Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000019.1 Hibiscus syriacus cultivar Beakdansim tig00000035_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: 51935
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3461 original size:18 final size:17
Alignment explanation
Indices: 3438--3471 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3428 TAGAAAAAGT
3438 TAAAATATGATCTATTTA
1 TAAAATATGAT-TATTTA
*
3456 TAAAATTTGATTATTT
1 TAAAATATGATTATTT
3472 GCTTTGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
TAAAATATGATTATTTA
Found at i:3986 original size:2 final size:2
Alignment explanation
Indices: 3979--4010 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3969 TAAGCACGTA
3979 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4011 CATAAGATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4003 original size:17 final size:17
Alignment explanation
Indices: 3981--4015 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3971 AGCACGTAAT
*
3981 ATATATATATATATATA
1 ATATATATATATACATA
3998 ATATATATATATACATA
1 ATATATATATATACATA
4015 A
1 A
4016 GATGATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATATATATACATA
Found at i:5353 original size:13 final size:13
Alignment explanation
Indices: 5335--5364 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5325 AAGTCTATAT
5335 TGGGTCAGGTTAC
1 TGGGTCAGGTTAC
*
5348 TGGGTCAGGTTGC
1 TGGGTCAGGTTAC
5361 TGGG
1 TGGG
5365 ACTGGTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.47, T:0.30
Consensus pattern (13 bp):
TGGGTCAGGTTAC
Found at i:5965 original size:46 final size:46
Alignment explanation
Indices: 5914--6001 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
5904 AACGGTAGAC
* *
5914 CATCTA-AGGGTGATAACACGGTT-TATATGTGATGAAGACGACATAT
1 CATCTATA-GGTGAGAACACGGTTCT-TACGTGATGAAGACGACATAT
* *
5960 CATCTATATGTGAGAACACGGTTCTTACGTGATGAGGACGAC
1 CATCTATAGGTGAGAACACGGTTCTTACGTGATGAAGACGAC
6002 TGGTTATCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
46 34 0.94
47 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (46 bp):
CATCTATAGGTGAGAACACGGTTCTTACGTGATGAAGACGACATAT
Found at i:6071 original size:40 final size:40
Alignment explanation
Indices: 5975--6076 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 40
5965 ATATGTGAGA
* *
5975 ACACGGTTCTTACGTGATGAGGACGACTGGTTATCTGGGGTG
1 ACACGGATCTTACGTGATGAGGACGACTGG-T-TCGGGGGTG
*
6017 ACACGGATCTTACGTGATGAGGACGGCTGG-TCGGGGGATG
1 ACACGGATCTTACGTGATGAGGACGACTGGTTCGGGGG-TG
* *
6057 ACACGGCTCATACGTGATGA
1 ACACGGATCTTACGTGATGA
6077 AGAGTTCTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
39 6 0.11
40 20 0.37
42 28 0.52
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.24
Consensus pattern (40 bp):
ACACGGATCTTACGTGATGAGGACGACTGGTTCGGGGGTG
Found at i:6402 original size:59 final size:59
Alignment explanation
Indices: 6318--6431 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
6308 CAATAGAATG
* * *
