Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003398.1 Hibiscus syriacus cultivar Beakdansim tig00007147_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: 59737
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:2686 original size:37 final size:39
Alignment explanation
Indices: 2607--2810 Score: 130
Period size: 39 Copynumber: 5.2 Consensus size: 39
2597 TAGTGGTATT
* * * *
2607 TTTAGTGGCGTTTTTAGAACAAATGCCGCTAAATACTCGTAA
1 TTTAGTGGC--TTTTA-TACAAACGCCACTAAAGACTCGTAA
*
2649 TTTAGTGG-TTTTATATAAACGCCACTAAAGACT-GTAA
1 TTTAGTGGCTTTTATACAAACGCCACTAAAGACTCGTAA
* ** * *
2686 TTTAGTGGCTTTTTATACAAACGCCGCTGGAGACT-ATAC
1 TTTAGTGGC-TTTTATACAAACGCCACTAAAGACTCGTAA
* * *
2725 TTTAGTGGCGTTTTATTCAAACGCCGA--AAAGAGTCGTAC
1 TTTAGTGGC-TTTTATACAAACGCC-ACTAAAGACTCGTAA
** * * * *
2764 TTTAGTGATATTTTTATATAAACGCCGCTATAGACTCGTAC
1 TTTAGTG--GCTTTTATACAAACGCCACTAAAGACTCGTAA
2805 TTTAGT
1 TTTAGT
2811 TATATTTTTA
Statistics
Matches: 129, Mismatches: 25, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
37 12 0.09
38 19 0.15
39 61 0.47
40 13 0.10
41 16 0.12
42 8 0.06
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (39 bp):
TTTAGTGGCTTTTATACAAACGCCACTAAAGACTCGTAA
Found at i:2708 original size:39 final size:40
Alignment explanation
Indices: 2607--2886 Score: 210
Period size: 41 Copynumber: 7.0 Consensus size: 40
2597 TAGTGGTATT
* * * *
2607 TTTAGTGGCGTTTTTAGAACAAATGCCGCTAAATACTCGTAA
1 TTTAGTGGC-TTTTTA-TACAAACGCCGCTAAAGACTCGTAC
* * *
2649 TTTAGTGG--TTTTATATAAACGCCACTAAAGACT-GTAA
1 TTTAGTGGCTTTTTATACAAACGCCGCTAAAGACTCGTAC
** *
2686 TTTAGTGGCTTTTTATACAAACGCCGCTGGAGACT-ATAC
1 TTTAGTGGCTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * *
2725 TTTAGTGGCGTTTTATTCAAACGCCG-AAAAGAGTCGTAC
1 TTTAGTGGCTTTTTATACAAACGCCGCTAAAGACTCGTAC
** * *
2764 TTTAGTGATATTTTTATATAAACGCCGCTATAGACTCGTAC
1 TTTAGTG-GCTTTTTATACAAACGCCGCTAAAGACTCGTAC
*** * * **
2805 TTTAGTTATATTTTTATACAAACACCGCTATAGACTAATAC
1 TTTAG-TGGCTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * ** *
2846 TTTAGTGACGTTTTTATATAAATACCGCTAAAAACTCGTAC
1 TTTAGTGGC-TTTTTATACAAACGCCGCTAAAGACTCGTAC
2887 AATAGTGATA
Statistics
Matches: 191, Mismatches: 40, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
37 12 0.06
38 19 0.10
39 62 0.32
40 15 0.08
41 74 0.39
42 9 0.05
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (40 bp):
TTTAGTGGCTTTTTATACAAACGCCGCTAAAGACTCGTAC
Found at i:2738 original size:78 final size:78
Alignment explanation
Indices: 2625--2810 Score: 175
Period size: 78 Copynumber: 2.4 Consensus size: 78
2615 CGTTTTTAGA
* * * * *
2625 ACAAATGCCGCTAAATACTCGTAATTTAGTGGTTTTATAT-AAACGCC-ACTAAAGACT-GTAAT
1 ACAAACGCCGCTAGAGACTCATACTTTAGTGGTTTTAT-TCAAACGCCGA--AAAGACTCGTAAT
*
2687 TTAGTG-GCTTTTTAT
63 TTAGTGAGATTTTTAT
* * *
2702 ACAAACGCCGCTGGAGACT-ATACTTTAGTGGCGTTTTATTCAAACGCCGAAAAGAGTCGTACTT
1 ACAAACGCCGCTAGAGACTCATACTTTAGT-G-GTTTTATTCAAACGCCGAAAAGACTCGTAATT
*
2766 TAGTGATATTTTTAT
64 TAGTGAGATTTTTAT
* * *
2781 ATAAACGCCGCTATAGACTCGTACTTTAGT
1 ACAAACGCCGCTAGAGACTCATACTTTAGT
2811 TATATTTTTA
Statistics
Matches: 88, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
76 8 0.09
77 23 0.26
78 24 0.27
79 24 0.27
80 9 0.10
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (78 bp):
ACAAACGCCGCTAGAGACTCATACTTTAGTGGTTTTATTCAAACGCCGAAAAGACTCGTAATTTA
GTGAGATTTTTAT
Found at i:2816 original size:41 final size:41
Alignment explanation
Indices: 2758--2903 Score: 175
Period size: 41 Copynumber: 3.5 Consensus size: 41
2748 CCGAAAAGAG
*
2758 TCGTACTTTAGTGATATTTTTATATAAACGCCGCTATAGAC
1 TCGTACTTTAGTGATATTTTTATATAAACACCGCTATAGAC
* *
2799 TCGTACTTTAGTTATATTTTTATACAAACACCGCTATAGAC
1 TCGTACTTTAGTGATATTTTTATATAAACACCGCTATAGAC
** ** * * *
2840 TAATACTTTAGTGACGTTTTTATATAAATACCGCTAAAAAC
1 TCGTACTTTAGTGATATTTTTATATAAACACCGCTATAGAC
