Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002921.1 Hibiscus syriacus cultivar Beakdansim tig00006038_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: 74271
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4477 original size:21 final size:22
Alignment explanation
Indices: 4453--4493 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4443 ATAATAGTAG
4453 TAAAATTAAAA-A-AAGAATTTT
1 TAAAA-TAAAAGATAAGAATTTT
4474 TAAAATAAAAGATAAGAATT
1 TAAAATAAAAGATAAGAATT
4494 AAATAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (22 bp):
TAAAATAAAAGATAAGAATTTT
Found at i:4512 original size:17 final size:18
Alignment explanation
Indices: 4476--4517 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
4466 AGAATTTTTA
4476 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
4494 AAATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATT
4511 AAATAAA
1 AAATAAA
4518 TAATTTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:4515 original size:35 final size:35
Alignment explanation
Indices: 4434--4517 Score: 86
Period size: 35 Copynumber: 2.4 Consensus size: 35
4424 AGGAAAAATA
*
4434 AAATAA-TAAATAATAGTAGTAAAATTAAAAAAAG
1 AAATAATTAAATAAAAGTAGTAAAATTAAAAAAAG
**
4468 -AATTTTTAAAATAAAAG-A-TAAGAATTAAATAAAAG
1 AAATAATT-AAATAAAAGTAGTAA-AATTAAA-AAAAG
4503 AAATAATTAAATAAA
1 AAATAATTAAATAAA
4518 TAATTTAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
33 6 0.15
34 9 0.22
35 20 0.50
36 5 0.12
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (35 bp):
AAATAATTAAATAAAAGTAGTAAAATTAAAAAAAG
Found at i:5191 original size:24 final size:25
Alignment explanation
Indices: 5164--5220 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
5154 TATCCTTATA
* **
5164 AAAATACTTAAAAC-TATTTAAACT
1 AAAATACTTAAAACAAAGATAAACT
*
5188 AAAATACCTAAAACAAAGATAAACT
1 AAAATACTTAAAACAAAGATAAACT
5213 AAAATACT
1 AAAATACT
5221 ATTTAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.25
Consensus pattern (25 bp):
AAAATACTTAAAACAAAGATAAACT
Found at i:15657 original size:23 final size:23
Alignment explanation
Indices: 15629--15673 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
15619 GACATTAGTT
15629 TTATGTTTCTTCATGTGTATCAG
1 TTATGTTTCTTCATGTGTATCAG
15652 TTATGTTTCTTCATGTGTATCA
1 TTATGTTTCTTCATGTGTATCA
15674 AAAAAAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (23 bp):
TTATGTTTCTTCATGTGTATCAG
Found at i:19234 original size:21 final size:21
Alignment explanation
Indices: 19196--19235 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19186 ATCAAAATGA
* *
19196 TAAGTCCTTTAATTGAAAGAT
1 TAAGTCATTTAATCGAAAGAT
*
19217 TAAGTCATTTTATCGAAAG
1 TAAGTCATTTAATCGAAAG
19236 GTCTTAACCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (21 bp):
TAAGTCATTTAATCGAAAGAT
Found at i:19628 original size:3 final size:3
Alignment explanation
Indices: 19622--19676 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
19612 ATAATAATAT
19622 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19670 TTA TTA T
1 TTA TTA T
19677 CTCGGATTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19914 original size:22 final size:22
Alignment explanation
Indices: 19888--19932 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
19878 ATCCCTTTAT
*
19888 GTTTGGGGTTATTGCGCACAAA
1 GTTTGGAGTTATTGCGCACAAA
*
19910 GTTTGGAGTTATTGCGTACAAA
1 GTTTGGAGTTATTGCGCACAAA
19932 G
1 G
19933 CCAAGCGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.33
Consensus pattern (22 bp):
GTTTGGAGTTATTGCGCACAAA
Found at i:21463 original size:24 final size:24
Alignment explanation
Indices: 21393--21502 Score: 165
Period size: 24 Copynumber: 4.8 Consensus size: 24
21383 CACATATTTA
21393 TCCCGAAGGACCACATA---TTTG
1 TCCCGAAGGACCACATAGGTTTTG
21414 TCCCGAAGGACCACATA-GTTTTG
1 TCCCGAAGGACCACATAGGTTTTG
*
