Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000725.1 Hibiscus syriacus cultivar Beakdansim tig00001406_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: 59351
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:674 original size:17 final size:20
Alignment explanation
Indices: 652--690 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
642 ATGAAGTTGT
652 GGATGA-TT-GAG-CGTTTG
1 GGATGATTTGGAGCCGTTTG
669 GGATGATTTGGAGCCGTTTG
1 GGATGATTTGGAGCCGTTTG
689 GG
1 GG
691 GATAAAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 3 0.16
20 8 0.42
ACGTcount: A:0.15, C:0.08, G:0.44, T:0.33
Consensus pattern (20 bp):
GGATGATTTGGAGCCGTTTG
Found at i:836 original size:20 final size:21
Alignment explanation
Indices: 806--845 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
796 AGTCGTTGGA
*
806 GCCTGATGGTATTGATACTAT
1 GCCTGATGGTATCGATACTAT
827 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
846 CTATGTGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:1367 original size:2 final size:2
Alignment explanation
Indices: 1360--1404 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1350 TCTTTTTAGA
1360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
1401 AT AT
1 AT AT
1405 TTCCTTATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5233 original size:88 final size:89
Alignment explanation
Indices: 5060--5234 Score: 232
Period size: 88 Copynumber: 2.0 Consensus size: 89
5050 ACCTTACGGG
* * *
5060 TCTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTTCCTTTGTT
1 TCTAAGGATACCCTTGGATAGGCCCATAGGCCCCAAGGAATATCCTTAGGTTGGTCTCCTTTGTT
*
5125 GTATGCTTAGGTTAACCCTACGAA
66 GTATGCTTAGGGTAACCCTACGAA
* *
5149 TCTAAGGATACCCTTGGATAGGTCCATAGG-CCCAAGGAATATCCTTTGGTTGG-CT-CTATT-T
1 TCTAAGGATACCCTTGGATAGGCCCATAGGCCCCAAGGAATATCCTTAGGTTGGTCTCCT-TTGT
*
5210 TGCTATGTTTAGGGTAAGCCCTACG
65 TG-TATGCTTAGGGTAA-CCCTACG
5235 GACGCAGTCT
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
86 5 0.07
87 15 0.20
88 28 0.37
89 28 0.37
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (89 bp):
TCTAAGGATACCCTTGGATAGGCCCATAGGCCCCAAGGAATATCCTTAGGTTGGTCTCCTTTGTT
GTATGCTTAGGGTAACCCTACGAA
Found at i:8865 original size:58 final size:58
Alignment explanation
Indices: 8771--8885 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
8761 AAGAAAATAG
8771 AGTTTGGTTGCTTAGAAAATGGAAAATGCCAATAGCATGATGTTACATCAAACTCTCT
1 AGTTTGGTTGCTTAGAAAATGGAAAATGCCAATAGCATGATGTTACATCAAACTCTCT
* * * *
8829 AGTTTTGTTTCTTAGAAAATGG-AAATGGTCAGTAGCATGATGTTACATCAAACTCTC
1 AGTTTGGTTGCTTAGAAAATGGAAAAT-GCCAATAGCATGATGTTACATCAAACTCTC
8886 AACGTGCTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 4 0.08
58 48 0.92
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (58 bp):
AGTTTGGTTGCTTAGAAAATGGAAAATGCCAATAGCATGATGTTACATCAAACTCTCT
Found at i:11685 original size:21 final size:21
Alignment explanation
Indices: 11659--11703 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
11649 CCGTAAATGT
*
11659 TAAAAACATTAATGTTTTAGG
1 TAAAAACAATAATGTTTTAGG
*
11680 TAAAAATAATAATGTTTTAGG
1 TAAAAACAATAATGTTTTAGG
11701 TAA
1 TAA
11704 TTATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.38
Consensus pattern (21 bp):
TAAAAACAATAATGTTTTAGG
Found at i:16968 original size:15 final size:15
Alignment explanation
Indices: 16948--16979 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16938 AAAATCTTTC
*
16948 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
16963 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
16978 TT
1 TT
16980 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:18222 original size:36 final size:35
Alignment explanation
Indices: 18177--18245 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
18167 AACATCTACC
* *
18177 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTAAAAAACAGTTTTCAAAG
*
18212 AAACATTTACCAAACTTTAAAAAATAGTTTTCAA
1 AAAC-TTTACCAAACTTTAAAAAACAGTTTTCAA
18246 GGTTGGTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (35 bp):
AAACTTTACCAAACTTTAAAAAACAGTTTTCAAAG
Found at i:21374 original size:45 final size:45
