Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005260.1 Hibiscus syriacus cultivar Beakdansim tig00011898_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: 70409
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:2661 original size:55 final size:54
Alignment explanation
Indices: 2597--2892 Score: 362
Period size: 55 Copynumber: 5.4 Consensus size: 54
2587 TCCTTATTCC
* *
2597 TTCAAGGAGTATAAGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTT
1 TTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTT
* * *
2651 GTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCT
1 -TTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATT-T
* * *
2707 TTCAAGGAGTATAAGACTCGAACAATCTTCAGCAAATGGGTTCT-CTCCCTATTCT
1 TTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTG-TCTGCTCCCTATT-T
* *
2762 TTCAGGGAGTAT-AGAACTCGAACAATCTTCAGCGAACGTGTCTGCTCCCTATTCA
1 TTCAGGGAGTATAAG-ACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATT-T
* * ** *
2817 TTCAGGGAGTATAAGACTCGAACAATCTTCAACTAACGTGTCCACTCCCTATTCC
1 TTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATT-T
* *
2872 TTCAGAGAGTATAGGACTCGA
1 TTCAGGGAGTATAAGACTCGA
2893 TCTTCATAAA
Statistics
Matches: 215, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
54 5 0.02
55 205 0.95
56 5 0.02
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (54 bp):
TTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTT
Found at i:2725 original size:110 final size:108
Alignment explanation
Indices: 2585--2892 Score: 402
Period size: 110 Copynumber: 2.8 Consensus size: 108
2575 TGATGGGTGT
* *
2585 GCTCCTTATTCCTTCAAGGAGTATAAGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATT
1 GCTCCCTATTCATTCAAGGAGTATAAGACTCGAACAATCTTCAGCAAATGTGTCT-CTCCCTATT
2650 TGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCC
65 T-TTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCC
* *
2695 GCTCCCTATTCTTTCAAGGAGTATAAGACTCGAACAATCTTCAGCAAATGGGTTCTCTCCCTATT
1 GCTCCCTATTCATTCAAGGAGTATAAGACTCGAACAATCTTCAGCAAATGTG-TCTCTCCCTATT
* * * *
2760 CTTTCAGGGAGTAT-AGAACTCGAACAATCTTCAGCGAACGTGTCT
65 -TTTCAGGGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCC
* * * * *
2805 GCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAACTAACGTGTCCACTCCCTATT
1 GCTCCCTATTCATTCAAGGAGTATAAGACTCGAACAATCTTCAGCAAATGTGT-CTCTCCCTATT
* * *
2870 CCTTCAGAGAGTATAGGACTCGA
65 -TTTCAGGGAGTATAAGACTCGA
2893 TCTTCATAAA
Statistics
Matches: 176, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
109 3 0.02
110 168 0.95
111 5 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (108 bp):
GCTCCCTATTCATTCAAGGAGTATAAGACTCGAACAATCTTCAGCAAATGTGTCTCTCCCTATTT
TTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCC
Found at i:2884 original size:165 final size:165
Alignment explanation
Indices: 2586--2892 Score: 474
Period size: 165 Copynumber: 1.9 Consensus size: 165
2576 GATGGGTGTG
* * *
2586 CTCCTTATTCCTTCAAGGAGTATAAGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTT
1 CTCCCTATTCCTTCAAGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTC
* * *
2651 GTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCTTTCAAGGAG
66 ATTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCACTCCCTATTCCTTCAAGGAG
2716 TATAAGACTCGAACAATCTTCAGCAAATGGGTTCT
131 TATAAGACTCGAACAATCTTCAGCAAATGGGTTCT
* * *
2751 CTCCCTATTCTTTCAGGGAGTAT-AGAACTCGAACAATCTTCAGCGAACGTGTCTGCTCCCTATT