6318 ACAAACTCAAAGATTTAATTTGTTTCAATGGAAACGATCTCAAAGATGTTTGTTTAGAA
1 ACAAACTCAAAGATTTAATTCGTTTCAAGGGAAACGATCTCAAAGATGATTGTTTAGAA
* * *
6377 ACAAACTCAAATATTTAATTCGTTTCAAGGGAAATGATTTCAAAGATGATTGTTT
1 ACAAACTCAAAGATTTAATTCGTTTCAAGGGAAACGATCTCAAAGATGATTGTTT
6432 TACAAGAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (59 bp):
ACAAACTCAAAGATTTAATTCGTTTCAAGGGAAACGATCTCAAAGATGATTGTTTAGAA
Found at i:7065 original size:23 final size:24
Alignment explanation
Indices: 7004--7065 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
6994 TTCTTCTTTT
* *
7004 ATTTTCAAAATA-TTAATTAGAAG
1 ATTTTGAAAATATTTAATCAGAAG
7027 AGTTTTGAAAAATATTTAATCA-AAG
1 A-TTTTG-AAAATATTTAATCAGAAG
7052 ATTTTGAAAATATT
1 ATTTTGAAAATATT
7066 GTCCATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 9 0.26
24 9 0.26
25 10 0.29
26 6 0.18
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (24 bp):
ATTTTGAAAATATTTAATCAGAAG
Found at i:7352 original size:22 final size:22
Alignment explanation
Indices: 7311--7358 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
7301 TTGTATGCCC
* *
7311 CAAAATTTTGTTTCTTGAGAGA
1 CAAAATTTTGTTTCTAGAGAAA
7333 CAAAATTTTGTTT-TAAGAGAAA
1 CAAAATTTTGTTTCT-AGAGAAA
7355 CAAA
1 CAAA
7359 CTCAAAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (22 bp):
CAAAATTTTGTTTCTAGAGAAA
Found at i:7806 original size:23 final size:24
Alignment explanation
Indices: 7745--7806 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
7735 TTCTTCTTTT
* *
7745 ATTTTCAAAATA-TTAATTAGAAG
1 ATTTTGAAAATATTTAATCAGAAG
7768 AGTTTTGAAAAATATTTAATCA-AAG
1 A-TTTTG-AAAATATTTAATCAGAAG
7793 ATTTTGAAAATATT
1 ATTTTGAAAATATT
7807 GTCCATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 9 0.26
24 9 0.26
25 10 0.29
26 6 0.18
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (24 bp):
ATTTTGAAAATATTTAATCAGAAG
Found at i:8007 original size:741 final size:741
Alignment explanation
Indices: 6582--8049 Score: 2774
Period size: 741 Copynumber: 2.0 Consensus size: 741
6572 TAAGAAGCTA
6582 TCTTGAGAGACAAAATTTTGTTTTAAGAGAAACAAACTCAAAGATTATTTATGCCTCAAATTAGA
1 TCTTGAGAGACAAAATTTTGTTTTAAGAGAAACAAACTCAAAGATTATTTATGCCTCAAATTAGA
*
6647 TAAAATTTGTTTTGAAAGAAAATTGTCTCAAGAGAGACAACATTTTATTTCGAGAGAAACAACAT
66 TAAAATTTATTTTGAAAGAAAATTGTCTCAAGAGAGACAACATTTTATTTCGAGAGAAACAACAT
6712 TAAATGATACTGATATTCTGCTTGTTCCCACTGGTGGAGGAAATGCCTTCAGAAGATCTAATAAT
131 TAAATGATACTGATATTCTGCTTGTTCCCACTGGTGGAGGAAATGCCTTCAGAAGATCTAATAAT
6777 TTGCATCAGGATATTAAATCCACAAAGATGTCCCAATATTCGATGTTAAATCTCCAAATATACCC
196 TTGCATCAGGATATTAAATCCACAAAGATGTCCCAATATTCGATGTTAAATCTCCAAATATACCC
*
6842 CAACATTTACTATTGAATCTTTAAATATGCCCCAATTATTCCTCCTTGCTTGCTTCAGCGCTGAT
261 CAACATTTACTATTGAATCTTTAAAGATGCCCCAATTATTCCTCCTTGCTTGCTTCAGCGCTGAT
*
6907 TTTGAGCATGAGCTTTGTGTCTGAGAGCTACATGTCATTTATCAAGATCTATTCTAGAGAGATTG
326 TTTGAGCATGAGCTTTGTGTCTGAGAGCTACATGTCATTTATCAAGATCTACTCTAGAGAGATTG
6972 TCTTGTTTGAAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAATATTAATTAGAAGAGTTTTGAAA
