Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004983.1 Hibiscus syriacus cultivar Beakdansim tig00011182_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: 58835
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:2685 original size:42 final size:42
Alignment explanation
Indices: 2621--2743 Score: 183
Period size: 42 Copynumber: 2.9 Consensus size: 42
2611 GATATCCGGA
* *
2621 TTAGGATTAGAGTGCATACCCAAGACACTTAGTGCAGGTGAT
1 TTAGCATTAGAGTGTATACCCAAGACACTTAGTGCAGGTGAT
* *
2663 TTAGCATTAGAGTGTATACCCAATACACTTAGTGCATGTGAT
1 TTAGCATTAGAGTGTATACCCAAGACACTTAGTGCAGGTGAT
* * *
2705 TTAGCACTAGAGTGTATGCCCATGACACTTAGTGCAGGT
1 TTAGCATTAGAGTGTATACCCAAGACACTTAGTGCAGGT
2744 TGTGGGCACG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (42 bp):
TTAGCATTAGAGTGTATACCCAAGACACTTAGTGCAGGTGAT
Found at i:3943 original size:21 final size:21
Alignment explanation
Indices: 3918--3966 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3908 CAATGTTGTA
3918 GTTGAAAATGAATTTGGGAGT
1 GTTGAAAATGAATTTGGGAGT
3939 GTTGAAAATGAATTTGGGAGT
1 GTTGAAAATGAATTTGGGAGT
*
3960 ATTGAAA
1 GTTGAAA
3967 CTAAAATAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.33
Consensus pattern (21 bp):
GTTGAAAATGAATTTGGGAGT
Found at i:4895 original size:20 final size:20
Alignment explanation
Indices: 4870--4908 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4860 TTATGTTAAG
4870 TTAGTTTATCCATAATTTAC
1 TTAGTTTATCCATAATTTAC
* *
4890 TTAGTTTTTCCATGATTTA
1 TTAGTTTATCCATAATTTA
4909 TATATGTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.54
Consensus pattern (20 bp):
TTAGTTTATCCATAATTTAC
Found at i:5614 original size:24 final size:24
Alignment explanation
Indices: 5562--5616 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
5552 TAGGTGTCTA
*
5562 GGTGAATGTACTTGTCTTTAGAAT
1 GGTGCATGTACTTGTCTTTAGAAT
5586 GGTGCATGTACTTGTCTTTAGAAT
1 GGTGCATGTACTTGTCTTTAGAAT
*
5610 TGTGCAT
1 GGTGCAT
5617 ATCATGGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (24 bp):
GGTGCATGTACTTGTCTTTAGAAT
Found at i:12058 original size:17 final size:18
Alignment explanation
Indices: 12030--12080 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
12020 TACTTTCACA
12030 TTTCAGGTTCATAACTC-T
1 TTTCA-GTTCATAACTCAT
12048 TTTCAGTTCATAACTCAT
1 TTTCAGTTCATAACTCAT
*
12066 TTTTAGATTCATAAC
1 TTTCAG-TTCATAAC
12081 CTAATTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 11 0.37
18 11 0.37
19 8 0.27
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (18 bp):
TTTCAGTTCATAACTCAT
Found at i:12076 original size:19 final size:19
Alignment explanation
Indices: 12037--12107 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
12027 ACATTTCAGG
*
12037 TTCATAACTC-TTTTCAG-
1 TTCATAACTCATTTTTAGA
12054 TTCATAACTCATTTTTAGA
1 TTCATAACTCATTTTTAGA
* *
12073 TTCATAAC-CTAATTTTATA
1 TTCATAACTC-ATTTTTAGA
*
12092 TTAATAACTCATTTTT
1 TTCATAACTCATTTTT
12108 CTAGTTTTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 10 0.22