1 CTCCCTATTCCTTCAAGGAGTATAAG-ACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATT
* *
2815 CATTCAGGGAGTATAAGACTCGAACAATCTTCAACTAACGTGTCCACTCCCTATTCCTTC-AGAG
65 CATTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCACTCCCTATTCCTTCAAG-G
*
2879 AGTATAGGACTCGA
129 AGTATAAGACTCGA
2893 TCTTCATAAA
Statistics
Matches: 128, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
164 4 0.03
165 124 0.97
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (165 bp):
CTCCCTATTCCTTCAAGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTC
ATTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCACTCCCTATTCCTTCAAGGAG
TATAAGACTCGAACAATCTTCAGCAAATGGGTTCT
Found at i:4214 original size:45 final size:45
Alignment explanation
Indices: 4129--4214 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
4119 TAAACAAAAC
* * *
4129 TCAAGTCGCCCTTTGCGGGTTTTCAACTTGAGACCTCCTTTGGTT
1 TCAAGACGCCCTTTGCGAGTTTTCAACTTGAGACCCCCTTTGGTT
* * *
4174 TCAAGACGCCCTTTGCGAATTTTTTATCTTGA-ACCCCCTTT
1 TCAAGACGCCCTTTGCG-AGTTTTCAACTTGAGACCCCCTTT
4215 TTATTTTTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
45 24 0.71
46 10 0.29
ACGTcount: A:0.16, C:0.28, G:0.17, T:0.38
Consensus pattern (45 bp):
TCAAGACGCCCTTTGCGAGTTTTCAACTTGAGACCCCCTTTGGTT
Found at i:4252 original size:11 final size:11
Alignment explanation
Indices: 4238--4370 Score: 89
Period size: 11 Copynumber: 12.0 Consensus size: 11
4228 TTTTGTTTTC
*
4238 TTTTTTCATCT
1 TTTTTTCATTT
4249 TTTTTTCATTT
1 TTTTTTCATTT
*
4260 ATTTTTTC-TTC
1 -TTTTTTCATTT
**
4271 AATTTTCTATTT
1 TTTTTTC-ATTT
4283 TTTTTTC-TATT
1 TTTTTTCAT-TT
4294 TTTTTTC----
1 TTTTTTCATTT
*
4301 TTTTTTCCTTT
1 TTTTTTCATTT
*
4312 TCCTTTTTCATGT
1 T--TTTTTCATTT
*
4325 TTTTCTCATTT
1 TTTTTTCATTT
4336 TTCTTTTCATTT
1 TT-TTTTCATTT
*
4348 TTTTCTCATTT
1 TTTTTTCATTT
4359 TTTTCTTCATTT
1 TTTT-TTCATTT
4371 CTTCATTTTT
Statistics
Matches: 96, Mismatches: 14, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
7 7 0.07
10 6 0.06
11 44 0.46
12 30 0.31
13 9 0.09
ACGTcount: A:0.09, C:0.16, G:0.01, T:0.74
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:4264 original size:23 final size:22
Alignment explanation
Indices: 4238--4370 Score: 80
Period size: 23 Copynumber: 6.0 Consensus size: 22
4228 TTTTGTTTTC
4238 TTTTTTCATCTTTTTTTCATTT
1 TTTTTTCATCTTTTTTTCATTT
* **
4260 ATTTTTTCTTC-AATTTTCTATTT
1 -TTTTTTCATCTTTTTTTC-ATTT
4283 TTTTTTCTAT-TTTTTTTC-TTT
1 TTTTTTC-ATCTTTTTTTCATTT
* *
4304 TTTCCTTT--TC-CTTTTTCATGT
1 TTT--TTTCATCTTTTTTTCATTT
* *
4325 TTTTCTCATTTTTCTTTTCATTT
1 TTTTTTCATCTTT-TTTTCATTT
* *
4348 TTTTCTCATTTTTTTCTTCATTT
1 TTTTTTCATCTTTTT-TTCATTT
4371 CTTCATTTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
19 2 0.02
20 7 0.08
21 12 0.14
22 15 0.17
23 50 0.58
ACGTcount: A:0.09, C:0.16, G:0.01, T:0.74
Consensus pattern (22 bp):
TTTTTTCATCTTTTTTTCATTT
Found at i:4283 original size:19 final size:19
Alignment explanation
Indices: 4259--4295 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4249 TTTTTTCATT
4259 TATTTTTTCTTCAATTTTC
1 TATTTTTTCTTCAATTTTC
* *
4278 TATTTTTTTTTCTATTTT
1 TATTTTTTCTTCAATTTT
4296 TTTTCTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTTTCTTCAATTTTC
Found at i:4300 original size:33 final size:29
Alignment explanation
Indices: 4218--4307 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 29
4208 CCCCTTTTTA
*
4218 TTTTTCTCTATTTTGTTTTCTTTTTTCATC
1 TTTTTTTCTATTTT-TTTTCTTTTTTCATC
*
4248 TTTTTTTC-ATTTATTTTTTCTTCAATTTTCTATT