Alignment explanation
Indices: 21315--21608 Score: 439
Period size: 45 Copynumber: 6.6 Consensus size: 45
21305 CATTTCTTAT
* *
21315 CAATCTACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
21360 CAATATATTTACCATTTGTTCCATAAGCTCATAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
21405 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
21450 CAATATATTTACCATTTGTTCCATAAGCTCATAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
21495 CAATATACTTACCA-TTATTCAATAAGATCGTAAGCTTATTTTAT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
21539 CAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
21584 CAATACACTTGCCA-TTATTCCATAA
1 CAATATACTTACCATTTATTCCATAA
21609 ACCATTTTCC
Statistics
Matches: 222, Mismatches: 26, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
44 49 0.22
45 173 0.78
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:21578 original size:89 final size:90
Alignment explanation
Indices: 21315--21608 Score: 484
Period size: 90 Copynumber: 3.3 Consensus size: 90
21305 CATTTCTTAT
*
21315 CAATCTACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATATTTACCATTTGTT
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATATTTACCATTTGTT
21380 CCATAAGCTCATAAGCTTATTTTAC
66 CCATAAGCTCATAAGCTTATTTTAC
21405 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATATTTACCATTTGTT
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATATTTACCATTTGTT
21470 CCATAAGCTCATAAGCTTATTTTAC
66 CCATAAGCTCATAAGCTTATTTTAC
* * * * *
21495 CAATATACTTACCA-TTATTCAATAAGATCGTAAGCTTATTTTATCAATATACTTACCATTTGTT
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATATTTACCATTTGTT
*
21559 CCATAAGCTCGTAAGCTTATTTTAC
66 CCATAAGCTCATAAGCTTATTTTAC
* * *
21584 CAATACACTTGCCA-TTATTCCATAA
1 CAATATACTTACCATTTATCCCATAA
21609 ACCATTTTCC
Statistics
Matches: 194, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
89 91 0.47
90 103 0.53
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (90 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATATTTACCATTTGTT
CCATAAGCTCATAAGCTTATTTTAC
Found at i:26169 original size:17 final size:18
Alignment explanation
Indices: 26142--26175 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
26132 GTTAAATTTT
26142 AAACGAAAAACTAAGATG
1 AAACGAAAAACTAAGATG
26160 AAAC-AAAAACTAAGAT
1 AAACGAAAAACTAAGAT
26176 ATAGGTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (18 bp):
AAACGAAAAACTAAGATG
Found at i:32608 original size:2 final size:2
Alignment explanation
Indices: 32601--32630 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
32591 AAAGAGAAGT
*
32601 AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
32631 GTAGTGGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33169 original size:20 final size:20
Alignment explanation
Indices: 33141--33292 Score: 135
Period size: 20 Copynumber: 7.5 Consensus size: 20
33131 GGGAAAATCA
*
33141 CAATACGATACTGACTATCG
1 CAATGCGATACTGACTATCG
33161 CAATGCGATACTGACTATCG
1 CAATGCGATACTGACTATCG
* *
33181 CAATGCGATACTTAATATCG
1 CAATGCGATACTGACTATCG
* *
33201 CAATGCGATACTTACAAAATCG
1 CAATGCGATACTGAC--TATCG
* * * *
33223 CAACGAGATACTAACTTTCG
1 CAATGCGATACTGACTATCG
* * *
33243 CAACGCGATTCTGACTTTCG
1 CAATGCGATACTGACTATCG
* *
33263 CAACGCGATAAT-ACATAATCG
1 CAATGCGATACTGAC-T-ATCG
33284 CAATGCGAT
1 CAATGCGAT
33293 TTTCAAAGCG
Statistics
Matches: 111, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
19 2 0.02
20 82 0.74
21 11 0.10
22 16 0.14
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (20 bp):
CAATGCGATACTGACTATCG
Found at i:33233 original size:62 final size:61
Alignment explanation
Indices: 33157--33286 Score: 143
Period size: 62 Copynumber: 2.1 Consensus size: 61
33147 GATACTGACT
* * * * * * *
33157 ATCGCAATGCGATACTGACTATCGCAATGCGATACTTAATATCGCAATGCGATACTTACAAA
1 ATCGCAACGAGATACTAACTATCGCAACGCGATACTGAATATCGCAACGCGATA-ATACAAA
* * * * *
33219 ATCGCAACGAGATACTAACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACATA
1 ATCGCAACGAGATACTAACTATCGCAACGCGATACTGAATATCGCAACGCGATAATACAAA
33280 ATCGCAA