18 7 0.16
19 27 0.60
20 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.49
Consensus pattern (19 bp):
TTCATAACTCATTTTTAGA
Found at i:12206 original size:15 final size:14
Alignment explanation
Indices: 12188--12217 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
12178 GATAAATTTG
12188 TCATTTATAATGCAA
1 TCATTTATAAT-CAA
12203 TCATTTATAATCAA
1 TCATTTATAATCAA
12217 T
1 T
12218 GGTAGTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.43
Consensus pattern (14 bp):
TCATTTATAATCAA
Found at i:12788 original size:35 final size:35
Alignment explanation
Indices: 12748--12826 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
12738 CCATATAATA
*
12748 TATTCGATACTTATTTGTTATAAAAATCATTTCGC
1 TATTCGATACTTATTCGTTATAAAAATCATTTCGC
12783 TATTCGATACTTATTCGTTATAAAAATCATTTCGC
1 TATTCGATACTTATTCGTTATAAAAATCATTTCGC
12818 TATTCGATA
1 TATTCGATA
12827 ACAACTTCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (35 bp):
TATTCGATACTTATTCGTTATAAAAATCATTTCGC
Found at i:14516 original size:29 final size:28
Alignment explanation
Indices: 14473--14551 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 28
14463 GACAAAACAT
** *
14473 AACTTTT-AAACATTACATTTTTTCCTTA
1 AACTTTTCAAA-ATTACATTTTGACCATA
* *
14501 AACTTTTTCAAAATTATACTTTGACCATA
1 AAC-TTTTCAAAATTACATTTTGACCATA
14530 AAC-TTTCAAAATTTACATTTTG
1 AACTTTTCAAAA-TTACATTTTG
14552 GTCACTAACC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
27 8 0.20
28 11 0.27
29 19 0.46
30 3 0.07
ACGTcount: A:0.35, C:0.16, G:0.03, T:0.46
Consensus pattern (28 bp):
AACTTTTCAAAATTACATTTTGACCATA
Found at i:18680 original size:19 final size:19
Alignment explanation
Indices: 18658--18719 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
18648 CTCTTTTGAG
18658 ATTCAGAACACATTTTCAA
1 ATTCAGAACACATTTTCAA
*
18677 ATTCAGAA-ATCAATTTT-AG
1 ATTCAGAACA-C-ATTTTCAA
**
18696 ATTCAGAACTTATTTTCAA
1 ATTCAGAACACATTTTCAA
18715 ATTCA
1 ATTCA
18720 TAAATTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 6 0.17
19 24 0.69
20 5 0.14
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (19 bp):
ATTCAGAACACATTTTCAA
Found at i:18701 original size:38 final size:39
Alignment explanation
Indices: 18651--18730 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 39
18641 TTCATAACTC
18651 TTTTGAGATTCAGAACACATTTTCAAATTCAGAAATCAA
1 TTTTGAGATTCAGAACACATTTTCAAATTCAGAAATCAA
** * *
18690 TTTT-AGATTCAGAACTTATTTTCAAATTCATAAATTAA
1 TTTTGAGATTCAGAACACATTTTCAAATTCAGAAATCAA
18728 TTT
1 TTT
18731 CATATTCACA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 33 0.89
39 4 0.11
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (39 bp):
TTTTGAGATTCAGAACACATTTTCAAATTCAGAAATCAA
Found at i:18731 original size:19 final size:19
Alignment explanation
Indices: 18671--18738 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
18661 CAGAACACAT
*
18671 TTTCAAATTCAGAAATCAA
1 TTTCAAATTCAGAAATTAA
* * * *
18690 TTTTAGATTCAGAACTTAT
1 TTTCAAATTCAGAAATTAA
