Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009440.1 Hibiscus syriacus cultivar Beakdansim tig00113501_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: 87774
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1392 original size:22 final size:22
Alignment explanation
Indices: 1358--1401 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1348 TCCATTTCAA
1358 CATCAACACCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
* *
1380 CATCAAGATCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
1402 GTAATTTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.25
Consensus pattern (22 bp):
CATCAACACCATCAACATCTTC
Found at i:4902 original size:80 final size:82
Alignment explanation
Indices: 4811--4985 Score: 214
Period size: 80 Copynumber: 2.2 Consensus size: 82
4801 TGGCATGGAC
* * * *
4811 TAATTCACAATTTGATTTAGT-TCAATCATGGA-AACATTCAATAATTCACCATTCGA-TCAATT
1 TAATTCACAATTTGATTCA-TCTCAATCAT-GACAACATGCAATAATTCACAATTCAACTCAATT
* *
4873 TGATCAT-GAATCATGCAA
64 CGATCATGGAAGCATGCAA
*
4891 TAATTCACAATTTGATTCATCTCAATCATGACAACATGCAATAATTCACAATTCAACTTAATTCG
1 TAATTCACAATTTGATTCATCTCAATCATGACAACATGCAATAATTCACAATTCAACTCAATTCG
*
4956 ATCATGGCAGCATGCAA
66 ATCATGGAAGCATGCAA
* *
4973 TAATCCATAATTT
1 TAATTCACAATTT
4986 CAATTCAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
79 3 0.04
80 47 0.58
81 11 0.14
82 20 0.25
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (82 bp):
TAATTCACAATTTGATTCATCTCAATCATGACAACATGCAATAATTCACAATTCAACTCAATTCG
ATCATGGAAGCATGCAA
Found at i:4960 original size:41 final size:39
Alignment explanation
Indices: 4811--5024 Score: 158
Period size: 41 Copynumber: 5.3 Consensus size: 39
4801 TGGCATGGAC
* * * *
4811 TAATTCACAATTTGATTTAGTTCAATCATGGAAACATTCAA
1 TAATTCACAATTCGA-TTAATTCGATCAT-GAAACATGCAA
* * * *
4852 TAATTCACCATTCGATCAATTTGATCATGAATCATGCAA
1 TAATTCACAATTCGATTAATTCGATCATGAAACATGCAA
* * *
4891 TAATTCACAATTTGATTCATCTCAATCATGACAACATGCAA
1 TAATTCACAATTCGATTAAT-TCGATCATGA-AACATGCAA
* * *
4932 TAATTCACAATTCAACTTAATTCGATCATGGCAGCATGCAA
1 TAATTCACAATTCGA-TTAATTCGATCAT-GAAACATGCAA
* * * * * *
4973 TAATCCATAATTTCAATTCAATTTGGTCATGGAAACATGCAT
1 TAATTCACAA-TTCGATT-AATTCGATCAT-GAAACATGCAA
*
5015 TTATTCACAA
1 TAATTCACAA
5025 CCTAATTCAA
Statistics
Matches: 136, Mismatches: 31, Indels: 11
0.76 0.17 0.06
Matches are distributed among these distances:
39 25 0.18
40 17 0.12
41 59 0.43
42 35 0.26
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (39 bp):
TAATTCACAATTCGATTAATTCGATCATGAAACATGCAA
Found at i:5051 original size:41 final size:41
Alignment explanation
Indices: 4986--5077 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
4976 TCCATAATTT
* * * * *
4986 CAATTCAATTTGGTCATGGAAACATGCATTTATTCACAA-C
1 CAATTCAATTAGATAATGGAAACATACATTAATTCACAATC
* *
5026 CTAATTCAATTAGATAATGGTAACATATATTAATTCACAATC
1 C-AATTCAATTAGATAATGGAAACATACATTAATTCACAATC
5068 CAATTCAATT
1 CAATTCAATT
5078 TAAATCAATG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.02
41 40 0.93
42 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (41 bp):
CAATTCAATTAGATAATGGAAACATACATTAATTCACAATC