21437 TCCCGAAGGGCCACATAGGTTTTG
1 TCCCGAAGGACCACATAGGTTTTG
*
21461 TCCCGAAGGGCCACATAGGTTTTG
1 TCCCGAAGGACCACATAGGTTTTG
*
21485 TCTCGAAGGACCACATAG
1 TCCCGAAGGACCACATAG
21503 AAACCTCGAC
Statistics
Matches: 83, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
21 17 0.20
23 20 0.24
24 46 0.55
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (24 bp):
TCCCGAAGGACCACATAGGTTTTG
Found at i:21475 original size:47 final size:46
Alignment explanation
Indices: 21393--21502 Score: 161
Period size: 47 Copynumber: 2.4 Consensus size: 46
21383 CACATATTTA
21393 TCCCGAAGGACCACATA-TTTGTCCCGAAGGACCACATA-GTTTTG
1 TCCCGAAGGACCACATAGTTTGTCCCGAAGGACCACATAGGTTTTG
* *
21437 TCCCGAAGGGCCACATAGGTTTTGTCCCGAAGGGCCACATAGGTTTTG
1 TCCCGAAGGACCACATA-G-TTTGTCCCGAAGGACCACATAGGTTTTG
*
21485 TCTCGAAGGACCACATAG
1 TCCCGAAGGACCACATAG
21503 AAACCTCGAC
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
44 16 0.28
47 21 0.36
48 21 0.36
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (46 bp):
TCCCGAAGGACCACATAGTTTGTCCCGAAGGACCACATAGGTTTTG
Found at i:22101 original size:22 final size:22
Alignment explanation
Indices: 22076--22136 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
22066 AGTACTCCTA
*
22076 CTATGGTA-CTGATACTTATTTT
1 CTATGGTATC-GATACCTATTTT
22098 CTATGGTATCGATACCTA-TTT
1 CTATGGTATCGATACCTATTTT
22119 C---GGTATCGATACC-ATTTT
1 CTATGGTATCGATACCTATTTT
22137 GGCATTCTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 1 0.03
18 15 0.42
21 4 0.11
22 15 0.42
23 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (22 bp):
CTATGGTATCGATACCTATTTT
Found at i:26862 original size:3 final size:3
Alignment explanation
Indices: 26854--26951 Score: 99
Period size: 3 Copynumber: 31.7 Consensus size: 3
26844 TTCATTTAAA
* *
26854 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
26902 AAT TAAT AAT T-T TAT TATT TAT TAC TAA TAT TATT TAT TAAT TAT TAT
1 TAT T-AT TAT TAT TAT TA-T TAT TAT TAT TAT TA-T TAT T-AT TAT TAT
26950 TA
1 TA
26952 CAAACGGGCC
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
2 2 0.03
3 66 0.84
4 11 0.14
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:27356 original size:17 final size:17
Alignment explanation
Indices: 27331--27367 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
27321 AGAGAACGAC
27331 AAGAAAAAAAACAGA-A
1 AAGAAAAAAAACAGAGA
27347 AAGAAAAAAAACAGAGA
1 AAGAAAAAAAACAGAGA
27364 AAGA
1 AAGA
27368 GAACACAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAACAGAGA
Found at i:28338 original size:19 final size:21
Alignment explanation
Indices: 28316--28356 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
28306 ATAGTTATAA
28316 ATATATA-TAAT-AATTATTT
1 ATATATATTAATAAATTATTT
28335 ATATATATTTAATAAATTATTT
1 ATATATA-TTAATAAATTATTT
28357 TGATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATATATTAATAAATTATTT
Found at i:28342 original size:21 final size:22
Alignment explanation
Indices: 28316--28356 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28306 ATAGTTATAA
28316 ATATATATAAT-AATTATTTAT
1 ATATATATAATAAATTATTTAT
*
28337 ATATATTTAATAAATTATTT
1 ATATATATAATAAATTATTT
28357 TGATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATATATAATAAATTATTTAT
Found at i:28993 original size:20 final size:21
Alignment explanation
Indices: 28970--29021 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
28960 AGAAATTAAA
28970 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
28990 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
29012 -ATT-ATTTATT
1 AATTCATTTATT
29022 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:33716 original size:6 final size:6
Alignment explanation
Indices: 33699--33743 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
33689 CTCATCCAGC
*