*
18709 TTTCAAATTCATAAATTAA
1 TTTCAAATTCAGAAATTAA
*
18728 TTTCATATTCA
1 TTTCAAATTCA
18739 CAACCCAATA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (19 bp):
TTTCAAATTCAGAAATTAA
Found at i:21234 original size:15 final size:15
Alignment explanation
Indices: 21205--21233 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21195 TTACAGGCCA
21205 AAATATATAAATTTT
1 AAATATATAAATTTT
21220 AAATAT-TAAATTTT
1 AAATATATAAATTTT
21234 TGGTCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATATATAAATTTT
Found at i:22393 original size:59 final size:59
Alignment explanation
Indices: 22264--22613 Score: 558
Period size: 59 Copynumber: 5.9 Consensus size: 59
22254 TAAATTTAAT
* * * * *
22264 TGGAATTTCATACAATCAATATGATTTCCTTACCATTTTA-CACACAAAGTACCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
22322 TGGAAATTCATACACTTTGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
22381 TAGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGTACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * *
22440 TGGAAATTAATACACTTAGTATGATTTCCTTACAATTTTAGCAAACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
22499 TAGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAATGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
22558 TGGAAATTCATACACTTAGTATGAATTCCTTACCATTTTAGCACACAAAGTACCCT
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
22614 TTGGTAATTT
Statistics
Matches: 268, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
58 35 0.13
59 233 0.87
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (59 bp):
TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:24571 original size:187 final size:187
Alignment explanation
Indices: 24251--24628 Score: 738
Period size: 187 Copynumber: 2.0 Consensus size: 187
24241 TGATATGTAC
*
24251 CTCCTAAGCATCGATACATGGAAAACATTGTGGATCTTGTCCATATCCGAAGGCAGAGATAATTG
1 CTCCTAACCATCGATACATGGAAAACATTGTGGATCTTGTCCATATCCGAAGGCAGAGATAATTG
*
24316 ATAAGCCACGGGTCCAATCATTTTCAATATCTCATACAGTCCAATAAACCTCGGACTTAGCTTTC
66 ATAAGCCACGGGTCCAATCATTTTCAATATCTCATACAGTCCAATAAACCTCGGACTTAGCCTTC
24381 CTTTTCGCCCAAATCGTAATACCTTCTTCCAAGGCGATACTTTTAAAAATACTTTAT
131 CTTTTCGCCCAAATCGTAATACCTTCTTCCAAGGCGATACTTTTAAAAATACTTTAT
24438 CTCCTAACCATCGATACATGGAAAACATTGTGGATCTTGTCCATATCCGAAGGCAGAGATAATTG
1 CTCCTAACCATCGATACATGGAAAACATTGTGGATCTTGTCCATATCCGAAGGCAGAGATAATTG
24503 ATAAGCCACGGGTCCAATCATTTTCAATATCTCATACAGTCCAATAAACCTCGGACTTAGCCTTC
66 ATAAGCCACGGGTCCAATCATTTTCAATATCTCATACAGTCCAATAAACCTCGGACTTAGCCTTC
24568 CTTTTCGCCCAAATCGTAATACCTTCTTCCAAGGCGATACTTTTAAAAATACTTTAT
131 CTTTTCGCCCAAATCGTAATACCTTCTTCCAAGGCGATACTTTTAAAAATACTTTAT
24625 CTCC
1 CTCC
24629 CTCCTGGTAT
Statistics
Matches: 189, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
187 189 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (187 bp):
CTCCTAACCATCGATACATGGAAAACATTGTGGATCTTGTCCATATCCGAAGGCAGAGATAATTG
ATAAGCCACGGGTCCAATCATTTTCAATATCTCATACAGTCCAATAAACCTCGGACTTAGCCTTC