Found at i:7079 original size:31 final size:31
Alignment explanation
Indices: 7035--7098 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
7025 ATGCAACACA
7035 CAATCTACATAGCATTTCGAATTCAATAATT
1 CAATCTACATAGCATTTCGAATTCAATAATT
** * * *
7066 CAATCTATGTAGCATTTTGATTTGAATAATT
1 CAATCTACATAGCATTTCGAATTCAATAATT
7097 CA
1 CA
7099 TGCATATACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (31 bp):
CAATCTACATAGCATTTCGAATTCAATAATT
Found at i:7602 original size:41 final size:40
Alignment explanation
Indices: 7554--7918 Score: 220
Period size: 41 Copynumber: 8.9 Consensus size: 40
7544 CAGCATTCAC
*
7554 TAATTCACAATTCGATTCATCTCAATCATGGAAACATGCAA
1 TAATTCACAATTCAATTCAT-TCAATCATGGAAACATGCAA
* * * * * * ***
7595 TAGTTCACCATTCAACTCAACTCGATCATGTCATGTATGCAA
1 TAATTCACAATTCAATTC-ATTCAATCATG-GAAACATGCAA
*
7637 TAATTCACAATTCAATTGAATTCAATCATGGTAAA-ATGCAA
1 TAATTCACAATTCAATT-CATTCAATCATGG-AAACATGCAA
*** *
7678 TAATTCACAATTCAACAAATTCGATCAT-GACAACATGCAA
1 TAATTCACAATTCAATTCATTCAATCATGGA-AACATGCAA
* * * *
7718 TAATTCACAATTCGATTCGATTCTATCATGGCATCATGCAA
1 TAATTCACAATTCAATTC-ATTCAATCATGGAAACATGCAA
* * * * * *
7759 TAATTCATAATTCATTTCAATTCAATCATGGCAGCAAGAAA
1 TAATTCACAATTCAATTC-ATTCAATCATGGAAACATGCAA
* * *
7800 TAATTCATAATTCAACTT-ATGTCGATCAT-GACAGCATGCAA
1 TAATTCACAATTCAA-TTCAT-TCAATCATGGA-AACATGCAA
* ** * *
7841 TAATCCATC-ATTCAATTCAATTTGATCATGGCAACATGCAT
1 TAATTCA-CAATTCAATTC-ATTCAATCATGGAAACATGCAA
* ** *
7882 TTATTCACAAACCAATTCAATT-AGATCATGGTAACAT
1 TAATTCACAATTCAATTC-ATTCA-ATCATGGAAACAT
7919 TTGTTAATTC
Statistics
Matches: 253, Mismatches: 54, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
38 1 0.00
39 3 0.01
40 36 0.14
41 175 0.69
42 38 0.15
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (40 bp):
TAATTCACAATTCAATTCATTCAATCATGGAAACATGCAA
Found at i:7705 original size:40 final size:40
Alignment explanation
Indices: 7578--7730 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 40
7568 ATTCATCTCA
* * * *
7578 ATCATGG-AAACATGCAATAGTTCACCATTCAACTCAACTCG
1 ATCATGGTAAA-ATGCAATAATTCACAATTCAAC-AAATTCG
** ** *
7619 ATCAT-GTCATGTATGCAATAATTCACAATTCAATTGAATTCA
1 ATCATGGT-A-AAATGCAATAATTCACAATTCAA-CAAATTCG
7661 ATCATGGTAAAATGCAATAATTCACAATTCAACAAATTCG
1 ATCATGGTAAAATGCAATAATTCACAATTCAACAAATTCG
** *
7701 ATCATGACAACATGCAATAATTCACAATTC
1 ATCATGGTAAAATGCAATAATTCACAATTC
7731 GATTCGATTC
Statistics
Matches: 91, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
40 33 0.36
41 26 0.29
42 30 0.33
43 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.29
Consensus pattern (40 bp):
ATCATGGTAAAATGCAATAATTCACAATTCAACAAATTCG
Found at i:7746 original size:123 final size:123
Alignment explanation
Indices: 7578--7912 Score: 338
Period size: 123 Copynumber: 2.7 Consensus size: 123
7568 ATTCATCTCA
* * * *
7578 ATCATGGA-AACATGCAATAGTTCACCATTCAACTCAACTCGATCATGTCATGTATGCAATAATT
1 ATCAT-GACAACATGCAATAATTCACAATTCAACTCAACTCGATCATGGCAT-CATGCAATAATT
* * *
7642 CACAATTCAATTGAATTCAATCATGGTA-AAATGCAATAATTCACAATTCAACAAAT-TCG
64 CACAATTCAATTCAATTCAATCATGGCAGAAA-GAAATAATTCACAATTCAACAAATGTCG
* * * * *
7701 ATCATGACAACATGCAATAATTCACAATTCGATTCGATTCTATCATGGCATCATGCAATAATTCA