**
2881 TCGTACAATAGTGATAGTTTTTA
1 TCGTACTTTAGTGATA-TTTTTA
2904 AATCCCACAC
Statistics
Matches: 86, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
41 80 0.93
42 6 0.07
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (41 bp):
TCGTACTTTAGTGATATTTTTATATAAACACCGCTATAGAC
Found at i:4738 original size:37 final size:38
Alignment explanation
Indices: 4688--4763 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
4678 TGCACATGTA
*
4688 TAATCTCAATC-TTTGGTCTGTTTTGACCTCATATTTG
1 TAATCTCAATCTTTTGGTCTGTTTTGACCTCAGATTTG
4725 TAATCTCAATCTTTTGGTCTGTTTTGACCTCAGATTTG
1 TAATCTCAATCTTTTGGTCTGTTTTGACCTCAGATTTG
4763 T
1 T
4764 TAAAACAAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 11 0.30
38 26 0.70
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.49
Consensus pattern (38 bp):
TAATCTCAATCTTTTGGTCTGTTTTGACCTCAGATTTG
Found at i:8583 original size:20 final size:20
Alignment explanation
Indices: 8555--8599 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
8545 ACTAATCCTG
8555 TAACAGATTTCTAACTTCCC
1 TAACAGATTTCTAACTTCCC
* *
8575 TAACTGATTTCTAATTTCCC
1 TAACAGATTTCTAACTTCCC
8595 TAACA
1 TAACA
8600 ACTTTTATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (20 bp):
TAACAGATTTCTAACTTCCC
Found at i:10964 original size:23 final size:23
Alignment explanation
Indices: 10914--10969 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
10904 GTCGAGGGTT
* * *
10914 CTATGTGGTCCTTCAAGATAAAT
1 CTATGTGGTCCTTCAAAACAAAC
*
10937 TTATGTGGTCCTTCAAAACAAAC
1 CTATGTGGTCCTTCAAAACAAAC
10960 CTATGTGGTC
1 CTATGTGGTC
10970 ATTCGGGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (23 bp):
CTATGTGGTCCTTCAAAACAAAC
Found at i:20929 original size:13 final size:13
Alignment explanation
Indices: 20908--20975 Score: 82
Period size: 13 Copynumber: 5.2 Consensus size: 13
20898 AATGACGCTT
*
20908 AATGAGCGTCATA
1 AATGCGCGTCATA
*
20921 AATGTGCGTCATA
1 AATGCGCGTCATA
*
20934 AATGCCCGTCATA
1 AATGCGCGTCATA
* *
20947 TATGCGTGTCATA
1 AATGCGCGTCATA
*
20960 AATGCGCGTTATA
1 AATGCGCGTCATA
20973 AAT
1 AAT
20976 TTATGACGCA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:21458 original size:23 final size:23
Alignment explanation
Indices: 21395--21458 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
21385 GGATTCTAAG
* *
21395 TAGTCCTTCGGGACAAACCTATG
1 TAGTCCTTCGGGACAAATCTATA
*
21418 TAGTCCTTCGGGACAAATCTGTA
1 TAGTCCTTCGGGACAAATCTATA
*
21441 TGGTCCTTCGGGACAAAT
1 TAGTCCTTCGGGACAAAT
21459 ATTTGGCACT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (23 bp):
TAGTCCTTCGGGACAAATCTATA
Found at i:25553 original size:2 final size:2
Alignment explanation
Indices: 25546--25590 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
25536 CTAAAAAGTT
25546 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
25588 TA T
1 TA T
25591 CCAAAAAGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32595 original size:22 final size:22
Alignment explanation
Indices: 32526--32596 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 22
32516 AGAGTTAATT
*
32526 AAATATATGTTTTAA-TAATCTTG
1 AAATATA-GATTTAATTAAT-TTG
*
32549 AATATTTA-ATTTCAATTAA-TT-
1 AA-ATATAGATTT-AATTAATTTG
32570 AAATATAGATTTAATTAATTTG
1 AAATATAGATTTAATTAATTTG
32592 AAATA
1 AAATA
32597 ATAAAATCCC
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
20 10 0.26
21 8 0.21
22 10 0.26
23 4 0.10
24 7 0.18
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (22 bp):
AAATATAGATTTAATTAATTTG
Found at i:40120 original size:64 final size:63
Alignment explanation
Indices: 40026--40163 Score: 145
Period size: 64 Copynumber: 2.2 Consensus size: 63
40016 CACATTCAAT
* * * *
40026 GTGCATCGATGCACTCTTTAAAGAAGAAACATTGAATGCAATTGGTGCATTGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGTA
* * * * * *
40089 GTGCATCGATTCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