CTTTTCGCCCAAATCGTAATACCTTCTTCCAAGGCGATACTTTTAAAAATACTTTAT
Found at i:32924 original size:58 final size:59
Alignment explanation
Indices: 32793--33055 Score: 428
Period size: 59 Copynumber: 4.5 Consensus size: 59
32783 TTTTACATGC
*
32793 TTTCCTTACCATTTTAGCACATAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGA
1 TTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGA
*
32852 TTTCCTTACCATTTTAGCACACAAAGTGCCCTATCT-GAAATTTATACACTTAGTATGA
1 TTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGA
* *
32910 TTTCCTTACTATTTTAGCACACAAAGTGCCCTATTTGGAAATTCATACAC----TATGA
1 TTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGA
* *
32965 TTTCCTTACCAGTTTAGCACAAAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGA
1 TTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGA
*
33024 TTTCCTTACCATTTTAGCACACAAAGTACCCT
1 TTTCCTTACCATTTTAGCACACAAAGTGCCCT
33056 TTGGTAATTT
Statistics
Matches: 187, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
55 51 0.27
58 55 0.29
59 81 0.43
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (59 bp):
TTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGA
Found at i:33487 original size:19 final size:21
Alignment explanation
Indices: 33436--33491 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 21
33426 TACCCTCATC
33436 ATGGTATCGATA-CCCCTAAGCT
1 ATGGTATCGATACCCCCT-A-CT
*
33458 ATGGTACCGATACCCCCT-CT
1 ATGGTATCGATACCCCCTACT
33478 A-GGTATCGATACCC
1 ATGGTATCGATACCC
33492 AAATTAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 12 0.39
20 3 0.10
22 11 0.35
23 5 0.16
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (21 bp):
ATGGTATCGATACCCCCTACT
Found at i:35785 original size:55 final size:55
Alignment explanation
Indices: 35718--36722 Score: 1064
Period size: 55 Copynumber: 18.3 Consensus size: 55
35708 TTTTATTAGA
*
35718 ATGCACA-AGTAGTGCATATACGG-TAATTCATCAATTCATGATGAATTACGTGGTT
1 ATGCACACA-TAGTGCATATACGGCT-ATTCATCAACTCATGATGAATTACGTGGTT
* * * * * * *
35773 TTGCACACGTAGTGCCTATAAGACTATTCATCAACTTATGATGAATTCCGTGGTT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
* **
35828 ATGCACACATAGTGCTTATACGAATATTCATCAACTCATGATGAATT-CTGTGGTT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTAC-GTGGTT
* ** * * *
35883 ATGCACATATAGTGTTTGTACGGCTATTCATCAACTCATAATGAATTTCGTGGTT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
* * *
35938 ATGCACACATAGTGCTTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGTT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
** * * *
35993 ATGCACACATAGTGTTTGTACGGCTATTCATCAACTCATGATGAATTCCATGGTT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
* * * * * *
36048 ATGAACACATAGTTCCAGTAT--GACTATTCATCAACTCATGGTCAATTTCGTGGTT
1 ATGCACACATAG-TGCA-TATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
* * **
36103 ATGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGAACAATTACGTGGTT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
* * * * * **
