729 AATACCTAAA
20739 AAATAATATTCT
1 AAATAATATTCT
20751 AAATAATATTCT
1 AAATAATATTCT
20763 AAAT
1 AAAT
20767 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTCT
Found at i:20858 original size:76 final size:75
Alignment explanation
Indices: 20682--20902 Score: 254
Period size: 76 Copynumber: 3.0 Consensus size: 75
20672 AAAACAAGTT
* * * * *
20682 ATAACATCTTAAATCCTTATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT--AA-AAAAT
1 ATAATATCCTAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAAT
* **
20743 AATAT-TCTAA
65 AAAATATAAAA
* *
20753 ATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGAT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAA-AT
20818 AAAATATAAAA
65 AAAATATAAAA
* * * *
20829 ATAATATCCTAAAACTTAATTAAAGTACTAAAACCTATTTAAACTAAAATATCTAAAACATATAT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACA-AAAT
20894 AAAATATAA
65 AAAATATAA
20903 TTTTAAAATA
Statistics
Matches: 129, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
70 5 0.04
71 43 0.33
73 2 0.02
74 3 0.02
75 6 0.05
76 69 0.53
77 1 0.01
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (75 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAATA
AAATATAAAA
Found at i:24264 original size:14 final size:14
Alignment explanation
Indices: 24247--24277 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
24237 TACGCTATTA
24247 TATATAATAAATAT
1 TATATAATAAATAT
*
24261 TATATTATAAATAT
1 TATATAATAAATAT
24275 TAT
1 TAT
24278 TATTTGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATATAATAAATAT
Found at i:24329 original size:26 final size:26
Alignment explanation
Indices: 24294--24351 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
24284 TAAAGCCCGA
* *
24294 AGGCCTGGTTACAAAGTAAGGCACAC
1 AGGCCCGGTTAAAAAGTAAGGCACAC
*
24320 ATGCCCGGTTAAAAAGTAAGGCACAC
1 AGGCCCGGTTAAAAAGTAAGGCACAC
24346 AGGCCC
1 AGGCCC
24352 AATTACAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.34, C:0.26, G:0.26, T:0.14
Consensus pattern (26 bp):
AGGCCCGGTTAAAAAGTAAGGCACAC
Found at i:25083 original size:20 final size:20
Alignment explanation
Indices: 25058--25097 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
25048 GAGGAGAAAG
25058 AGAGCTACATTTTTTGGTAA
1 AGAGCTACATTTTTTGGTAA
25078 AGAGCTACATTTTTTGGTAA
1 AGAGCTACATTTTTTGGTAA
25098 GTTTGGTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (20 bp):
AGAGCTACATTTTTTGGTAA
Found at i:25800 original size:16 final size:16
Alignment explanation
Indices: 25767--25801 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
25757 AATAATGATT
**
25767 TAAATTAAATTATTTA
1 TAAATTAAATTAAATA
25783 TAAATTAAATTAAATA
1 TAAATTAAATTAAATA
25799 TAA
1 TAA
25802 GTTTATCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTAAATTAAATA
Found at i:31570 original size:22 final size:22
Alignment explanation
Indices: 31528--31570 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
31518 TCGAGTTAAC
*
31528 CATACATTATTATTTTACCCAT
1 CATACATTATTATTATACCCAT
*
31550 CATACGATTA-TATTATCCCCA
1 CATAC-ATTATTATTATACCCA
31571 CAGGTGCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.40
Consensus pattern (22 bp):
CATACATTATTATTATACCCAT
Found at i:33636 original size:26 final size:25
Alignment explanation
Indices: 33607--33696 Score: 103
Period size: 26 Copynumber: 3.6 Consensus size: 25
33597 AAGCCCGAAG
33607 GCCCGGTTACAAAGTAAGGCACACAA