40153 GTGCATCGATG
1 GTGCATCGATG
40164 AACATGTTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
63 16 0.26
64 45 0.74
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:40181 original size:24 final size:20
Alignment explanation
Indices: 40154--40207 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
40144 GCATGGGTAG
40154 TGCATCGATGAACATGTTAAAGAA
1 TGCATCGATGAAC-TG-T--AGAA
*
40178 TGCATCGATGCACTGTAGAA
1 TGCATCGATGAACTGTAGAA
40198 TGCATCGATG
1 TGCATCGATG
40208 CCCTTCAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 14 0.48
22 1 0.03
23 2 0.07
24 12 0.41
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCATCGATGAACTGTAGAA
Found at i:41897 original size:23 final size:23
Alignment explanation
Indices: 41871--41931 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
41861 TATGGCATTT
41871 CGGTGCATTTCTACGCGGCACTA
1 CGGTGCATTTCTACGCGGCACTA
* * *
41894 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCATTTCTACGCGGCACTA
*
41917 CGGTGCATTTATACG
1 CGGTGCATTTCTACG
41932 AATTGTGGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGGCACTA
Found at i:44199 original size:3 final size:3
Alignment explanation
Indices: 44183--44275 Score: 107
Period size: 3 Copynumber: 30.7 Consensus size: 3
44173 TTTGGGCTTG
* * * *
44183 TAA TAA TATT TAA TAA TAA TAT TAA TAA TAAA TAA TAA TAA TAT TAG
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* *
44230 TAA TTA TAA TTA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
44276 TTTAAATGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.03
3 69 0.91
4 5 0.07
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:44568 original size:36 final size:36
Alignment explanation
Indices: 44516--44605 Score: 144
Period size: 36 Copynumber: 2.5 Consensus size: 36
44506 TTGAACAAGC
* * * *
44516 TCTTTTCATTGTGAACTTCTTCTTTTTCAGATTAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
44552 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
44588 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
44606 TCTCTGGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.19, C:0.20, G:0.10, T:0.51
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
Found at i:44877 original size:113 final size:112
Alignment explanation
Indices: 44551--45430 Score: 1219
Period size: 113 Copynumber: 7.8 Consensus size: 112
44541 TTCAGATTAG
****
44551 TTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
44612 GAAAAGCTGATCTATCAAGTGATGGATTTGAACAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGAT-GATTTGAGCAAAAGGTTGAACAAA
* * *
44660 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTGTGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCGAA
* * * * ** * * *
44725 CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG
63 CTGGAAAAGCTGATCCATCAAGTGATG-ATTTGAGCAAAAGGTTGAACAAA
* ****
44776 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* * *
44841 GAAAAGCGGATCCATCAAGTGATGTATTTGAGCAAAAGATTGAATAAA
66 GAAAAGCTGATCCATCAAGTGATG-ATTTGAGCAAAAGGTTGAACAAA
* **** *
44889 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
44954 GAAAAGCTGATCCATCAAGTGATGGATTTGGGCAAAAGGTTGAATAAA
66 GAAAAGCTGATCCATCAAGTGAT-GATTTGAGCAAAAGGTTGAACAAA
45002 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* * *
45067 GAAAAGCTAATCTATCAAGTGATAGATTTGAGCAAAAAGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGAT-GATTTGAGCAAAAGGTTGAACAAA
*
45115 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
45180 GAAAAGCTAATCTATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGAT-GATTTGAGCAAAAGGTTGAACAAA
* *
45228 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGGACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
45293 GAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGAT-GATTTGAGCAAAAGGTTGAACAAA
* * *
45341 TTCTTCTCATTATGAACTTTTTCATCATTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