36158 ATACATACATAGTGCCTATACGACTATTCATTAACTCATGATGAATTATATGGTT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
* * * **
36213 ATGCACACATAATGCTTGTACGGCTATTCATCAACTCATGATGAATTTTGTGGTT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
* * * * *
36268 ATGCACACATGGTCCTTATACGGCTATTCATCAACTCATGATGAATTCCGTGATT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
* * * * * * *
36323 ATGCACACGTAGTGCCTGA-ACGACTATCCATCAACTTATGACGAATTATGTGGTT
1 ATGCACACATAGTGCAT-ATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
* *
36378 ATGAACA-AGTAGTGCCA-ATACGACTATTCATCAACTCATGATGAATT-CTGTGGTT
1 ATGCACACA-TAGTG-CATATACGGCTATTCATCAACTCATGATGAATTAC-GTGGTT
* * *
36433 ATACACACATAGCGCATGTACGGCTATTCATCAACTCATGATGAATT-CTGTGGTT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTAC-GTGGTT
* * * ** *
36488 ATGCACACATAGTGCCTGTACGGCTATTCATCAATTCATGATGAATTTTGTTGTT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
* * *
36543 ATGCACATATAGTGCATGTACGGCTATTCATAAACTCATGATGAATT-CTGTGGTT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTAC-GTGGTT
* * * *
36598 ATGAACACATAGTGCGAGTAT--GGCTATTCATCAACTCATGATCAATTTCATGGTT
1 ATGCACACATAGTGC-A-TATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
* * * *
36653 ATGCACACATAGTGCATGTACGGCTATTCATCAACTCATGTTGAATTATGTGATT
1 ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
*
36708 ATGCACTCATAGTGC
1 ATGCACACATAGTGC
36723 CTGTAGTACA
Statistics
Matches: 809, Mismatches: 119, Indels: 44
0.83 0.12 0.05
Matches are distributed among these distances:
53 4 0.00
54 7 0.01
55 786 0.97
56 8 0.01
57 4 0.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (55 bp):
ATGCACACATAGTGCATATACGGCTATTCATCAACTCATGATGAATTACGTGGTT
Found at i:35867 original size:110 final size:110
Alignment explanation
Indices: 35718--36724 Score: 1172
Period size: 110 Copynumber: 9.2 Consensus size: 110
35708 TTTTATTAGA
* * * * *
35718 ATGCACA-AGTAGTGCATATACG-GTAATTCATCAATTCATGATGAATTACGTGGTTTTGCACAC
1 ATGCACACA-TAGTGCCTATACGACT-ATTCATCAACTCATGATGAATTTCGTGGTTATGCACAC
* * * * * * *
35781 GTAGTGCCTATAAGACTATTCATCAACTTATGATGAATTCCGTGGTT
64 ATAGTGCATGTACGGCTATTCATCAACTCATGATGAATTCTGTGGTT
* * *
35828 ATGCACACATAGTGCTTATACGAATATTCATCAACTCATGATGAA-TTCTGTGGTTATGCACATA
1 ATGCACACATAGTGCCTATACGACTATTCATCAACTCATGATGAATTTC-GTGGTTATGCACACA
** *
35892 TAGTGTTTGTACGGCTATTCATCAACTCATAATGAATT-TCGTGGTT
65 TAGTGCATGTACGGCTATTCATCAACTCATGATGAATTCT-GTGGTT
* * * *
35938 ATGCACACATAGTGCTTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGTTATGCACACAT
1 ATGCACACATAGTGCCTATACGACTATTCATCAACTCATGATGAATTTCGTGGTTATGCACACAT
** **
36003 AGTGTTTGTACGGCTATTCATCAACTCATGATGAATTCCATGGTT
66 AGTGCATGTACGGCTATTCATCAACTCATGATGAATTCTGTGGTT
* * * * *
36048 ATGAACACATAGTTCC-AGTATGACTATTCATCAACTCATGGTCAATTTCGTGGTTATGCACACA
1 ATGCACACATAGTGCCTA-TACGACTATTCATCAACTCATGATGAATTTCGTGGTTATGCACACA
* **
36112 TAGTGCCTGTACGGCTATTCATCAACTCATGAACAATTAC-GTGGTT
65 TAGTGCATGTACGGCTATTCATCAACTCATGATGAATT-CTGTGGTT