1 ATCATGACAACATGCAATAATTCACAATTCAACTCAACTCGATCATGGCATCATGCAATAATTCA
* * * * **
7766 TAATTCATTTCAATTCAATCATGGCAGCAAGAAATAATTCATAATTCAACTTATGTCG
66 CAATTCAATTCAATTCAATCATGGCAGAAAGAAATAATTCACAATTCAACAAATGTCG
* * * * * * * *
7824 ATCATGACAGCATGCAATAATCCATC-ATTCAATTCAATTTGATCATGGCAACATGCATTTATTC
1 ATCATGACAACATGCAATAATTCA-CAATTCAACTCAACTCGATCATGGCATCATGCAATAATTC
**
7888 ACAAACCAATTCAATT-AGATCATGG
65 ACAATTCAATTCAATTCA-ATCATGG
7913 TAACATTTGT
Statistics
Matches: 176, Mismatches: 31, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
122 58 0.33
123 117 0.66
124 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (123 bp):
ATCATGACAACATGCAATAATTCACAATTCAACTCAACTCGATCATGGCATCATGCAATAATTCA
CAATTCAATTCAATTCAATCATGGCAGAAAGAAATAATTCACAATTCAACAAATGTCG
Found at i:7757 original size:81 final size:83
Alignment explanation
Indices: 7554--7772 Score: 268
Period size: 81 Copynumber: 2.7 Consensus size: 83
7544 CAGCATTCAC
* * *
7554 TAATTCACAATTCGATTC-ATCTCAATCATGGAAACATGCAATAGTTCACCATTCAACTCAACTC
1 TAATTCACAATTCGATTCGAT-TCAATCATGGAAACATGCAATAATTCACAATTCAACTAAACTC
* **
7618 GATCATGTCATGTATGCAA
65 GATCATGACATACATGCAA
* *
7637 TAATTCACAATTCAATT-GAATTCAATCATGGTAAA-ATGCAATAATTCACAATTCAAC-AAATT
1 TAATTCACAATTCGATTCG-ATTCAATCATGG-AAACATGCAATAATTCACAATTCAACTAAACT
7699 CGATCATGACA-ACATGCAA
64 CGATCATGACATACATGCAA
* * * *
7718 TAATTCACAATTCGATTCGATTCTATCATGGCATCATGCAATAATTCATAATTCA
1 TAATTCACAATTCGATTCGATTCAATCATGGAAACATGCAATAATTCACAATTCA
7773 TTTCAATTCA
Statistics
Matches: 118, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
80 1 0.01
81 52 0.44
82 14 0.12
83 46 0.39
84 5 0.04
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (83 bp):
TAATTCACAATTCGATTCGATTCAATCATGGAAACATGCAATAATTCACAATTCAACTAAACTCG
ATCATGACATACATGCAA
Found at i:9534 original size:36 final size:37
Alignment explanation
Indices: 9494--9563 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
9484 TGGGTCATTT
*
9494 TCCAATAAAATTAATTTAAATTTAAA-TTCAATTTGA
1 TCCAATAAAATTAAATTAAATTTAAATTTCAATTTGA
* *
9530 TCCAATATAATTAAATTAATTTTAAATTTCAATT
1 TCCAATAAAATTAAATTAAATTTAAATTTCAATT
9564 CAATTATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 23 0.77
37 7 0.23
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (37 bp):
TCCAATAAAATTAAATTAAATTTAAATTTCAATTTGA
Found at i:14901 original size:22 final size:23
Alignment explanation
Indices: 14868--14938 Score: 56
Period size: 24 Copynumber: 3.1 Consensus size: 23
14858 AAGGGTAAAC
*
14868 AAAAAT-AGAGAATAAAT-CTAT
1 AAAAATAAAAGAATAAATACTAT
* *
14889 AAAAATAAAAGAAAAAATACAAT
1 AAAAATAAAAGAATAAATACTAT
* * *
14912 AATAAAGAAAAAAATATAATGCTAT
1 AA-AAATAAAAGAATA-AATACTAT
14937 AA
1 AA
14939 TAAAACTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 6 0.16
22 9 0.24
23 5 0.13
24 10 0.26
25 8 0.21
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (23 bp):
AAAAATAAAAGAATAAATACTAT
Found at i:24550 original size:2 final size:2
Alignment explanation
Indices: 24543--24581 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
24533 TATGCACTGT