391 TCTTGTTTGAAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAATATTAATTAGAAGAGTTTTGAAA
7037 AATATTTAATCAAAGATTTTGAAAATATTGTCCATTTATAGGTTTTACAATTGACAAATCATAAA
456 AATATTTAATCAAAGATTTTGAAAATATTGTCCATTTATAGGTTTTACAATTGACAAATCATAAA
*
7102 ACAAGAGTTAATTGGATATCAAAGAATTAATTACACTGTTAATCATTCAATAAATTATAGTTATT
521 ACAAGAGTTAATTGGATATCAAAGAATTAATTACACTGTTAATCATTCAATAAATTATAGCTATT
7167 TGACAAGTGTCAAGAACAAAGCTATCTTTGGGAAATGGGTAGGTGAGAAAATGGTAAAATGTCTC
586 TGACAAGTGTCAAGAACAAAGCTATCTTTGGGAAATGGGTAGGTGAGAAAATGGTAAAATGTCTC
*
7232 AGGTTGTTATTTTTTGTCAATGGTTTGACCTTCTTGTTTCTTTGATGTTCACTGATTTAATGGGG
651 AGATTGTTATTTTTTGTCAATGGTTTGACCTTCTTGTTTCTTTGATGTTCACTGATTTAATGGGG
7297 TAGCTTGTATGCCCCAAAATTTTGTT
716 TAGCTTGTATGCCCCAAAATTTTGTT
7323 TCTTGAGAGACAAAATTTTGTTTTAAGAGAAACAAACTCAAAGATTATTTATGCCTCAAATTAGA
1 TCTTGAGAGACAAAATTTTGTTTTAAGAGAAACAAACTCAAAGATTATTTATGCCTCAAATTAGA
*
7388 TAAAATTTATTTTGAAAGAAAATTGTCTCAAGAGAGACAACATTTTGTTTCGAGAGAAACAACAT
66 TAAAATTTATTTTGAAAGAAAATTGTCTCAAGAGAGACAACATTTTATTTCGAGAGAAACAACAT
* * *
7453 TAAATGATATTGATATTCTGCTTGTTCCCATTGGTGGAGGAAATGCTTTCAGAAGATCTAATAAT
131 TAAATGATACTGATATTCTGCTTGTTCCCACTGGTGGAGGAAATGCCTTCAGAAGATCTAATAAT
*
7518 TTGCATCAGGATATTAAATCCACAAAGATGTCCCAATATTCGATGTTAAATCTCCAAATATGCCC
196 TTGCATCAGGATATTAAATCCACAAAGATGTCCCAATATTCGATGTTAAATCTCCAAATATACCC
*
7583 CAACATTTACTATTGAATCTTTAAAGATGCCCCAATTGTTCCTCCTTGCTTGCTTCAGCGCTGAT
261 CAACATTTACTATTGAATCTTTAAAGATGCCCCAATTATTCCTCCTTGCTTGCTTCAGCGCTGAT
7648 TTTGAGCATGAGCTTTGTGTCTGAGAGCTACATGTCATTTATCAAGATCTACTCTAGAGAGATTG
326 TTTGAGCATGAGCTTTGTGTCTGAGAGCTACATGTCATTTATCAAGATCTACTCTAGAGAGATTG
*
7713 TCTTGTTTGAAAATTGTTTTTCTTCTTCTTTTATTTTCAAAATATTAATTAGAAGAGTTTTGAAA
391 TCTTGTTTGAAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAATATTAATTAGAAGAGTTTTGAAA
*
7778 AATATTTAATCAAAGATTTTGAAAATATTGTCCATTTATATGTTTTACAATTGACAAATCATAAA
456 AATATTTAATCAAAGATTTTGAAAATATTGTCCATTTATAGGTTTTACAATTGACAAATCATAAA
*
7843 ACAAGAGTTAATTGGATATCAAAGAATTAATTACACTGTTAATCCTTCAATAAATTATAGCTATT
521 ACAAGAGTTAATTGGATATCAAAGAATTAATTACACTGTTAATCATTCAATAAATTATAGCTATT
* *
7908 TGACAAGTGTCAAGATCAAAGCTATCTTTGGGAAATGGGTAGGTGAGGAAATGGTAAAATGTCTC
586 TGACAAGTGTCAAGAACAAAGCTATCTTTGGGAAATGGGTAGGTGAGAAAATGGTAAAATGTCTC
* *
7973 AGATTGTTATTTTTTGTCAATGGTTTGGCCTTCTTGTTTCTTTGATGTTCACTGATTTGATGGGG
651 AGATTGTTATTTTTTGTCAATGGTTTGACCTTCTTGTTTCTTTGATGTTCACTGATTTAATGGGG
8038 TAGCTTGTATGC
716 TAGCTTGTATGC
8050 TCTTCTACTG
Statistics
Matches: 709, Mismatches: 18, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
741 709 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (741 bp):
TCTTGAGAGACAAAATTTTGTTTTAAGAGAAACAAACTCAAAGATTATTTATGCCTCAAATTAGA
TAAAATTTATTTTGAAAGAAAATTGTCTCAAGAGAGACAACATTTTATTTCGAGAGAAACAACAT
TAAATGATACTGATATTCTGCTTGTTCCCACTGGTGGAGGAAATGCCTTCAGAAGATCTAATAAT
TTGCATCAGGATATTAAATCCACAAAGATGTCCCAATATTCGATGTTAAATCTCCAAATATACCC
CAACATTTACTATTGAATCTTTAAAGATGCCCCAATTATTCCTCCTTGCTTGCTTCAGCGCTGAT