* * * *
36158 ATACATACATAGTGCCTATACGACTATTCATTAACTCATGATGAATTAT-ATGGTTATGCACACA
1 ATGCACACATAGTGCCTATACGACTATTCATCAACTCATGATGAATT-TCGTGGTTATGCACACA
* * *
36222 TAATGCTTGTACGGCTATTCATCAACTCATGATGAATTTTGTGGTT
65 TAGTGCATGTACGGCTATTCATCAACTCATGATGAATTCTGTGGTT
* * * * *
36268 ATGCACACATGGT-CCTTATACGGCTATTCATCAACTCATGATGAATTCCGTGATTATGCACACG
1 ATGCACACATAGTGCC-TATACGACTATTCATCAACTCATGATGAATTTCGTGGTTATGCACACA
* * * * * * *
36332 TAGTGCCTGAACGACTATCCATCAACTTATGACGAATTATGTGGTT
65 TAGTGCATGTACGGCTATTCATCAACTCATGATGAATTCTGTGGTT
* * *
36378 ATGAACA-AGTAGTGCCAATACGACTATTCATCAACTCATGATGAA-TTCTGTGGTTATACACAC
1 ATGCACACA-TAGTGCCTATACGACTATTCATCAACTCATGATGAATTTC-GTGGTTATGCACAC
*
36441 ATAGCGCATGTACGGCTATTCATCAACTCATGATGAATTCTGTGGTT
64 ATAGTGCATGTACGGCTATTCATCAACTCATGATGAATTCTGTGGTT
* * * * * *
36488 ATGCACACATAGTGCCTGTACGGCTATTCATCAATTCATGATGAATTTTGTTGTTATGCACATAT
1 ATGCACACATAGTGCCTATACGACTATTCATCAACTCATGATGAATTTCGTGGTTATGCACACAT
*
36553 AGTGCATGTACGGCTATTCATAAACTCATGATGAATTCTGTGGTT
66 AGTGCATGTACGGCTATTCATCAACTCATGATGAATTCTGTGGTT
* * * * * *
36598 ATGAACACATAGTG-CGAGTATGGCTATTCATCAACTCATGATCAATTTCATGGTTATGCACACA
1 ATGCACACATAGTGCCTA-TACGACTATTCATCAACTCATGATGAATTTCGTGGTTATGCACACA
* * *
36662 TAGTGCATGTACGGCTATTCATCAACTCATGTTGAATTATGTGATT
65 TAGTGCATGTACGGCTATTCATCAACTCATGATGAATTCTGTGGTT
*
36708 ATGCACTCATAGTGCCT
1 ATGCACACATAGTGCCT
36725 GTAGTACACT
Statistics
Matches: 765, Mismatches: 112, Indels: 39
0.84 0.12 0.04
Matches are distributed among these distances:
109 8 0.01
110 744 0.97
111 13 0.02
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (110 bp):
ATGCACACATAGTGCCTATACGACTATTCATCAACTCATGATGAATTTCGTGGTTATGCACACAT
AGTGCATGTACGGCTATTCATCAACTCATGATGAATTCTGTGGTT
Found at i:35990 original size:165 final size:165
Alignment explanation
Indices: 35718--36727 Score: 1190
Period size: 165 Copynumber: 6.1 Consensus size: 165
35708 TTTTATTAGA
* * * * *
35718 ATGCACA-AGTAGTGCATATACGG-TAATTCATCAATTCATGATGAATTACGTGGTTTTGCACAC
1 ATGCACATA-TAGTGCCTGTACGGCT-ATTCATCAACTCATGATGAATTTCGTGGTTATGCACAC
* * * * *
35781 GTAGTGCCTATAAGACTATTCATCAACTTATGATGAATTCCGTGGTTATGCACACATAGTGCTTA
64 ATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGTTATGCACACATAGTGCTTA
* *
35846 TACGAATATTCATCAACTCATGATGAATTCTGTGGTT
129 TACGACTATTCATCAACTCATGATGAATTATGTGGTT
** *
35883 ATGCACATATAGTGTTTGTACGGCTATTCATCAACTCATAATGAATTTCGTGGTTATGCACACAT
1 ATGCACATATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTCGTGGTTATGCACACAT
* * *
35948 AGTGCTTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGTTATGCACACATAGTGTTTGTA
66 AGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGTTATGCACACATAGTGCTTATA
* ***
36013 CGGCTATTCATCAACTCATGATGAATTCCATGGTT
131 CGACTATTCATCAACTCATGATGAATTATGTGGTT
* * * * * * * *
36048 ATGAACACATAGTTCCAGTATGACTATTCATCAACTCATGGTCAATTTCGTGGTTATGCACACAT
1 ATGCACATATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTCGTGGTTATGCACACAT
** * * * *
36113 AGTGCCTGTACGGCTATTCATCAACTCATGAACAATTACGTGGTTATACATACATAGTGCCTATA
66 AGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGTTATGCACACATAGTGCTTATA
* *
36178 CGACTATTCATTAACTCATGATGAATTATATGGTT
131 CGACTATTCATCAACTCATGATGAATTATGTGGTT
* * * *
36213 ATGCACACATAATGCTTGTACGGCTATTCATCAACTCATGATGAATTTTGTGGTTATGCACACAT
1 ATGCACATATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTCGTGGTTATGCACACAT
* * * * *
36278 GGT-CCTTATACGGCTATTCATCAACTCATGATGAATTCCGTGATTATGCACACGTAGTGCCTGA
66 AGTGCC-TGTACGGCTATTCATCAACTCATGATGAATTCCGTGGTTATGCACACATAGTG-CTTA
* * *
36342 -ACGACTATCCATCAACTTATGACGAATTATGTGGTT
129 TACGACTATTCATCAACTCATGATGAATTATGTGGTT
* ** * *
36378 ATGAACA-AGTAGTGCCAATACGACTATTCATCAACTCATGATGAA-TTCTGTGGTTATACACAC
1 ATGCACATA-TAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTC-GTGGTTATGCACAC
* * * * *
36441 ATAGCGCATGTACGGCTATTCATCAACTCATGATGAATTCTGTGGTTATGCACACATAGTGCCTG
64 ATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGTTATGCACACATAGTGCTTA
* * * *
36506 TACGGCTATTCATCAATTCATGATGAATTTTGTTGTT
129 TACGACTATTCATCAACTCATGATGAATTATGTGGTT
* * *
36543 ATGCACATATAGTGCATGTACGGCTATTCATAAACTCATGATGAA-TTCTGTGGTTATGAACACA
1 ATGCACATATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTC-GTGGTTATGCACACA
** * * * * * *
36607 TAGTGCGAGTATGGCTATTCATCAACTCATGATCAATTTCATGGTTATGCACACATAGTGCATGT
65 TAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGTTATGCACACATAGTGCTTAT
* * *
36672 ACGGCTATTCATCAACTCATGTTGAATTATGTGATT
130 ACGACTATTCATCAACTCATGATGAATTATGTGGTT
36708 ATGCAC-TCATAGTGCCTGTA
1 ATGCACAT-ATAGTGCCTGTA
36728 GTACACTTAG
Statistics
Matches: 718, Mismatches: 117, Indels: 20
0.84 0.14 0.02
Matches are distributed among these distances:
164 7 0.01
165 705 0.98
166 6 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (165 bp):
ATGCACATATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTCGTGGTTATGCACACAT
AGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGTTATGCACACATAGTGCTTATA
CGACTATTCATCAACTCATGATGAATTATGTGGTT
Found at i:37111 original size:19 final size:21
Alignment explanation
Indices: 37068--37121 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 21
37058 TACCCCTACC
37068 ATGGTATCGATACTACTATACT
1 ATGGTATCGATACTACTATA-T
*
37090 ATGGTATCGATACT-CTGT-T
1 ATGGTATCGATACTACTATAT
37109 ATGGTATCGATAC
1 ATGGTATCGATAC
37122 CATTTTTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 14 0.45
21 3 0.10
22 14 0.45
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (21 bp):
ATGGTATCGATACTACTATAT
Found at i:53106 original size:18 final size:19
Alignment explanation
Indices: 53075--53110 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
53065 TCCCCATTTC
*
53075 TTTTTCTTTGTCTATTCTA
1 TTTTTCGTTGTCTATTCTA
53094 TTTTTCGTT-TCTATTCT
1 TTTTTCGTTGTCTATTCT
53111 TGCTAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.08, C:0.17, G:0.06, T:0.69
Consensus pattern (19 bp):
TTTTTCGTTGTCTATTCTA
Done.