1 ATCGCAA
33287 TGCGATTTTC
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
61 12 0.21
62 44 0.79
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (61 bp):
ATCGCAACGAGATACTAACTATCGCAACGCGATACTGAATATCGCAACGCGATAATACAAA
Found at i:33488 original size:22 final size:22
Alignment explanation
Indices: 33460--33501 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
33450 CACTCTCTCA
33460 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
33482 CCCATCTCCGGCGAAATCCG
1 CCCATCTCCGACGAAATCCG
33502 CCTATCTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.45, G:0.17, T:0.17
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:33820 original size:20 final size:20
Alignment explanation
Indices: 33766--33824 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
33756 GCGATTCTCT
**
33766 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
33786 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
33806 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
33825 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:34015 original size:25 final size:24
Alignment explanation
Indices: 33961--34015 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
33951 TGTTTATTAT
* *
33961 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
33985 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
34011 TGTTT
1 TGTTT
34016 ATTGCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:35159 original size:18 final size:18
Alignment explanation
Indices: 35138--35182 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
35128 TCCACTTCGG
*
35138 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
35156 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
35174 GAGCCATCA
1 GAGCCATCA
35183 TCTGATCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:35689 original size:20 final size:20
Alignment explanation
Indices: 35664--35705 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
35654 TAGTTTACTT
35664 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
35684 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
35704 TC
1 TC
35706 ACAATGCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:35718 original size:19 final size:19
Alignment explanation
Indices: 35675--35738 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
35665 CGCAACACGA
*
35675 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAATGC-G
* *
35695 AAATGGCTATCACAATGCG
1 AAATGACTATCGCAATGCG
**
35714 AAATGAAAATCGCAATGCG
1 AAATGACTATCGCAATGCG
35733 AAATGA
1 AAATGA
35739 AATCGCAACG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 22 0.59
20 15 0.41
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (19 bp):
AAATGACTATCGCAATGCG
Found at i:35739 original size:19 final size:19
Alignment explanation
Indices: 35707--35784 Score: 87
Period size: 19 Copynumber: 4.4 Consensus size: 19
35697 ATGGCTATCA
35707 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
35726 CAATGCGAAATG-AAATCG
1 CAATGCGAAATGAAAATCG
*
35744 CAA--CG--A-CAAAATCG
1 CAATGCGAAATGAAAATCG
* *
35758 CAACGCGAAATAAAAATCG
1 CAATGCGAAATGAAAATCG
35777 CAATGCGA
1 CAATGCGA
35785 TTTGTGTTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
14 10 0.20
16 4 0.08
18 10 0.20
19 26 0.52
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (19 bp):
CAATGCGAAATGAAAATCG
Found at i:35815 original size:14 final size:14
Alignment explanation
Indices: 35796--35886 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
35786 TTGTGTTTCG
35796 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
35810 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
35826 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
35842 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
*
35859 CGCATTGCAATTTTGT
1 CG--TTGCGATTTTGT
35875 CGTTGCGATTTT
1 CGTTGCGATTTT
35887 CATTTCGCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 26 0.42
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 5 0.08
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:35860 original size:33 final size:33