24543 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24582 GGCATTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25176 original size:13 final size:13
Alignment explanation
Indices: 25155--25192 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
25145 TATGTCCAAC
*
25155 ATACTTTTTTCTT
1 ATACATTTTTCTT
25168 ATACATTTTTCTT
1 ATACATTTTTCTT
*
25181 TTA-ATTTTTCTT
1 ATACATTTTTCTT
25193 TAGTAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (13 bp):
ATACATTTTTCTT
Found at i:25187 original size:12 final size:13
Alignment explanation
Indices: 25160--25193 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
25150 CCAACATACT
*
25160 TTTTTCTTATACA
1 TTTTTCTTTTACA
25173 TTTTTCTTTTA-A
1 TTTTTCTTTTACA
25185 TTTTTCTTT
1 TTTTTCTTT
25194 AGTAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTCTTTTACA
Found at i:34204 original size:28 final size:31
Alignment explanation
Indices: 34123--34215 Score: 77
Period size: 32 Copynumber: 3.1 Consensus size: 31
34113 ACATTGTTTG
* *
34123 AACAATGT-AGTTTGGTTCTAATAGTGCAGAA
1 AACAAT-TAAGTTTGGTTCGAACAGTGCAGAA
* *
34154 AATCAATTAAGTTTAGTTGGAACAGTGCA-AA
1 AA-CAATTAAGTTTGGTTCGAACAGTGCAGAA
* * *
34185 AA-AA-TCAGTTTGGTTCGAACTGTACAGAA
1 AACAATTAAGTTTGGTTCGAACAGTGCAGAA
34214 AA
1 AA
34216 AAATATATAC
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
28 17 0.34
29 6 0.12
31 7 0.14
32 20 0.40
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (31 bp):
AACAATTAAGTTTGGTTCGAACAGTGCAGAA
Found at i:34646 original size:144 final size:144
Alignment explanation
Indices: 34481--34770 Score: 544
Period size: 144 Copynumber: 2.0 Consensus size: 144
34471 GAAATTGGAT
34481 TTAATTACAAGCTTATAGTAATGCTTTAACTTGTTTTGGCTTGAGCGTTTCTTTGTCCTTAAACA
1 TTAATTACAAGCTTATAGTAATGCTTTAACTTGTTTTGGCTTGAGCGTTTCTTTGTCCTTAAACA
34546 CTTTGAGTAGAATGAGAGAATCTTTTGTGAGGGTATTGAGTTTTGCATCATGGAATTTTTGAGTC
66 CTTTGAGTAGAATGAGAGAATCTTTTGTGAGGGTATTGAGTTTTGCATCATGGAATTTTTGAGTC
34611 ATTGGAATATCTTG
131 ATTGGAATATCTTG
*
34625 TTAATTACAAGCTTATGGTAATGCTTTAACTTGTTTTGGCTTGAGCGTTTCTTTGTCCTTAAACA
1 TTAATTACAAGCTTATAGTAATGCTTTAACTTGTTTTGGCTTGAGCGTTTCTTTGTCCTTAAACA
* * *
34690 CTTTGAGTAGAATGGGTGAATCTTTTGTGAGGGTATTGAGTTTTGCATCATGGGATTTTTGAGTC
66 CTTTGAGTAGAATGAGAGAATCTTTTGTGAGGGTATTGAGTTTTGCATCATGGAATTTTTGAGTC
34755 ATTGGAATATCTTG
131 ATTGGAATATCTTG
34769 TT
1 TT
34771 TTACTTTAAC
Statistics
Matches: 142, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 142 1.00
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.43
Consensus pattern (144 bp):
TTAATTACAAGCTTATAGTAATGCTTTAACTTGTTTTGGCTTGAGCGTTTCTTTGTCCTTAAACA
CTTTGAGTAGAATGAGAGAATCTTTTGTGAGGGTATTGAGTTTTGCATCATGGAATTTTTGAGTC
ATTGGAATATCTTG
Found at i:35377 original size:77 final size:75
Alignment explanation
Indices: 35250--35397 Score: 197
Period size: 77 Copynumber: 1.9 Consensus size: 75
35240 TTAAATTCAA
* ** * * *
35250 GATTTATCTTTTTTTATGATATAATTTCAAGAATGATCTTTTATGGTTTTTAATGTGATTTTAGG
1 GATTTATCTTTTTTTAGGATATAATTAAAAGAATGATCTTTTACGATTTTTAATGTAATTTTAGG
35315 CTTTTTAGTG
66 CTTTTTAGTG
* *
35325 GATTTATCTTTATTTTTAGGATGTAATTAAAAGAATTATCTTTTACGATTTTTAATGTAATTTTA