TTTGAGCATGAGCTTTGTGTCTGAGAGCTACATGTCATTTATCAAGATCTACTCTAGAGAGATTG
TCTTGTTTGAAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAATATTAATTAGAAGAGTTTTGAAA
AATATTTAATCAAAGATTTTGAAAATATTGTCCATTTATAGGTTTTACAATTGACAAATCATAAA
ACAAGAGTTAATTGGATATCAAAGAATTAATTACACTGTTAATCATTCAATAAATTATAGCTATT
TGACAAGTGTCAAGAACAAAGCTATCTTTGGGAAATGGGTAGGTGAGAAAATGGTAAAATGTCTC
AGATTGTTATTTTTTGTCAATGGTTTGACCTTCTTGTTTCTTTGATGTTCACTGATTTAATGGGG
TAGCTTGTATGCCCCAAAATTTTGTT
Found at i:12019 original size:15 final size:13
Alignment explanation
Indices: 11995--12037 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
11985 CTTAAAAATG
11995 AAATGCAGATGCA
1 AAATGCAGATGCA
12008 AAATGCAAAGATGC-
1 AAATGC--AGATGCA
12022 AAATGCAGATGCA
1 AAATGCAGATGCA
12035 AAA
1 AAA
12038 AATGTTGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.22
13 9 0.33
14 6 0.22
15 6 0.22
ACGTcount: A:0.51, C:0.14, G:0.21, T:0.14
Consensus pattern (13 bp):
AAATGCAGATGCA
Found at i:12021 original size:21 final size:20
Alignment explanation
Indices: 11997--12036 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
11987 TAAAAATGAA
*
11997 ATGCAGATGCAAAATGCAAAG
1 ATGCAAATGC-AAATGCAAAG
*
12018 ATGCAAATGCAGATGCAAA
1 ATGCAAATGCAAATGCAAA
12037 AAATGTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (20 bp):
ATGCAAATGCAAATGCAAAG
Found at i:12033 original size:12 final size:12
Alignment explanation
Indices: 11995--12036 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 12
11985 CTTAAAAATG
11995 AAATGCAGATGC
1 AAATGCAGATGC
12007 AAAATGCAAAGATGC
1 -AAATGC--AGATGC
12022 AAATGCAGATGC
1 AAATGCAGATGC
12034 AAA
1 AAA
12037 AAATGTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.33
13 6 0.22
14 6 0.22
15 6 0.22
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (12 bp):
AAATGCAGATGC
Found at i:12791 original size:32 final size:32
Alignment explanation
Indices: 12755--12816 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
12745 ATGAAAAATG
12755 ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
*
12787 ACACAAACAAAAGAAAAGAAATTAGTTAGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGT
12817 ACATGAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
Found at i:14609 original size:2 final size:2
Alignment explanation
Indices: 14602--14629 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14592 TAAGCACGTA
14602 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
14630 GTGTGTATGT
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:16673 original size:50 final size:51
Alignment explanation
Indices: 16591--16772 Score: 197
Period size: 50 Copynumber: 3.6 Consensus size: 51
16581 AAAACTGTAG
* * * * * *
16591 CACTTAACATATATTTACATCGGTGCAAGTGAATAAAATAAACAAGTATAT
1 CACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAGTATAA
* * * *
16642 CACTTAATACATA-TTATACCGGTGTAAGTGAATAAAATAAAAAAACTGTAA
1 CACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT-AAAAAAGTATAA
* ** *
16693 CACTTAACATATACTTACACCAATGTAAGTAAATAAAA-AAAAAAGTATAA