1 GCCCGGTTACAAAGTAAGG-ACACAA
*
33633 GCCCGGTTACAAAGCAA--ATCACAA
1 GCCCGGTTACAAAGTAAGGA-CACAA
* * *
33657 GCTCGGTTACAAAATAAGGAACACAT
1 GCCCGGTTACAAAGTAAGG-ACACAA
33683 GCCCGGTTACAAAG
1 GCCCGGTTACAAAG
33697 AAAATCACAG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
23 1 0.02
24 19 0.36
26 32 0.60
27 1 0.02
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.14
Consensus pattern (25 bp):
GCCCGGTTACAAAGTAAGGACACAA
Found at i:33663 original size:24 final size:24
Alignment explanation
Indices: 33628--33718 Score: 94
Period size: 24 Copynumber: 3.7 Consensus size: 24
33618 AAGTAAGGCA
*
33628 CACAAGCCCGGTTACAAAGCAAAT
1 CACAAGCCCGGTTACAAAGAAAAT
* *
33652 CACAAGCTCGGTTACAAA-ATAAGGAA
1 CACAAGCCCGGTTACAAAGA-AA--AT
*
33678 CACATGCCCGGTTACAAAGAAAAT
1 CACAAGCCCGGTTACAAAGAAAAT
* *
33702 CACAGGCCTGGTTACAA
1 CACAAGCCCGGTTACAA
33719 CAAAACCCGA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
24 35 0.64
26 19 0.35
27 1 0.02
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (24 bp):
CACAAGCCCGGTTACAAAGAAAAT
Found at i:33669 original size:50 final size:49
Alignment explanation
Indices: 33609--33718 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 49
33599 GCCCGAAGGC
* * *
33609 CCGGTTACAAAGTAAGGCACACAAGCCCGGTTACAAAGCAAATCACAAG
1 CCGGTTACAAAATAAGGAACACAAGCCCGGTTACAAAGAAAATCACAAG
* *
33658 CTCGGTTACAAAATAAGGAACACATGCCCGGTTACAAAGAAAATCACAGG
1 C-CGGTTACAAAATAAGGAACACAAGCCCGGTTACAAAGAAAATCACAAG
33708 CCTGGTTACAA
1 CC-GGTTACAA
33719 CAAAACCCGA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
49 2 0.04
50 52 0.96
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (49 bp):
CCGGTTACAAAATAAGGAACACAAGCCCGGTTACAAAGAAAATCACAAG
Found at i:39651 original size:31 final size:30
Alignment explanation
Indices: 39605--39680 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
39595 TTCAACGTTC
*
39605 AAGTGACC-AAACTTAATAAGACAATAACGT
1 AAGTGACCAAAACTTAATAA-AAAATAACGT
*
39635 TAGTGACCAAAACTTAATAAAAAATAACGT
1 AAGTGACCAAAACTTAATAAAAAATAACGT
39665 AAGTGACCAAAACTTA
1 AAGTGACCAAAACTTA
39681 TGTTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
30 31 0.74
31 11 0.26
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.21
Consensus pattern (30 bp):
AAGTGACCAAAACTTAATAAAAAATAACGT
Found at i:39880 original size:31 final size:31
Alignment explanation
Indices: 39845--39913 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
39835 ATTAAACTTC
*
39845 AGTGACCACATTTTAATT-AAATCGAAATGAA
1 AGTGACCACATCTTAATTAAAAT-GAAATGAA
*
39876 AGTGACCAGATCTTAATTAAAATGAAATGAA
1 AGTGACCACATCTTAATTAAAATGAAATGAA
39907 AGTGACC
1 AGTGACC
39914 GAACCTTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (31 bp):
AGTGACCACATCTTAATTAAAATGAAATGAA
Found at i:43067 original size:33 final size:33
Alignment explanation
Indices: 43030--43097 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
43020 TAAAACTATC
43030 ATCTTTGGAGAAAGAAGATTAAAAAAGGGAAAA
1 ATCTTTGGAGAAAGAAGATTAAAAAAGGGAAAA
43063 ATCTTTGGAGAAAGAAGATTAAAAAAGGGAAAA
1 ATCTTTGGAGAAAGAAGATTAAAAAAGGGAAAA
43096 AT
1 AT
43098 AATATGGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.19
Consensus pattern (33 bp):
ATCTTTGGAGAAAGAAGATTAAAAAAGGGAAAA
Found at i:43258 original size:12 final size:12
Alignment explanation
Indices: 43243--43268 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43233 TTTAATTAAT
43243 AAAAGAAAATTA