1 TTTTTTTCTA-TT-TTTTTTCTT---TTTTC-ATC
4282 TTTTTTTCTATTTTTTTTCTTTTTTC
1 TTTTTTTCTATTTTTTTTCTTTTTTC
4308 CTTTTCCTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
29 1 0.02
30 21 0.41
31 2 0.04
33 14 0.27
34 12 0.24
35 1 0.02
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (29 bp):
TTTTTTTCTATTTTTTTTCTTTTTTCATC
Found at i:4303 original size:63 final size:60
Alignment explanation
Indices: 4213--4428 Score: 158
Period size: 63 Copynumber: 3.4 Consensus size: 60
4203 TGAACCCCCT
4213 TTTTATTTTTCTCTATTTTGTTTTCTTTTTTCATCTTTTTTTCATTTATTTTTTCTTCAATTTTC
1 TTTT-TTTTT-TCTATTTT-TTTTCTTTTTTC-TCTTTTTTT-ATTTATTTTTTCTTCAATTTTC
* *
4278 TATTTTTTTTTCTATTTTTTTTCTTTTTTC-CTTTTCCTTT-TTCATGTTTTTC-TCATTTTTC
1 T-TTTTTTTTTCTATTTTTTTTCTTTTTTCTCTTTT--TTTATTTAT-TTTTTCTTCAATTTTC
* *
4339 TTTTCATTTTTTTCTCA-TTTTTTTCTTCATTTCTTCATTTTTTTAATTT-TTTCAATT-TTCAA
1 -TTT--TTTTTTTCT-ATTTTTTTTCTT-TTTTC-TC-TTTTTTT-ATTTATTT--TTTCTTCAA
4401 TTTTC
56 TTTTC
4406 TTTTTATTTTTC-ATTTCTTTTTC
1 TTTTT-TTTTTCTATTT-TTTTTC
4429 AGGCGAAATA
Statistics
Matches: 125, Mismatches: 6, Indels: 40
0.73 0.04 0.23
Matches are distributed among these distances:
61 19 0.15
62 7 0.06
63 35 0.28
64 17 0.14
65 23 0.18
66 8 0.06
67 16 0.13
ACGTcount: A:0.11, C:0.15, G:0.01, T:0.74
Consensus pattern (60 bp):
TTTTTTTTTTCTATTTTTTTTCTTTTTTCTCTTTTTTTATTTATTTTTTCTTCAATTTTC
Found at i:4350 original size:31 final size:30
Alignment explanation
Indices: 4259--4379 Score: 93
Period size: 31 Copynumber: 3.7 Consensus size: 30
4249 TTTTTTCATT
*
4259 TATTTTTTCTTCAATTTTCTATTT-TTTTTTC
1 TATTTTTTC-TCATTTTTCT-TTTCTTTTTTC
* * *
4290 TATTTTTTTTCTTTTTTCCTTTTCCTTTTTC
1 TATTTTTTCTCATTTTT-CTTTTCTTTTTTC
4321 -ATGTTTTTCTCATTTTTCTTTTCATTTTTTTC
1 TAT-TTTTTCTCATTTTTCTTTTC--TTTTTTC
4353 TCATTTTTTTCTTCATTTCTTCATTTT
1 T-A-TTTTTTC-TCATTT-TTC-TTTT
4380 TTTAATTTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
30 17 0.24
31 28 0.39
32 6 0.08
34 7 0.10
35 7 0.10
36 3 0.04
37 4 0.06
ACGTcount: A:0.09, C:0.17, G:0.01, T:0.74
Consensus pattern (30 bp):
TATTTTTTCTCATTTTTCTTTTCTTTTTTC
Found at i:4381 original size:76 final size:75
Alignment explanation
Indices: 4233--4382 Score: 162
Period size: 76 Copynumber: 2.0 Consensus size: 75
4223 CTCTATTTTG
* * *
4233 TTTTCTTTTTTCATCTTTTTTTCATTTATTTTTTCTTCAATTTTCTATTTTTTTTTCTATTTTTT
1 TTTTCCTTTTTCATCTTTTTCTCATTTATTTTTTCTT-AATTTTCTATTTTTTTTTCTATTTCTT
**
4298 TTCTTTTTTCC
65 CACTTTTTTCC
* *
4309 TTTTCCTTTTTCATGTTTTTCTCATTT-TTCTTTTCATT-TTTTTCTCATTTTTTTCTTC-ATTT
1 TTTTCCTTTTTCATCTTTTTCTCATTTATT-TTTTC-TTAATTTTCT-ATTTTTTT-TTCTATTT
*
4371 CTTCATTTTTTT
62 CTTCACTTTTTT
4383 AATTTTTTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
75 8 0.13
76 49 0.79
77 5 0.08
ACGTcount: A:0.09, C:0.16, G:0.01, T:0.75
Consensus pattern (75 bp):
TTTTCCTTTTTCATCTTTTTCTCATTTATTTTTTCTTAATTTTCTATTTTTTTTTCTATTTCTTC
ACTTTTTTCC
Found at i:24665 original size:20 final size:20
Alignment explanation
Indices: 24640--24747 Score: 76
Period size: 20 Copynumber: 5.1 Consensus size: 20
24630 CTTTGCCTGA
24640 AGAAAAAAGAAAGAAAAAAG
1 AGAAAAAAGAAAGAAAAAAG
* *
24660 AGAAAAAATTAGAAAAAAAAGAAAA
1 AG-AAAAA--AG-AAAGAAA-AAAG
24685 ACGAAAAAAGAAAGAAAAAA-
1 A-GAAAAAAGAAAGAAAAAAG
*
24705 AGGGAAAAAGAAAGAAGAAAAG
1 A-GAAAAAAGAAAGAA-AAAAG
* * *
24727 A-AAAAAATAAATAAAAGAG
1 AGAAAAAAGAAAGAAAAAAG
24746 AG
1 AG
24748 TTCAAGATGA
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
19 5 0.07