45406 GAAAAGCTGATCCATCAAGTGATGA
66 GAAAAGCTGATCCATCAAGTGATGA
45431 ATTTAAATTT
Statistics
Matches: 703, Mismatches: 59, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
109 16 0.02
112 8 0.01
113 579 0.82
114 1 0.00
115 1 0.00
116 98 0.14
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
GAAAAGCTGATCCATCAAGTGATGATTTGAGCAAAAGGTTGAACAAA
Found at i:46296 original size:83 final size:83
Alignment explanation
Indices: 46159--46712 Score: 966
Period size: 83 Copynumber: 6.7 Consensus size: 83
46149 GGTTTTATAT
* * *
46159 CAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
46224 TTCAATAACTGGTTTTAC
66 TTCAATAACTGGTTTTAC
46242 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
46307 TTCAATGACTGGTTTTAC
66 TTCAATAACTGGTTTTAC
*
46325 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
46390 TTCAATAACTGGTTTTAC
66 TTCAATAACTGGTTTTAC
*
46408 CAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
46473 TTCAATGACTGGTTTTAC
66 TTCAATAACTGGTTTTAC
* *
46491 CAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
46556 TTCCATAACTGGTTTTAC
66 TTCAATAACTGGTTTTAC
46574 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACAT-TTGTCA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT-CATCTT-TCA
* *
46638 AATTCAATGATTGGTTTTTAC
64 AATTCAATAACTGG-TTTTAC
46659 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
46713 ACATTTGTTT
Statistics
Matches: 451, Mismatches: 17, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
83 375 0.83
84 16 0.04
85 60 0.13
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
TTCAATAACTGGTTTTAC
Found at i:47882 original size:13 final size:13
Alignment explanation
Indices: 47860--47902 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
47850 CTTGACCCCC
*
47860 TTTTTCCTTTTCT
1 TTTTTTCTTTTCT
47873 TTTTTTCTTTTC-
1 TTTTTTCTTTTCT
*
47885 TCTTTT-TTTTCT
1 TTTTTTCTTTTCT
47897 TTTTTT
1 TTTTTT
47903 TCTTCAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 5 0.19
12 10 0.38
13 11 0.42
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCTTTTCT
Found at i:47888 original size:15 final size:15
Alignment explanation
Indices: 47860--47900 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
47850 CTTGACCCCC
*
47860 TTTTTCCTTTTC-TT
1 TTTTTCTTTTTCTTT
47874 TTTTTCTTTTCTCTTT
1 TTTTTCTTTT-TCTTT
47890 TTTTTCTTTTT
1 TTTTTCTTTTT
47901 TTTCTTCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 9 0.38
15 3 0.12
16 12 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCTTTTTCTTT
Found at i:47889 original size:20 final size:20
Alignment explanation
Indices: 47861--47905 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
47851 TTGACCCCCT
47861 TTTTC-CTTTTCTTTT-TTTC
1 TTTTCTCTTTT-TTTTCTTTC
*
47880 TTTTCTCTTTTTTTTCTTTT
1 TTTTCTCTTTTTTTTCTTTC
47900 TTTTCT
1 TTTTCT
47906 TCAAGCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTCTCTTTTTTTTCTTTC
Found at i:47897 original size:9 final size:9
Alignment explanation
Indices: 47860--47906 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
47850 CTTGACCCCC
*
47860 TTTTTCCTT
1 TTTTTTCTT
47869 TTCTTTT-TT
1 TT-TTTTCTT
47878 TCTTTTCTCTT
1 T-TTTT-TCTT
47889 TTTTTTCTT
1 TTTTTTCTT
47898 TTTTTTCTT
1 TTTTTTCTT
47907 CAAGCATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 21 0.64
10 9 0.27
11 3 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:58429 original size:20 final size:22
Alignment explanation
Indices: 58389--58432 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
58379 ATGAAATATT
58389 AATAATATATATAATACTATAA
1 AATAATATATATAATACTATAA
*
58411 AATAATATGTAT-ATA-TATAA
1 AATAATATATATAATACTATAA
58431 AA
1 AA
58433 AAGAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 3 0.14
22 11 0.52
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAATATATATAATACTATAA
Done.