1 AAAAGAAAATTA
43255 AAAAGAAAATTA
1 AAAAGAAAATTA
43267 AA
1 AA
43269 TGATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAAGAAAATTA
Found at i:44044 original size:27 final size:27
Alignment explanation
Indices: 44014--44104 Score: 67
Period size: 28 Copynumber: 3.1 Consensus size: 27
44004 GATTAGAGGT
44014 AGTATTGTAACTTATCTTTCAATTGAG
1 AGTATTGTAACTTATCTTTCAATTGAG
* * * * *
44041 AGTAATATCT-TCGTAACTTATAAGATTAGAGG
1 AGT-AT-TGTAACTTATCTT-TCA-ATT-GA-G
44073 TAGTATTGTAACTTATCTTTCAATTGAG
1 -AGTATTGTAACTTATCTTTCAATTGAG
44101 AGTA
1 AGTA
44105 ATATCAACAC
Statistics
Matches: 46, Mismatches: 10, Indels: 16
0.64 0.14 0.22
Matches are distributed among these distances:
27 7 0.15
28 9 0.20
29 6 0.13
30 6 0.13
31 6 0.13
32 9 0.20
33 3 0.07
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (27 bp):
AGTATTGTAACTTATCTTTCAATTGAG
Found at i:44083 original size:60 final size:60
Alignment explanation
Indices: 43990--44109 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
43980 TATGAAAAAA
43990 TTCGTAACTTATAAGATTAGAGGTAGTATTGTAACTTATCTTTCAATTGAGAGTAATATC
1 TTCGTAACTTATAAGATTAGAGGTAGTATTGTAACTTATCTTTCAATTGAGAGTAATATC
44050 TTCGTAACTTATAAGATTAGAGGTAGTATTGTAACTTATCTTTCAATTGAGAGTAATATC
1 TTCGTAACTTATAAGATTAGAGGTAGTATTGTAACTTATCTTTCAATTGAGAGTAATATC
44110 AACACATACG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (60 bp):
TTCGTAACTTATAAGATTAGAGGTAGTATTGTAACTTATCTTTCAATTGAGAGTAATATC
Found at i:46736 original size:410 final size:409
Alignment explanation
Indices: 45977--46796 Score: 1613
Period size: 410 Copynumber: 2.0 Consensus size: 409
45967 GTACTTGTGG
45977 ACACATTAAGCCATGTACTTGTCCACATCGTTTTTTTTTCACAATTGACGTAACCGAGTGACGTA
1 ACACATTAAGCCATGTACTTGTCCACATCGTTTTTTTTTCACAATTGACGTAACCGAGTGACGTA
46042 ATTATAATTCTTTTCGGCATAATCAGCCATGTACCTAACGTGACGTGATAGGCAACTCGCATTTT
66 ATTATAATTCTTTTCGGCATAATCAGCCATGTACCTAACGTGACGTGATAGGCAACTCGCATTTT
46107 GCATAACACGAGTTCACTACCACATCAGTAATAGATGCAATTGTACGCTCGACTTTCTTGCTTAT
131 GCATAACACGAGTTCACTACCACATCAGTAATAGATGCAATTGTACGCTCGACTTTCTTGCTTAT
46172 TTAAATTCCTCTTATTCCACCGAACCTAACCATCTCCGCGAAACCTTCTTATTTCTTAATAAATG
196 TTAAATTCCTCTTATTCCACCGAACCTAACCATCTCCGCGAAACCTTCTTATTTCTTAATAAATG
46237 ATTTATCGATTCTGGAAAATTTCTAGTTTAAAAATGGCATCCTTTTCTGGTGGCATCATTTTTGT
261 ATTTATCGATTCTGGAAAATTTCTAGTTTAAAAATGGCATCCTTTTCTGGTGGCATCATTTTTGT
46302 ACTCGACCGTATCAGATATATCAAAATATTCTTCTTCATCGTCAAGATCATTCTGCGCGACATGA
326 ACTCGACCGTATCAGATATATCAAAATATTCTTCTTCATCGTCAAGATCATTCTGCGCGACATGA
46367 GGTTCTTCTATACTTCTCA
391 GGTTCTTCTATACTTCTCA
46386 ACACATTAAGCCATGTACTTGTCCACATCGTTTTTTTTTCACAATTGACGTAACCGAGTGACGTA
1 ACACATTAAGCCATGTACTTGTCCACATCGTTTTTTTTTCACAATTGACGTAACCGAGTGACGTA
*
46451 CATTATAATTCTTTTCGGCATAATCAGCCATGTACCTTACGTGACGTGATAGGCAACTCGCATTT
66 -ATTATAATTCTTTTCGGCATAATCAGCCATGTACCTAACGTGACGTGATAGGCAACTCGCATTT
*
46516 TGCATAACACGAGTTCACTACCACATCAGTAATAGATGCATTTGTACGCTCGACTTTCTTGCTTA
130 TGCATAACACGAGTTCACTACCACATCAGTAATAGATGCAATTGTACGCTCGACTTTCTTGCTTA
46581 TTTAAATTCCTCTTATTCCACCGAACCTAACCATCTCCGCGAAACCTTCTTATTTCTTAATAAAT
195 TTTAAATTCCTCTTATTCCACCGAACCTAACCATCTCCGCGAAACCTTCTTATTTCTTAATAAAT
46646 GATTTATCGATTCTGGAAAATTTCTAGTTTAAAAATGGCATCCTTTTCTGGTGGCATCATTTTTG
260 GATTTATCGATTCTGGAAAATTTCTAGTTTAAAAATGGCATCCTTTTCTGGTGGCATCATTTTTG
46711 TACTCGACCGTATCAGATATATCAAAATATTCTTCTTCATCGTCAAGATCATTCTGCGCGACATG