20 26 0.37
21 12 0.17
22 7 0.10
23 4 0.06
24 6 0.09
25 9 0.13
26 1 0.01
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.04
Consensus pattern (20 bp):
AGAAAAAAGAAAGAAAAAAG
Found at i:24726 original size:46 final size:46
Alignment explanation
Indices: 24641--24731 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
24631 TTTGCCTGAA
*
24641 GAAAAAAGAAAGAAAAAAGAGAAAAAATTAGAAAAAAAAGAAAAAC
1 GAAAAAAGAAAGAAAAAAGAGAAAAAATAAGAAAAAAAAGAAAAAC
* *
24687 GAAAAAAGAAAGAAAAAAAGGGAAAAAGA-AAG-AAGAAAAGAAAAA
1 GAAAAAAGAAAG-AAAAAAGAGAAAAA-ATAAGAAAAAAAAGAAAAA
24732 AATAAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 24 0.60
47 15 0.38
48 1 0.03
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.02
Consensus pattern (46 bp):
GAAAAAAGAAAGAAAAAAGAGAAAAAATAAGAAAAAAAAGAAAAAC
Found at i:24732 original size:27 final size:27
Alignment explanation
Indices: 24643--24733 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 27
24633 TGCCTGAAGA
* *
24643 AAAAAGAAAGAAAAAAGAGAAAAA-ATTAG
1 AAAAA-AAAGAAAAACGA-AAAAAGA-AAG
24672 AAAAAAAAGAAAAACGAAAAAAGAAAG
1 AAAAAAAAGAAAAACGAAAAAAGAAAG
* *
24699 AAAAAAAGGGAAAAA-GAAAGAAGAAAAG
1 AAAAAAA-AGAAAAACGAAAAAAG-AAAG
24727 AAAAAAA
1 AAAAAAA
24734 TAAATAAAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
27 21 0.38
28 29 0.53
29 5 0.09
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.02
Consensus pattern (27 bp):
AAAAAAAAGAAAAACGAAAAAAGAAAG
Found at i:27081 original size:75 final size:76
Alignment explanation
Indices: 26975--27161 Score: 250
Period size: 75 Copynumber: 2.5 Consensus size: 76
26965 CCCCCTGGGG
* ** *
26975 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAATGTTTAGGGGGGAATCG
1 GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAAAAACATTCAGGGGGGAATCG
*
27040 GTTCCTCTTAT
66 GTTCCTCCTAT
* * * *
27051 -GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCAAACCATTCAGGGGGGAATCG
1 GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAAAAACATTCAGGGGGGAATCG
27115 GTTCCTCCTAT
66 GTTCCTCCTAT
* * *
27126 GGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 -GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
27162 TTTGGCTTTG
Statistics
Matches: 96, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
75 66 0.69
77 30 0.31
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.25
Consensus pattern (76 bp):
GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAAAAACATTCAGGGGGGAATCG
GTTCCTCCTAT
Found at i:29786 original size:21 final size:21
Alignment explanation
Indices: 29760--29799 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29750 CAGAACCCCA
*
29760 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
29781 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
29800 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:33689 original size:22 final size:21
Alignment explanation
Indices: 33647--33686 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33637 TGAGTTGTTT
*
33647 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
33668 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
33687 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:35777 original size:75 final size:74
Alignment explanation
Indices: 35606--35808 Score: 253
Period size: 74 Copynumber: 2.7 Consensus size: 74
35596 GACCGTTGAA
* * ** * *
35606 CAGGGGGAATCGGTACCCCCTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAAC
1 CAGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAAC
**
35671 AAAAATGTT
66 AAAAACATT
* *
35680 TAGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC
1 CAGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAAC
* *
35745 CAAACCATT
66 AAAAACATT
* *
35754 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 CA-GGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTTCCCTCCGAGCATTCTG
35809 TAATTTTTGG
Statistics
Matches: 111, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
74 63 0.57
75 21 0.19
77 27 0.24
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.23
Consensus pattern (74 bp):
CAGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAAC
AAAAACATT
Found at i:36203 original size:21 final size:21
Alignment explanation
Indices: 36177--36236 Score: 120
Period size: 21 Copynumber: 2.9 Consensus size: 21
36167 TTACTTGAAA
36177 AAGTGGAGCAGATCAAGTTTT
1 AAGTGGAGCAGATCAAGTTTT
36198 AAGTGGAGCAGATCAAGTTTT
1 AAGTGGAGCAGATCAAGTTTT
36219 AAGTGGAGCAGATCAAGT
1 AAGTGGAGCAGATCAAGT
36237 CTGACCTTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (21 bp):
AAGTGGAGCAGATCAAGTTTT
Found at i:37336 original size:16 final size:16
Alignment explanation
Indices: 37307--37373 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
37297 CGTTCATTTA
37307 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
37321 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
37337 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
37353 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
37369 ATAAA
1 ATAAA
37374 CGTTGGAGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 41 0.84
ACGTcount: A:0.60, C:0.18, G:0.10, T:0.12
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:38433 original size:14 final size:14
Alignment explanation
Indices: 38416--38471 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
38406 AATGAACATA
38416 AACGAACATAACCG
1 AACGAACATAACCG
38430 AACGAACAT-A---
1 AACGAACATAACCG
* *
38440 AACGAATATAACTG
1 AACGAACATAACCG
38454 AACGAACATAACCG
1 AACGAACATAACCG
38468 AACG
1 AACG
38472 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:38436 original size:24 final size:24
Alignment explanation
Indices: 38409--38470 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
38399 ATAAATGAAT
38409 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
* *
38433 GAACATAAACGAATATAACTGAAC
1 GAACATAAACGAACATAACCGAAC
*
38457 GAACATAACCGAAC
1 GAACATAAACGAAC
38471 GTTCACGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.53, C:0.23, G:0.13, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:39670 original size:2 final size:2
Alignment explanation
Indices: 39663--39737 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
39653 ACATATGCGC
39663 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
39705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39738 CGCATATGTG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41368 original size:13 final size:13
Alignment explanation
Indices: 41352--41396 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
41342 TACAATTAAT
41352 TTAATAATTATAA
1 TTAATAATTATAA
* *
41365 TTAATATTTATAG
1 TTAATAATTATAA
* *
41378 TAAAGAATTATAA
1 TTAATAATTATAA
41391 TTAATA
1 TTAATA
41397 TAAAAAGTAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (13 bp):
TTAATAATTATAA
Found at i:41405 original size:26 final size:26
Alignment explanation