Alignment explanation
Indices: 35791--35902 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
35781 GCGATTTGTG
*
35791 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
35823 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
35856 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
35889 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
35903 AGCCATTTCC
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 26 0.34
33 50 0.66
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:35871 original size:19 final size:19
Alignment explanation
Indices: 35812--35945 Score: 83
Period size: 20 Copynumber: 7.5 Consensus size: 19
35802 GATTTTGTCG
35812 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
35830 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
35844 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
35863 TTGC-AATTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
35877 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*** * *
35896 TTGCGATAGCCATTTCCTCG
1 TTGCGATTTTCATTT-CGCA
**
35916 TTGCGATAGTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
35936 TTGCGATTTT
1 TTGCGATTTT
35946 AAGTTTCGTG
Statistics
Matches: 88, Mismatches: 16, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
14 10 0.11
15 7 0.08
16 8 0.09
17 8 0.09
18 13 0.15
19 16 0.18
20 23 0.26
21 3 0.03
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:36405 original size:41 final size:42
Alignment explanation
Indices: 36309--36396 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
36299 GACTCACCTG
* *
36309 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * *
36351 TCCTCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
36392 TCATC
1 TCATC
36397 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:37831 original size:14 final size:14
Alignment explanation
Indices: 37812--37847 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
37802 ATTGTTTAAT
37812 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
37826 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
37840 TGATTTGT
1 TGATTTGT
37848 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:37991 original size:14 final size:15
Alignment explanation
Indices: 37972--38049 Score: 52
Period size: 19 Copynumber: 4.7 Consensus size: 15
37962 GAAACTGACT
37972 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
37986 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
*
38005 ATCGCAATGCGAAATTAAA
1 ATCGCAA-GCG--A-GAAA
38024 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
38038 ATCGCAATGCGA
1 ATCGCAA-GCGA
38050 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 17 0.31
15 1 0.02
16 5 0.09
17 2 0.04
18 1 0.02
19 29 0.53
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:38006 original size:19 final size:19
Alignment explanation
Indices: 37982--38049 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
37972 ATCGCAACGA
37982 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
38001 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
38020 TAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
38034 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
38050 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
19 29 0.66
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:38099 original size:20 final size:20
Alignment explanation
Indices: 38076--38163 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
38066 CGATTTTCTA
*
38076 GTTGTGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
38096 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
38116 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
38136 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
38156 GTTGCGAT
1 GTTGCGAT
38164 TTCCCGTTGC
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
19 3 0.05
20 49 0.89
21 3 0.05
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:38101 original size:34 final size:36
Alignment explanation
Indices: 38056--38143 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 36