33699 AAAAGA AGAAGA AAAAGA AAAA-A AAAAGA AAAAGA AAAAGGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA-GA AAA
33744 TCGAATAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
5 5 0.14
6 25 0.71
7 5 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:33725 original size:23 final size:23
Alignment explanation
Indices: 33699--33743 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
33689 CTCATCCAGC
*
33699 AAAAGAAGAAGAAAAAGAAAAAA
1 AAAAGAAAAAGAAAAAGAAAAAA
*
33722 AAAAGAAAAAGAAAAAGGAAAA
1 AAAAGAAAAAGAAAAAGAAAAA
33744 TCGAATAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAAGAAAAAGAAAAAGAAAAAA
Found at i:36070 original size:83 final size:83
Alignment explanation
Indices: 35969--36233 Score: 442
Period size: 83 Copynumber: 3.2 Consensus size: 83
35959 AATGGAACAA
* *
35969 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGGCAAAATC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
36034 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
36052 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
36117 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
* * * *
36135 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
36199 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
*
36218 ATGAATTTGCTCATAG
1 ATGAATGTGCTCATAG
36234 TAGAAATAAG
Statistics
Matches: 172, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
82 4 0.02
83 168 0.98
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
AATCATTGAATTTGGAAG
Found at i:38777 original size:22 final size:22
Alignment explanation
Indices: 38751--38805 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
38741 ATCTACACTC
*
38751 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
38773 TTCAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
38795 TTCAAAGATGA
1 TTCAAAGATGA
38806 AAACTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:39643 original size:113 final size:113
Alignment explanation
Indices: 39274--39976 Score: 907
Period size: 113 Copynumber: 6.2 Consensus size: 113
39264 CATTTGAAGA
* ** ** * * * ** *
39274 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGT-CAGTTAGAG
1 AGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGATGGATTAGCA-TTTCCAGAGAAAG
39338 TTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATAATG
65 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * * *** * *
39386 AGAAGAATTTGTTCAACCTTTT-CCCTGAATTCATTACTTGATGAATTATTTTTTCCAAAGGAAG
1 AGAAGAACTTGTTCAACCTTTTGCTC-GAATTCATCACTTGATGGATTAGCATTTCCAGAGAAAG
*
39450 TTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAA-AAAGTTCATAATG
65 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTCATAATG
* *
39498 AGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGATGGATTAGCATTTCCAGAGAAAGT
39563 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * * * *
39611 AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGT
1 AGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGATGGATTAGCATTTCCAGAGAAAGT
39676 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * * *
39724 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCA-TTCGATAGATCAGCATTTCCAGAGAAAG
1 AGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTT-GATGGATTAGCATTTCCAGAGAAAG
*
39788 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
65 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * *
39837 AGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCA-TTCGATGGATCAGCATTTCCAGAGAAAG
1 AGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTT-GATGGATTAGCATTTCCAGAGAAAG
* * *
39901 TTCATAATGAGAAGAACTCTTCATCTGAAGAAGAAAGAAGAAGTTCATAATA
65 TTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAATTCATAATG
*
39953 AGAAGAACTTGTTCAACTTTTTGC
1 AGAAGAACTTGTTCAACCTTTTGC
39977 ATAATTCTAT
Statistics