325 TACTCGACCGTATCAGATATATCAAAATATTCTTCTTCATCGTCAAGATCATTCTGCGCGACATG
46776 AGGTTCTTCTATACTTCTCA
390 AGGTTCTTCTATACTTCTCA
46796 A
1 A
46797 AACGCTATTG
Statistics
Matches: 408, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
409 65 0.16
410 343 0.84
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (409 bp):
ACACATTAAGCCATGTACTTGTCCACATCGTTTTTTTTTCACAATTGACGTAACCGAGTGACGTA
ATTATAATTCTTTTCGGCATAATCAGCCATGTACCTAACGTGACGTGATAGGCAACTCGCATTTT
GCATAACACGAGTTCACTACCACATCAGTAATAGATGCAATTGTACGCTCGACTTTCTTGCTTAT
TTAAATTCCTCTTATTCCACCGAACCTAACCATCTCCGCGAAACCTTCTTATTTCTTAATAAATG
ATTTATCGATTCTGGAAAATTTCTAGTTTAAAAATGGCATCCTTTTCTGGTGGCATCATTTTTGT
ACTCGACCGTATCAGATATATCAAAATATTCTTCTTCATCGTCAAGATCATTCTGCGCGACATGA
GGTTCTTCTATACTTCTCA
Found at i:48650 original size:21 final size:20
Alignment explanation
Indices: 48626--48698 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
48616 TTTTTTGGAT
* *
48626 AGTATCGATACTGATTGAATC
1 AGTATCGATACCG-TTGAAGC
* *
48647 AGTATCGAAACCGTTGAGGC
1 AGTATCGATACCGTTGAAGC
*
48667 AGTATCGATACCATTGTAAG-
1 AGTATCGATACCGTTG-AAGC
*
48687 GGTATCGATACC
1 AGTATCGATACC
48699 AAGCAAACAT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
20 30 0.70
21 13 0.30
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (20 bp):
AGTATCGATACCGTTGAAGC
Found at i:48842 original size:95 final size:96
Alignment explanation
Indices: 48667--48852 Score: 245
Period size: 95 Copynumber: 1.9 Consensus size: 96
48657 CCGTTGAGGC
* * *
48667 AGTATCGATACCATTGTAAGGGTATCGATACCAAGCAAACATTGAATCTAATTTCGGTATCGATA
1 AGTATCAATACCATTGTAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTCGGTATCGATA
*
48732 CCGTAAGAGAGTATCGGTACCATAGTAGGGT
66 CCATAAGAGAGTATCGGTACCATAGTAGGGT
* * *
48763 AGTATCAATACCA-TGTTAAGGGTATCGATACCATG-AAACATCGAGCCTAATTTTGGTATCGAT
1 AGTATCAATACCATTG-TAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTCGGTATCGAT
*
48826 ACCATGAAG-G-GCTATCGGTACCCTAGT
65 ACCAT-AAGAGAG-TATCGGTACCATAGT
48853 GTAGAAGTAT
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
94 1 0.01
95 45 0.57
96 33 0.42
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (96 bp):
AGTATCAATACCATTGTAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTCGGTATCGATA
CCATAAGAGAGTATCGGTACCATAGTAGGGT
Found at i:49386 original size:45 final size:45
Alignment explanation
Indices: 49337--49657 Score: 493
Period size: 45 Copynumber: 7.1 Consensus size: 45
49327 AAAGGATTCC
49337 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
49382 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
49427 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* ** *
49472 ATAGTTGAAATGCATATGGGTGTATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
49517 ATAGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
49562 ATAGTTGAAATGCATATGGGTGAC-TTATTAACAGAAAAGAATACT
1 ATAGTTGAAATGTATATGGGT-ACATTATCAACAGAAAAGTATACT
** * * *
49607 ATAGTAT-AAATACATATGAGTACATTATCAATAGAAAAGTATGCT
1 ATAGT-TGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
49652 ATAGTT
1 ATAGTT
49658 AAAAGTGCAT
Statistics
Matches: 256, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
44 3 0.01
45 251 0.98
46 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:49458 original size:90 final size:90
Alignment explanation
Indices: 49300--49685 Score: 510
Period size: 90 Copynumber: 4.3 Consensus size: 90
49290 TGAAAATAAT
* ** * * *