38046 GCGATTTTCA
* * *
38056 TTTCGCATTGCGATTTTC-T-AGTTGTGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
38090 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAT
38130 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
38144 AGCCATTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
34 12 0.27
35 5 0.11
38 1 0.02
39 1 0.02
40 26 0.58
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
Found at i:38396 original size:20 final size:20
Alignment explanation
Indices: 38371--38482 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
38361 TTTGAAGATG
38371 ATTGCGATTTTCAGAATCTC
1 ATTGCGATTTTCAGAATCTC
***
38391 ATTGCGAAAGTCAGAATCTC
1 ATTGCGATTTTCAGAATCTC
* * **
38411 GTTGCGATTTTGTATTATCTC
1 ATTGCGATTTT-CAGAATCTC
* ** * *
38432 GTTGCGATAGTCAGTATCGC
1 ATTGCGATTTTCAGAATCTC
*
38452 ATTGCGATTTTCCA-AATTCGC
1 ATTGCGATTTT-CAGAA-TCTC
38473 ATTGCGATTT
1 ATTGCGATTT
38483 ACTTATCGCA
Statistics
Matches: 70, Mismatches: 19, Indels: 5
0.74 0.20 0.05
Matches are distributed among these distances:
20 39 0.56
21 31 0.44
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTGCGATTTTCAGAATCTC
Found at i:38493 original size:19 final size:20
Alignment explanation
Indices: 38446--38498 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
38436 CGATAGTCAG
*
38446 TATCGCATTGCGATTTTCCA
1 TATCGCATTGCGATTTTACA
* *
38466 AATTCGCATTGCGA-TTTACT
1 TA-TCGCATTGCGATTTTACA
38486 TATCGCATTGCGA
1 TATCGCATTGCGA
38499 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 11 0.39
20 6 0.21
21 11 0.39
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (20 bp):
TATCGCATTGCGATTTTACA
Found at i:38707 original size:12 final size:12
Alignment explanation
Indices: 38688--38721 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
38678 CTCTCCGGCG
38688 ACATCCGTTCCT
1 ACATCCGTTCCT
*
38700 ATATCCGTTCCT
1 ACATCCGTTCCT
38712 ACATCC-TTCC
1 ACATCCGTTCC
38722 CCATCCGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:39289 original size:24 final size:24
Alignment explanation
Indices: 39262--39315 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
39252 GTATTCGAAA
*
39262 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATATTGGTCAATACTCGGAC
*
39286 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACTCGGAC
39310 TTTGAT
1 TTTGAT
39316 GATGTTGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCGGAC
Found at i:41811 original size:19 final size:19
Alignment explanation
Indices: 41789--41886 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
41779 GGAAATTACT
41789 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
41808 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
41822 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
41841 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
41855 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
41874 ATCGCAACGCGAA
1 ATCGCAATGCGAA
41887 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.50
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:41889 original size:33 final size:33
Alignment explanation
Indices: 41790--41889 Score: 157
Period size: 33 Copynumber: 3.0 Consensus size: 33
41780 GAAATTACTA
* *
41790 TCGCAATGCGAAATGAAAATCGCAACGAGAGA-A
1 TCGCAATGCGAAATGAAAATCGCAACGCGA-ATT
*
41823 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
41856 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
41889 T
1 T
41890 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
32 1 0.02
33 61 0.98
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:41914 original size:14 final size:14
Alignment explanation
Indices: 41897--41953 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
41887 TTTAATTTCG
41897 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
41911 CGTTGCAATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
41930 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
41944 CGTTGCGATT
1 CGTTGCGATT
41954 TCATTTCGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:41928 original size:33 final size:32
Alignment explanation