1 CACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAGTATAA
**
16743 CACTTAACACATACTTACACTTGTGTAAGT
1 CACTTAACACATACTTACACCGGTGTAAGT
16773 ATGTACATCT
Statistics
Matches: 108, Mismatches: 21, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
50 58 0.54
51 30 0.28
52 20 0.19
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (51 bp):
CACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAGTATAA
Found at i:16697 original size:51 final size:51
Alignment explanation
Indices: 16580--16755 Score: 162
Period size: 51 Copynumber: 3.5 Consensus size: 51
16570 TTCATACTAC
* * * *
16580 AAAAACTGTAGCACTTAACATATATT-TACATCGGTGCAAGTGAATAAAAT-A
1 AAAAACTATAACACTTAACACATATTATAC--CGGTGTAAGTGAATAAAATAA
* * * *
16631 AACAAGTATATCACTTAATACATATTATACCGGTGTAAGTGAATAAAATAA
1 AAAAACTATAACACTTAACACATATTATACCGGTGTAAGTGAATAAAATAA
* * * ** *
16682 AAAAACTGTAACACTTAACATATACTTACACCAATGTAAGTAAAT-AAA-AA
1 AAAAACTATAACACTTAACACATA-TTATACCGGTGTAAGTGAATAAAATAA
*
16732 AAAAAGTATAACACTTAACACATA
1 AAAAACTATAACACTTAACACATA
16756 CTTACACTTG
Statistics
Matches: 102, Mismatches: 20, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
50 41 0.40
51 42 0.41
52 19 0.19
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (51 bp):
AAAAACTATAACACTTAACACATATTATACCGGTGTAAGTGAATAAAATAA
Found at i:16769 original size:102 final size:102
Alignment explanation
Indices: 16580--16772 Score: 253
Period size: 102 Copynumber: 1.9 Consensus size: 102
16570 TTCATACTAC
* * * ** * * *
16580 AAAAACTGTAGCACTTAACATATATTTACATCGGTGCAAGTGAATAAAATAAACAAGTATATCAC
1 AAAAACTGTAACACTTAACATATACTTACACCAATGCAAGTAAATAAAATAAAAAAGTATAACAC
* *
16645 TTAATACATATTATACCGGTGTAAGTGAATAAAATAA
66 TTAACACATATTACACCGGTGTAAGTGAATAAAATAA
*
16682 AAAAACTGTAACACTTAACATATACTTACACCAATGTAAGTAAATAAAA-AAAAAAGTATAACAC
1 AAAAACTGTAACACTTAACATATACTTACACCAATGCAAGTAAATAAAATAAAAAAGTATAACAC
**
16746 TTAACACATACTTACACTTGTGTAAGT
66 TTAACACATA-TTACACCGGTGTAAGT
16773 ATGTACATCT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 22 0.29
102 55 0.71
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (102 bp):
AAAAACTGTAACACTTAACATATACTTACACCAATGCAAGTAAATAAAATAAAAAAGTATAACAC
TTAACACATATTACACCGGTGTAAGTGAATAAAATAA
Found at i:21836 original size:95 final size:95
Alignment explanation
Indices: 21672--21872 Score: 260
Period size: 95 Copynumber: 2.1 Consensus size: 95
21662 TCAGAGGTGC
* * ** * *
21672 AGTATCGATACTAGGAGAAAGATATTGATACCTTGGAATCCAGAATGTAGAAATTGTATCGATAC
1 AGTATCGATACTAGAAGAAAGATATCGATACCAGGGAATACAGAATGTAGAAATGGTATCGATAC
*
21737 TGAAAGGGAGTATCGGTACCATAGTATAAA
66 TGAAAGGGAGTATCAGTACCATAGTATAAA
* * *
21767 AGTATCGGTACTAGAAGAAATATATCGATACCAGGGATTACAGAATGCT-GAAATGGTATCGATA
1 AGTATCGATACTAGAAGAAAGATATCGATACCAGGGAATACAGAATG-TAGAAATGGTATCGATA
* * * *
21831 TTGAAAGGGAGTATCATTACCGTAGTATATA
65 CTGAAAGGGAGTATCAGTACCATAGTATAAA
21862 AGTATCGATAC
1 AGTATCGATAC
21873 CATGGTAGGG
Statistics