Indices: 41357--41407 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
41347 TTAATTTAAT
** *
41357 AATTATAATTAATATTTATAGTAAAG
1 AATTATAATTAATATAAAAAGTAAAG
41383 AATTATAATTAATATAAAAAGTAAA
1 AATTATAATTAATATAAAAAGTAAA
41408 TTTATTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (26 bp):
AATTATAATTAATATAAAAAGTAAAG
Found at i:48420 original size:12 final size:12
Alignment explanation
Indices: 48398--48432 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
48388 TATATATATA
*
48398 TATATATATACG
1 TATATAAATACG
48410 TATATAAATACG
1 TATATAAATACG
48422 TATATAAATAC
1 TATATAAATAC
48433 CATCTCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (12 bp):
TATATAAATACG
Found at i:48427 original size:2 final size:2
Alignment explanation
Indices: 48370--48407 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
48360 CTCATGCATT
48370 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
48408 CGTATATAAA
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):
TA
Found at i:57083 original size:46 final size:45
Alignment explanation
Indices: 56981--57116 Score: 191
Period size: 46 Copynumber: 3.0 Consensus size: 45
56971 GAAATATTCA
* * *
56981 TAGTCATACATTATTACCACCTACTCCACTACTCAATTAAATTAC
1 TAGTCATACATTATTGCCACCTACTCCACTACTCCATTAAATTGC
* * *
57026 TAGTCATACATTACTGTCACCTACTCCATCTAATCCATTAAATTGC
1 TAGTCATACATTATTGCCACCTACTCCA-CTACTCCATTAAATTGC
*
57072 TAGTCATACATTATTGCCACCTATTCCACCTACTCCATTAAATTG
1 TAGTCATACATTATTGCCACCTACTCCA-CTACTCCATTAAATTG
57117 AGAAACTTCC
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
45 25 0.32
46 54 0.68
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.35
Consensus pattern (45 bp):
TAGTCATACATTATTGCCACCTACTCCACTACTCCATTAAATTGC
Found at i:58439 original size:10 final size:10
Alignment explanation
Indices: 58424--58462 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
58414 AACAAACACA
58424 ATAAATGAAC
1 ATAAATGAAC
58434 ATAAATGAAC
1 ATAAATGAAC
* *
58444 GTAAACGAAC
1 ATAAATGAAC
58454 ATAAATGAA
1 ATAAATGAA
58463 AATATATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:58453 original size:20 final size:20
Alignment explanation
Indices: 58425--58462 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58415 ACAAACACAA
*
58425 TAAATGAACATAAATGAACG
1 TAAACGAACATAAATGAACG
58445 TAAACGAACATAAATGAA
1 TAAACGAACATAAATGAA
58463 AATATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (20 bp):
TAAACGAACATAAATGAACG
Found at i:59679 original size:19 final size:19
Alignment explanation
Indices: 59652--59689 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
59642 GAATTCAACA
*
59652 AAAATAATATTTTATAATT
1 AAAAGAATATTTTATAATT
59671 AAAAGAATATTTTATAATT
1 AAAAGAATATTTTATAATT
59690 TCTGATGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
AAAAGAATATTTTATAATT
Found at i:59987 original size:31 final size:31
Alignment explanation
Indices: 59952--60074 Score: 183
Period size: 31 Copynumber: 4.0 Consensus size: 31
59942 ACAATCCTCT
* * *
59952 AACATTTAGTTCGTTTACAATATGATCCTCC
1 AACATTTAGTCCGTTTGCAATATGATCCCCC
* *
59983 AACATTTAGTCTGTTTGCAATATGGTCCCCC
1 AACATTTAGTCCGTTTGCAATATGATCCCCC
60014 AACATTTAGTCCGTTTGCAATATGATCCCCC
1 AACATTTAGTCCGTTTGCAATATGATCCCCC
* *
60045 TACATTTAGTCCGTTTGCAATATGGTCCCC
1 AACATTTAGTCCGTTTGCAATATGATCCCC
60075 GACCATTTGA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 83 1.00
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (31 bp):
AACATTTAGTCCGTTTGCAATATGATCCCCC
Done.