1 GATTTATC-TT-TTTTTAGGATATAATTAAAAGAATGATCTTTTACGATTTTTAATGTAATTTTA
*
35390 GGTTTTTT
64 GGCTTTTT
35398 CATAAACTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 8 0.13
76 2 0.03
77 52 0.84
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.55
Consensus pattern (75 bp):
GATTTATCTTTTTTTAGGATATAATTAAAAGAATGATCTTTTACGATTTTTAATGTAATTTTAGG
CTTTTTAGTG
Found at i:41939 original size:178 final size:178
Alignment explanation
Indices: 41640--41997 Score: 716
Period size: 178 Copynumber: 2.0 Consensus size: 178
41630 TAGATGAATT
41640 TGACAAAAGATACAATATCTTATTTTTAAATTAAGTGTTTGCAAAATTGATTGACATTGCATCTA
1 TGACAAAAGATACAATATCTTATTTTTAAATTAAGTGTTTGCAAAATTGATTGACATTGCATCTA
41705 CTTTGATTATGCTTGCTGGTCATAGAATAGGAAACATATACATGGTGCATTTAGACTCTATAGAA
66 CTTTGATTATGCTTGCTGGTCATAGAATAGGAAACATATACATGGTGCATTTAGACTCTATAGAA
41770 ATGACTAATTTATGCCTAGTTGGTAAGGATGAGCATGATAGTTGGTTA
131 ATGACTAATTTATGCCTAGTTGGTAAGGATGAGCATGATAGTTGGTTA
41818 TGACAAAAGATACAATATCTTATTTTTAAATTAAGTGTTTGCAAAATTGATTGACATTGCATCTA
1 TGACAAAAGATACAATATCTTATTTTTAAATTAAGTGTTTGCAAAATTGATTGACATTGCATCTA
41883 CTTTGATTATGCTTGCTGGTCATAGAATAGGAAACATATACATGGTGCATTTAGACTCTATAGAA
66 CTTTGATTATGCTTGCTGGTCATAGAATAGGAAACATATACATGGTGCATTTAGACTCTATAGAA
41948 ATGACTAATTTATGCCTAGTTGGTAAGGATGAGCATGATAGTTGGTTA
131 ATGACTAATTTATGCCTAGTTGGTAAGGATGAGCATGATAGTTGGTTA
41996 TG
1 TG
41998 GCATAGGAGA
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
178 180 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (178 bp):
TGACAAAAGATACAATATCTTATTTTTAAATTAAGTGTTTGCAAAATTGATTGACATTGCATCTA
CTTTGATTATGCTTGCTGGTCATAGAATAGGAAACATATACATGGTGCATTTAGACTCTATAGAA
ATGACTAATTTATGCCTAGTTGGTAAGGATGAGCATGATAGTTGGTTA
Found at i:47765 original size:47 final size:47
Alignment explanation
Indices: 47666--47765 Score: 130
Period size: 47 Copynumber: 2.1 Consensus size: 47
47656 TTTATGCATT
* ** * *
47666 GATGCACTCTCCATGCATCGATGCACTCAAGTTTTTTTGAAAACATC
1 GATGCACTCACCATGCATCGATGCACTCAAGGCTTATTCAAAACATC
*
47713 GATGCACTCACCATGCATCGATGCACT-TAGGCTTATTCAAAACATC
1 GATGCACTCACCATGCATCGATGCACTCAAGGCTTATTCAAAACATC
47759 GAATGCA
1 G-ATGCA
47766 TTTTATGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 15 0.33
47 31 0.67
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (47 bp):
GATGCACTCACCATGCATCGATGCACTCAAGGCTTATTCAAAACATC
Found at i:57559 original size:4 final size:4
Alignment explanation
Indices: 57531--58811 Score: 1422
Period size: 4 Copynumber: 326.5 Consensus size: 4
57521 TTAGTGCATG
* * * * * *
57531 TACA TGCA TACA TCCA TATA TACA TACA TACA TGCA TGCA TGCA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * **
57579 TATA TGCA TACA TACA TGTA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
57627 TACA TACCA TACA TACA TACA TAC- TACA T--A TACA TACA TACA T--A
1 TACA TA-CA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
57671 TACA TACA TACA T--A TACA TACA TAATA TACA TACA TACA -ACA TACA
1 TACA TACA TACA TACA TACA TACA T-ACA TACA TACA TACA TACA TACA
*
57717 TACA TACA TACA TACA TACA TACA TACA -ACA TACA TACA TACA TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