Matches: 90, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 89 0.99
96 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (95 bp):
AGTATCGATACTAGAAGAAAGATATCGATACCAGGGAATACAGAATGTAGAAATGGTATCGATAC
TGAAAGGGAGTATCAGTACCATAGTATAAA
Found at i:22406 original size:81 final size:81
Alignment explanation
Indices: 22271--22622 Score: 501
Period size: 81 Copynumber: 4.3 Consensus size: 81
22261 TGTTTTAAAA
* *
22271 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCGATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTTCCAATATTGCAAGTTAGATGAAAG
22336 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * *
22352 TAAAATATTAATTGCCTAGCTGTGCATTTGGCATAAA-GTTACTAATATTGCAAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTT-CCAATATTGCAAGTTAGATGAAA
*
22416 GACTAAATGCCTTTGAG
65 GGCTAAATGCCTTTGAG
* * *
22433 TAAAAGATTAATTTCCTAGCTGTGCATTTGGCAGAAATGTTCCAATATTGCAAGTTAGATGAATG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTTCCAATATTGCAAGTTAGATGAAAG
22498 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * * * *
22514 TAAAAGATTAAATGCCTAACTGTGCATTTAGAAGAAAGGTTCCAATAATGTC-AGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTTCCAATATTG-CAAGTTAGATGAAA
*
22578 GGTTAAATGCCTTTGAG
65 GGCTAAATGCCTTTGAG
* * *
22595 ATAAAAGACTAATTGTCTATCTGTGCAT
1 -TAAAAGATTAATTGCCTAGCTGTGCAT
22623 AGCTGGCATG
Statistics
Matches: 242, Mismatches: 25, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
80 2 0.01
81 213 0.88
82 27 0.11
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTTCCAATATTGCAAGTTAGATGAAAG
GCTAAATGCCTTTGAG
Found at i:40274 original size:32 final size:32
Alignment explanation
Indices: 40224--40288 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
40214 ATGAAGATGC
*
40224 CCCAGGTGTAACTTTGGAGAAGGAAACAAAAA
1 CCCAGGTGCAACTTTGGAGAAGGAAACAAAAA
* * *
40256 CCCATGTGCAACTTTGGAGAAGGGAATAAAAA
1 CCCAGGTGCAACTTTGGAGAAGGAAACAAAAA
40288 C
1 C
40289 TATCACCGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (32 bp):
CCCAGGTGCAACTTTGGAGAAGGAAACAAAAA
Found at i:49821 original size:102 final size:102
Alignment explanation
Indices: 49645--49849 Score: 358
Period size: 102 Copynumber: 2.0 Consensus size: 102
49635 TCACGGGATG
49645 ACTCTACCTGACTAGCTCGAGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGT
1 ACTCTACCTGACTAGCTCGAGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGT
*
49710 GTGATGAGATGACTCCCCTTAAAGT-CTTCTTAAAAAA
66 GTGATGAGATGACTCCCCTTAAAGTAC-GCTTAAAAAA
* * *
49747 ACTCTACTTGACTAGCTCGGGGGTGGAAGGTATGTTCCCTTTCACTTAGAGTGTGGGATGGTAGT
1 ACTCTACCTGACTAGCTCGAGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGT
49812 GTGATGAGATGACTCCCCTTAAAGTACGCTTAAAAAA
66 GTGATGAGATGACTCCCCTTAAAGTACGCTTAAAAAA
49849 A
1 A
49850 GATATTTGAA
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 97 0.99
103 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (102 bp):
ACTCTACCTGACTAGCTCGAGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGT
GTGATGAGATGACTCCCCTTAAAGTACGCTTAAAAAA
Done.