Indices: 41885--41962 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 32
41875 TCGCAACGCG
*
41885 AATTTAATTTCGCGTTGCGATTCTCTCGTTGC
1 AATTTCATTTCGCGTTGCGATTCTCTCGTTGC
41917 AATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
1 AA-TTTCATTTCGCGTTGCGATTCTCTCGTTGC
*
41950 GATTTCATTTCGC
1 AATTTCATTTCGC
41963 ATTTCGATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 13 0.30
33 30 0.70
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (32 bp):
AATTTCATTTCGCGTTGCGATTCTCTCGTTGC
Found at i:43507 original size:42 final size:41
Alignment explanation
Indices: 43448--43595 Score: 156
Period size: 42 Copynumber: 3.6 Consensus size: 41
43438 GTGAATCGAG
* *
43448 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * * *
43490 CTCTTGAACGGTGGGAGGGACTC-TCGAGGAAGATAGGGGC
1 CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
* * * * *
43530 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
43572 CTCTTG-ACGGTGGGAGGGGACTCT
1 CTCTTGAACGGTGGGA-GGGACTCT
43596 CGAGGAATTA
Statistics
Matches: 85, Mismatches: 18, Indels: 7
0.77 0.16 0.06
Matches are distributed among these distances:
40 26 0.31
41 23 0.27
42 36 0.42
ACGTcount: A:0.21, C:0.20, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:43592 original size:82 final size:80
Alignment explanation
Indices: 43478--43647 Score: 281
Period size: 82 Copynumber: 2.1 Consensus size: 80
43468 CCTCTTCAAC
43478 GATGACAGTGGCCTCTTGAACGGTGGGAGGGACTCTCGAGGAA-GATAGGGGCCTCTTCAACGAT
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
43542 AGGAGTGGACTCTTGAGG
66 AGGAGTGGA--C-TGAGG
*
43560 GATGACAGTGGCCTCTTG-ACGGTGGGAGGGGACTCTCGAGGAATTATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGA-GGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
43624 TAGGAGTGGACTGAGG
65 TAGGAGTGGACTGAGG
43640 GATGACAG
1 GATGACAG
43648 CGAGTCGGGC
Statistics
Matches: 85, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
80 13 0.15
81 10 0.12
82 33 0.39
83 29 0.34
ACGTcount: A:0.24, C:0.18, G:0.38, T:0.21
Consensus pattern (80 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
AGGAGTGGACTGAGG
Found at i:43614 original size:41 final size:41
Alignment explanation
Indices: 43487--43617 Score: 149
Period size: 41 Copynumber: 3.2 Consensus size: 41
43477 CGATGACAGT
43487 GGCCTCTTGAACGGTGGGA-GGGACTCTCGAGGAA-GATAGG
1 GGCCTCTTG-ACGGTGGGAGGGGACTCTCGAGGAATGATAGG
* * * * * * * *
43527 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGT
1 GGCCTCTT-GACGGTGGGAGGGGACTCTCGAGGAATGATAGG
*
43569 GGCCTCTTGACGGTGGGAGGGGACTCTCGAGGAATTATAGG
1 GGCCTCTTGACGGTGGGAGGGGACTCTCGAGGAATGATAGG
43610 GGCCTCTT
1 GGCCTCTT
43618 CAACGATAGG
Statistics
Matches: 71, Mismatches: 17, Indels: 5
0.76 0.18 0.05
Matches are distributed among these distances:
40 15 0.21
41 44 0.62
42 12 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.22
Consensus pattern (41 bp):
GGCCTCTTGACGGTGGGAGGGGACTCTCGAGGAATGATAGG
Found at i:44021 original size:84 final size:89
Alignment explanation
Indices: 43861--44034 Score: 250
Period size: 84 Copynumber: 2.0 Consensus size: 89
43851 ATTTCAAACT
*
43861 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTT--A-AATACACAGTTTAGC
43926 AAAATTGGCAGCAACCGAATAAATTAC
63 AAAATTGGCAGCAACCGAATAAATTAC
**
43953 TTCAA-CAAAAGA-AAAAAAAAGACAAATACTAACTTCACAGTG-T-AATA-ACAGTTTAGCAGT
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAATACACAGTTTAGCAAA
*
44013 ATTGGCAGCAACTGAATAAATT
66 ATTGGCAGCAACCGAATAAATT
44035 TACTAAGCAA
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
84 32 0.41
85 4 0.05
89 1 0.01
90 29 0.37
91 7 0.09
92 5 0.06
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (89 bp):
TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAATACACAGTTTAGCAAA
ATTGGCAGCAACCGAATAAATTAC
Found at i:45796 original size:33 final size:29
Alignment explanation
Indices: 45725--45808 Score: 114
Period size: 33 Copynumber: 2.7 Consensus size: 29
45715 ACGAGATAAT
*
45725 GAGAATCGCAATGCGGAAATGACTATCGCA
1 GAGAATCGCAACGC-GAAATGACTATCGCA