57764 CATA TACA TACA TAC- TACA TACA TACA TACA TACA TACA TACA TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
57811 TACA TATA TACA AACA TACA TACA TACA TACA TACA TACA TACA TGCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
57859 T--A TACA TACA TACA TCCA TCCA TACA TACA TACA TCCA TCCA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
57905 TACA TACA TACA TCCA TCCA TCCA TACA TACA TACA TCCA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* *
57953 TATCCA TCCA TACA TCACA T--A TACA TACA TATA TACA TACA TACA TACA
1 TA--CA TACA TACA T-ACA TACA TACA TACA TACA TACA TACA TACA TACA
*
58002 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TGCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * *
58050 TGCA TGCA TGCA TGCA AACA TGCA TACA TACA T--A TACA TACA T--A
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
58094 TACA TACA TGCA TACA TACA TGCA TACA TACA TGCA TACA TACA TGCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
58142 TGCA TACA TATGCA TAC- -ACA TACA TACA TACA TACA TACA TAC- TACA
1 TACA TACA TA--CA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
58189 TACA TACA TACA TACA T--A TACA TATA TACA TACA T--A TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
58233 TACA -ACA TACA TACA TACA TACA TACA TACA TACA -ACA TATA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
** * *
58279 TACA TACA TACA TACA TACA TACA CGCA TACA CATA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
58327 TAC- TACA TACA T--A TACA TACA T--A TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
58370 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* ** * * * * *
58418 TAACA -ACA TAAA TTTA TACA TACA TACA TTCA TGCA TCCA TGCA TCCA
1 T-ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * * * * *
58466 TGCA TGCA TCCA TGCA TCCA TACA TAAA TACA TGCA TACA TGCA TGCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
** * * * * * *
58514 TGTA TACA TACA TCCA TGCA TGCA TGCA TACA TACA TCCA TACA TCCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * *
58562 TACA TCCA TACA TGCA TACA TACA TACA TGCA TACA TGCA TACA TGCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* *
58610 TACA TGCA TACA TACA TGCA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
58658 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
58706 TACA TACA TACA TACA TACA TATA TACA TACT TACA TGCA TGCA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * * * * * * *
58754 TGCA TGCA TGCA TCCA TGCA TCCA TGCA TCCA TGCA TCCA TGCA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
58802 TACA TACA TA
1 TACA TACA TA
58812 GGGTGAACCA
Statistics
Matches: 1109, Mismatches: 127, Indels: 82
0.84 0.10 0.06
Matches are distributed among these distances:
2 24 0.02
3 27 0.02
4 1037 0.94
5 14 0.01
6 7 0.01
ACGTcount: A:0.45, C:0.25, G:0.04, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:59350 original size:13 final size:13
Alignment explanation
Indices: 59332--59357 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59322 TTAGCCAAAG
59332 AGTTATCCAAGTT
1 AGTTATCCAAGTT
59345 AGTTATCCAAGTT
1 AGTTATCCAAGTT
59358 TAATGTGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