49300 AATGCATATGGGTGCATTATCGGCATG-AAAGGATTCCATAGTTGAAATGTATATGGGTACATTA
1 AATGCATATGGGTACATTATCAACA-GAAAAGTATACTATAGTTGAAATGTATATGGGTACATTA
49364 TCAACAGAAAAGTATACTATAGTTGA
65 TCAACAGAAAAGTATACTATAGTTGA
*
49390 AATGTATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGTATATGGGTACATTAT
1 AATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGTATATGGGTACATTAT
49455 CAACAGAAAAGTATACTATAGTTGA
66 CAACAGAAAAGTATACTATAGTTGA
** * *
49480 AATGCATATGGGTGTATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTGCATTAT
1 AATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGTATATGGGTACATTAT
49545 CAACAGAAAAGTATACTATAGTTGA
66 CAACAGAAAAGTATACTATAGTTGA
* * ** *
49570 AATGCATATGGGTGAC-TTATTAACAGAAAAGAATACTATAGTAT-AAATACATATGAGTACATT
1 AATGCATATGGGT-ACATTATCAACAGAAAAGTATACTATAGT-TGAAATGTATATGGGTACATT
* * *
49633 ATCAATAGAAAAGTATGCTATAGTTAA
64 ATCAACAGAAAAGTATACTATAGTTGA
* *
49660 AAGTGCATAAT-GGTGCATTATAAACA
1 AA-TGCAT-ATGGGTACATTATCAACA
49686 TGAATGGAGG
Statistics
Matches: 264, Mismatches: 26, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
89 1 0.00
90 244 0.92
91 17 0.06
92 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (90 bp):
AATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGTATATGGGTACATTAT
CAACAGAAAAGTATACTATAGTTGA
Found at i:55839 original size:95 final size:96
Alignment explanation
Indices: 55662--55847 Score: 261
Period size: 95 Copynumber: 1.9 Consensus size: 96
55652 CCGTTTAGGC
* *
55662 AGTATCGATACCATTGTAAGGGTATCGATGCCAAAGAAACATCGAATCTAATTTCGGTATCAATA
1 AGTATCGATACCATTGTAAGGGTATCGATACCAAAGAAACATCGAACCTAATTTCGGTATCAATA
* * *
55727 CTGTAAGGGAGTATCGGTACCGTAGTAGGGT
66 CAGGAAGGGAGTATCGGTACCCTAGTAGGGT
* * *
55758 AGTATCGATACCA-TGTTAAGGGTATCGATACC-ATGAAACATCGAACCTAATTTTGGTATCGAT
1 AGTATCGATACCATTG-TAAGGGTATCGATACCAAAGAAACATCGAACCTAATTTCGGTATCAAT
55821 ACCAGGAAGGG-GTATCGGTACCCTAGT
65 A-CAGGAAGGGAGTATCGGTACCCTAGT
55848 GTAGAAGTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
95 45 0.56
96 35 0.44
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (96 bp):
AGTATCGATACCATTGTAAGGGTATCGATACCAAAGAAACATCGAACCTAATTTCGGTATCAATA
CAGGAAGGGAGTATCGGTACCCTAGTAGGGT
Found at i:56381 original size:45 final size:45
Alignment explanation
Indices: 56295--56680 Score: 533
Period size: 45 Copynumber: 8.6 Consensus size: 45
56285 TGAAAATAAT
** * * * *
56295 AATGCATATGGGTGCATTATCGGCATG-AAAGGATTCCATAGTTTA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATACTATAGTTGA
* * *
56340 AATGTATATGGGTACATTATCAACAGAAAAATATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * *
56385 AATGTATATGGGTACATTATCAACAAAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * *
56430 AATGCATATGGATGTATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* *
56475 AATGCATATGGGTGTATTATCAACAGAAAAATATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
56520 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
56565 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTAA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
56610 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
** *
56655 CGGTGCATAAT-GGTGCATTATAAACA
1 -AATGCAT-ATGGGTGCATTATCAACA
56681 TGAATGGAGG
Statistics
Matches: 310, Mismatches: 28, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
44 1 0.00
45 288 0.93
46 19 0.06
47 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
Done.