45755 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTAT--CG-C-A
45788 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
45809 AAATCGCAAC
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
29 11 0.22
30 13 0.27
31 2 0.04
32 1 0.02
33 22 0.45
ACGTcount: A:0.38, C:0.21, G:0.27, T:0.13
Consensus pattern (29 bp):
GAGAATCGCAACGCGAAATGACTATCGCA
Found at i:45813 original size:19 final size:19
Alignment explanation
Indices: 45791--45836 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
45781 GCGACGAGAG
45791 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
45810 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
45829 AATCGCAA
1 AATCGCAA
45837 TGCAATTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:46516 original size:20 final size:20
Alignment explanation
Indices: 46431--46544 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
46421 CGCTATGTAA
* * *
46431 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
46451 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
46471 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
46492 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
46512 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
46532 ATCGCATTACGAT
1 ATCGCATTGCGAT
46545 TTTCCCAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.04
20 64 0.79
21 12 0.15
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:46545 original size:61 final size:61
Alignment explanation
Indices: 46431--46547 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
46421 CGCTATGTAA
* * * * *
46431 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTTGTATT
* * *
46492 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTACGATTTT
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTT
46548 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTTGTATT
Found at i:46563 original size:61 final size:61
Alignment explanation
Indices: 46431--46565 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
46421 CGCTATGTAA
* * * * * ** *
46431 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTTCCAAT
* * *
46492 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTACGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTT-CCAAT
46554 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
46566 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTTCCAAT
Found at i:46676 original size:21 final size:21
Alignment explanation
Indices: 46615--46668 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
46605 ACTGTAGACC
46615 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
46636 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
46657 ATCGCAACGCGA
1 ATCGCAACGCGA
46669 AATGCAACGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTCCAACT
Found at i:47842 original size:7 final size:8
Alignment explanation
Indices: 47825--47849 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
47815 AAATAGGTTG
47825 AAAATGAA
1 AAAATGAA
47833 AAAATGAA
1 AAAATGAA
47841 AAAATGAA
1 AAAATGAA
47849 A
1 A
47850 TATGTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:51067 original size:2 final size:2
Alignment explanation
Indices: 51060--51087 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51050 TGCGTAAATC
51060 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
51088 GCGTAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52690 original size:88 final size:88
Alignment explanation
Indices: 52485--52691 Score: 261
Period size: 88 Copynumber: 2.4 Consensus size: 88
52475 ATGATATGAA
** *
52485 AATGTCGATCCCTCTCCTTCTGTGATGGAATCAAACAAGATGTCGGTGCTGATCTACCTCATTCT
1 AATGTCGATCCAACTCCTTCTGTGATGGATTCAAACAAGATGTCGGTGCTGATCTACCTCATTCT
**
52550 ATGATAGAATCGAGCTAAAAGTT
66 ATGATAGAATCGAGAAAAAAGTT
* * * * ** * * *
52573 AACGTTGATCCAACTCATTCTGCGATGGATTTGAGCAAGATGTCGGTGCTGATCTATCTCTTTCT
1 AATGTCGATCCAACTCCTTCTGTGATGGATTCAAACAAGATGTCGGTGCTGATCTACCTCATTCT
* *
52638 GTGATAGAATCGAGAAAAAATTT
66 ATGATAGAATCGAGAAAAAAGTT
*
52661 GATGTCGATCCAACTCCTTCTGTGATGGATT
1 AATGTCGATCCAACTCCTTCTGTGATGGATT
52692 AAAATGTCAA
Statistics