AGTTATCCAAGTT
Found at i:60744 original size:43 final size:43
Alignment explanation
Indices: 60678--60760 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
60668 TAGCCTTTTC
*
60678 TTCTTGTGCATTAATATGCTTATCAATTCTTCCTTAACACTTA
1 TTCTGGTGCATTAATATGCTTATCAATTCTTCCTTAACACTTA
* * * *
60721 TTCTGGTGCATTAGTCTGCTTATCACTTCTTCCTTGACAC
1 TTCTGGTGCATTAATATGCTTATCAATTCTTCCTTAACAC
60761 CAGCTTGAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (43 bp):
TTCTGGTGCATTAATATGCTTATCAATTCTTCCTTAACACTTA
Found at i:61494 original size:16 final size:15
Alignment explanation
Indices: 61473--61542 Score: 77
Period size: 15 Copynumber: 4.5 Consensus size: 15
61463 GTAAAGTAAA
61473 TTTGGGTTGCTTTCGG
1 TTTGGGTTG-TTTCGG
*
61489 TTTGGGTTGTTTCAG
1 TTTGGGTTGTTTCGG
*
61504 TTCGGGTTGTTTTCGG
1 TTTGGGTTG-TTTCGG
* **
61520 TTTGGGTTGATTCAA
1 TTTGGGTTGTTTCGG
61535 TTTGGGTT
1 TTTGGGTT
61543 ACTTTTGGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
15 24 0.52
16 22 0.48
ACGTcount: A:0.06, C:0.09, G:0.34, T:0.51
Consensus pattern (15 bp):
TTTGGGTTGTTTCGG
Found at i:61518 original size:31 final size:31
Alignment explanation
Indices: 61471--61552 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
61461 TGGTAAAGTA
* *
61471 AATTTGGGTTGCTTTCGGTTTGGGTTGTTTC
1 AATTCGGGTTGCTTTCGGTTTGGGTTGATTC
* *
61502 AGTTCGGGTTGTTTTCGGTTTGGGTTGATTC
1 AATTCGGGTTGCTTTCGGTTTGGGTTGATTC
* * *
61533 AATTTGGGTTACTTTTGGTT
1 AATTCGGGTTGCTTTCGGTT
61553 CAACTAAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.09, C:0.09, G:0.32, T:0.51
Consensus pattern (31 bp):
AATTCGGGTTGCTTTCGGTTTGGGTTGATTC
Found at i:65530 original size:25 final size:25
Alignment explanation
Indices: 65502--65551 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
65492 CCTGATATCT
65502 TCCTCGAGGAGTTACCTGGACTGCC
1 TCCTCGAGGAGTTACCTGGACTGCC
65527 TCCTCGAGGAGTTACCTGGACTGCC
1 TCCTCGAGGAGTTACCTGGACTGCC
65552 ATCGGGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (25 bp):
TCCTCGAGGAGTTACCTGGACTGCC
Found at i:68490 original size:26 final size:26
Alignment explanation
Indices: 68461--68513 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
68451 AGTAATACCA
68461 TCCTAAGATAATAGGCTTAAGTTTCC
1 TCCTAAGATAATAGGCTTAAGTTTCC
* *
68487 TCCTGAGATAATAGGCTTATGTTTCC
1 TCCTAAGATAATAGGCTTAAGTTTCC
68513 T
1 T
68514 ATGTGACTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (26 bp):
TCCTAAGATAATAGGCTTAAGTTTCC
Found at i:69038 original size:62 final size:59
Alignment explanation
Indices: 68962--69085 Score: 160
Period size: 62 Copynumber: 2.1 Consensus size: 59
68952 CTGAAAGTTA
* * * *
68962 ATTAGTTTTGTCATAGGATTTTTATTTTACTTATTCAATTTTTATATATAGTTTTA-ATTGTT
1 ATTAGTTTTGTCATAGCATTATAATTTTACTTATT---TTTATATATATAGTTTTACA-TGTT
*
69024 ATTAGTTTTGTCATAGCATTATAATTTTACTTCTTTTTATATATATAGTTTTACATGTT
1 ATTAGTTTTGTCATAGCATTATAATTTTACTTATTTTTATATATATAGTTTTACATGTT
69083 ATT
1 ATT
69086 TTCCTTGTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
59 24 0.43
60 1 0.02
62 31 0.55
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (59 bp):
ATTAGTTTTGTCATAGCATTATAATTTTACTTATTTTTATATATATAGTTTTACATGTT