Matches: 98, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
88 98 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (88 bp):
AATGTCGATCCAACTCCTTCTGTGATGGATTCAAACAAGATGTCGGTGCTGATCTACCTCATTCT
ATGATAGAATCGAGAAAAAAGTT
Found at i:52705 original size:33 final size:33
Alignment explanation
Indices: 52657--53222 Score: 837
Period size: 33 Copynumber: 17.0 Consensus size: 33
52647 TCGAGAAAAA
* *
52657 ATTTG-ATGTCGATCCAACTCCTTCTGTGATGG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
** * *
52689 ATTAAAATGTCAATCCACCTCTTTTTGTGATGG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
*
52722 ATTTGAATGTCGATCCACCTCTTTCTGTGATAG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
* *
52755 ATTTGAACGTCGATCCACCTCTTTCTGTAATGG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
* *
52788 ATTTGAAATATCGATCCACTTCTTTCTGTGATGG
1 ATTTG-AATGTCGATCCACCTCTTTCTGTGATGG
52822 ATTTGAAATGTCGATCCACCTCTTTCTGTGATGG
1 ATTTG-AATGTCGATCCACCTCTTTCTGTGATGG
* *
52856 ATTTGAATGTTGATCCACCTCTTTCTGCGATGG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
* *
52889 ATTTGAACGTCGATTCACCTCTTTCTGTGATGG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
*
52922 ATTTGCAATGTCGATCCACCTCTTTCTATGATGG
1 ATTTG-AATGTCGATCCACCTCTTTCTGTGATGG
*
52956 ATTTGAAATGTCGATACACCTCTTTCTGTGATGG
1 ATTTG-AATGTCGATCCACCTCTTTCTGTGATGG
*
52990 ATTTGAATGTTGATCCACCTCTTTCTGTGATGG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
53023 ATTTGAAATGTCGATCCACCTCTTTCTGTGATGG
1 ATTTG-AATGTCGATCCACCTCTTTCTGTGATGG
* * *
53057 ATTTGAACGTCAATCCACCTCTTTCTGTTATGG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
* *
53090 ATTTGAACGTCGATCCACCTCTTTATGTGATGG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
*
53123 ATTTTAATGTCGATCCACCTCTTTCTGTGATGG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
* *
53156 ATGTGAATGTCGATTCACCTCTTTCTGTGATGG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
*
53189 ATTTAAATGTCGATCCACCTCTTTCTGTGATGG
1 ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
53222 A
1 A
53223 ATCAAGCAAA
Statistics
Matches: 480, Mismatches: 50, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
32 3 0.01
33 323 0.67
34 154 0.32
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (33 bp):
ATTTGAATGTCGATCCACCTCTTTCTGTGATGG
Found at i:52908 original size:134 final size:134
Alignment explanation
Indices: 52662--53222 Score: 851
Period size: 134 Copynumber: 4.2 Consensus size: 134
52652 AAAAAATTTG
* * * * *
52662 ATGTCGATCCAACTCCTTCTGTGATGGA-TTAAAATGTCAATCCACCTCTTTTTGTGATGGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
* *
52726 GAATGTCGATCCACCTCTTTCTGTGATAGATTTGAACGTCGATCCACCTCTTTCTGTAATGGATT
66 GAATGTCGATCCACCTCTTTCTGTGATGGATTTGAACGTCGATCCACCTCTTTCTGTGATGGATT
52791 TGAA
131 TGAA
* *
52795 ATATCGATCCACTTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
* * *
52860 GAATGTTGATCCACCTCTTTCTGCGATGGATTTGAACGTCGATTCACCTCTTTCTGTGATGGATT
66 GAATGTCGATCCACCTCTTTCTGTGATGGATTTGAACGTCGATCCACCTCTTTCTGTGATGGATT
*
52925 TGCA
131 TGAA
* *
52929 ATGTCGATCCACCTCTTTCTATGATGGATTTGAAATGTCGATACACCTCTTTCTGTGATGGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
* *
52994 GAATGTTGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGAT
66 GAATGTCGATCCACCTCTTTCTGTGATGGATTTG-AACGTCGATCCACCTCTTTCTGTGATGGAT
53059 TTG-A
130 TTGAA
* * * * *
53063 ACGTCAATCCACCTCTTTCTGTTATGGATTTG-AACGTCGATCCACCTCTTTATGTGATGGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
* * * *
53127 TAATGTCGATCCACCTCTTTCTGTGATGGATGTGAATGTCGATTCACCTCTTTCTGTGATGGATT
66 GAATGTCGATCCACCTCTTTCTGTGATGGATTTGAACGTCGATCCACCTCTTTCTGTGATGGATT
53192 T-AA
131 TGAA
53195 ATGTCGATCCACCTCTTTCTGTGATGGA
1 ATGTCGATCCACCTCTTTCTGTGATGGA
53223 ATCAAGCAAA
Statistics
Matches: 391, Mismatches: 34, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
132 57 0.15
133 84 0.21
134 219 0.56
135 31 0.08
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (134 bp):
ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
GAATGTCGATCCACCTCTTTCTGTGATGGATTTGAACGTCGATCCACCTCTTTCTGTGATGGATT
TGAA
Done.