Found at i:72374 original size:23 final size:22
Alignment explanation
Indices: 72321--72362 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
72311 TAGATAAAAT
72321 AATGTTTAAAAATCCATCAAAC
1 AATGTTTAAAAATCCATCAAAC
72343 AATGTTTAAAAATCCATCAA
1 AATGTTTAAAAATCCATCAA
72363 GCAGTAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.29
Consensus pattern (22 bp):
AATGTTTAAAAATCCATCAAAC
Found at i:81966 original size:20 final size:20
Alignment explanation
Indices: 81937--81977 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
81927 AGAGCTCATA
*
81937 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
81957 TAGGAGCATATAGTTGCATT
1 TAGGAGCATATAGATGCATT
81977 T
1 T
81978 GGTTGAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:87097 original size:3 final size:3
Alignment explanation
Indices: 87089--87244 Score: 61
Period size: 3 Copynumber: 50.7 Consensus size: 3
87079 TATATATACT
* * * *
87089 TAA TAA TAA TACA CAA TAA TAA TAAA TAA GAA -AA TATA TAA GAA -GA
1 TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TAA TA-A TAA TAA TAA
* * ** * * *
87135 TAA -AA TAA GTGA TAA TAA TAA TAA -AT TCT TAG TAA TAC TAA GAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
87179 TAA TAA TAA TTAA TAG TAA TAA T-A TAA TAA TATA TAT TACA TAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA
*
87226 TAA GCAA TATA TAA TAA TA
1 TAA -TAA TA-A TAA TAA TA
87245 GTACTTAACA
Statistics
Matches: 114, Mismatches: 25, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
2 8 0.07
3 83 0.73
4 23 0.20
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:87193 original size:22 final size:21
Alignment explanation
Indices: 87167--87209 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
87157 AAATTCTTAG
87167 TAATACTAAGAATAATAATAAT
1 TAATACTAAGAAT-ATAATAAT
* *
87189 TAATAGTAATAATATAATAAT
1 TAATACTAAGAATATAATAAT
87210 ATATATTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (21 bp):
TAATACTAAGAATATAATAAT
Found at i:87198 original size:13 final size:13
Alignment explanation
Indices: 87177--87243 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 13
87167 TAATACTAAG
87177 AATAATAATAATT
1 AATAATAATAATT
*
87190 AATAGTAATAATAT
1 AATAATAATAAT-T
87204 AATAAT-ATATATT
1 AATAATAATA-ATT
* **
87217 ACATAGTAATAAGC
1 A-ATAATAATAATT
87231 AATATATAATAAT
1 AATA-ATAATAAT
87244 AGTACTTAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 19 0.45
14 20 0.48
15 3 0.07
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (13 bp):
AATAATAATAATT
Found at i:87198 original size:28 final size:27
Alignment explanation
Indices: 87148--87228 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
87138 AATAAGTGAT
** *
87148 AATAATAATAAATTCTTAGTAATACTAAG
1 AATAATAAT-AATTAATAGTAATAAT-AG
*
87177 AATAATAATAATTAATAGTAATAATAT
1 AATAATAATAATTAATAGTAATAATAG
87204 AATAAT-ATATATTACATAGTAATAA
1 AATAATAATA-ATTA-ATAGTAATAA
87229 GCAATATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 3 0.07
27 11 0.24
28 23 0.50
29 9 0.20
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.36
Consensus pattern (27 bp):
AATAATAATAATTAATAGTAATAATAG
Done.