Matches: 527, Mismatches: 54, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
111 6 0.01
112 161 0.31
113 303 0.57
114 3 0.01
115 1 0.00
116 53 0.10
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
AGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGATGGATTAGCATTTCCAGAGAAAGT
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
Found at i:40214 original size:165 final size:166
Alignment explanation
Indices: 40025--40371 Score: 687
Period size: 166 Copynumber: 2.1 Consensus size: 166
40015 CTTTCTAGAA
40025 AAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTGCTTGAATTCATCATTTGATGGATCAACAT
1 AAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACAT
40089 TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCAAGAGCTTATTCAACCTTTTGAATGACTCTA
66 TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCAAGAGCTTATTCAACCTTTTGAATGACTCTA
40154 TCACAGAAAAAAGGAGGTCATCATCATCCCCAGCAG
131 TCACAGAAAAAAGGAGGTCATCATCATCCCCAGCAG
40190 AAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACAT
1 AAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACAT
40255 TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCAAGAGCTTATTCAACCTTTTGAATGACTCTA
66 TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCAAGAGCTTATTCAACCTTTTGAATGACTCTA
40320 TCACAGAAAAAAGGAGGTCATCATCATCCCCAGCAG
131 TCACAGAAAAAAGGAGGTCATCATCATCCCCAGCAG
40356 AAAGTTCATAATGAGA
1 AAAGTTCATAATGAGA
40372 GGAACTCATC
Statistics
Matches: 181, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
165 31 0.17
166 150 0.83
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (166 bp):
AAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACAT
TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCAAGAGCTTATTCAACCTTTTGAATGACTCTA
TCACAGAAAAAAGGAGGTCATCATCATCCCCAGCAG
Found at i:40541 original size:3 final size:3
Alignment explanation
Indices: 40533--40625 Score: 100
Period size: 3 Copynumber: 31.0 Consensus size: 3
40523 TCATTTAAAT
* * *
40533 TTA TTA TTA TTA -TA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
40580 TTA ATA TT- TTA TTA TTTA TTA CTA ATA TTA TTA TTAA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
40626 CAAACGGGCC
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
2 4 0.05
3 65 0.87
4 6 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:41803 original size:22 final size:22
Alignment explanation
Indices: 41776--41826 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
41766 TTTTATTATT
41776 ATTATTTATAATATATATAAT-A
1 ATTATTTAT-ATATATATAATAA
*
41798 ATTATTTATATATATTTAATAA
1 ATTATTTATATATATATAATAA
41820 ATTATTT
1 ATTATTT
41827 TGATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTATTTATATATATATAATAA
Found at i:44849 original size:11 final size:11
Alignment explanation
Indices: 44835--44859 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44825 CATATTTAAA
44835 ATAAAAAAAAT
1 ATAAAAAAAAT
44846 ATAAAAAAAAT
1 ATAAAAAAAAT
44857 ATA
1 ATA
44860 TAGGAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
ATAAAAAAAAT
Found at i:46166 original size:14 final size:14
Alignment explanation
Indices: 46147--46173 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46137 GTGAAGCTAC
46147 ATGTTTCCATGAGG
1 ATGTTTCCATGAGG
46161 ATGTTTCCATGAG
1 ATGTTTCCATGAG
46174 TAGCAGCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (14 bp):
ATGTTTCCATGAGG
Found at i:46761 original size:36 final size:35
Alignment explanation
Indices: 46715--46830 Score: 133
Period size: 36 Copynumber: 3.2 Consensus size: 35
46705 TATACTGCCG
* * * *
46715 CCACCCGCTCCGTTGATTCCAAATCCTTTTCAACCT
1 CCACCAGCTCCATT-ATTCCAAATCCATTTCAGCCT
* * *
46751 CCACCAGCTCCACTAATTCCAAACCCCTTTCAGCCT
1 CCACCAGCTCCA-TTATTCCAAATCCATTTCAGCCT
46787 CCACCAGCTCCACTTATTCCAAATCCATTTCAGCCT
1 CCACCAGCTCCA-TTATTCCAAATCCATTTCAGCCT
*
46823 CCTCCAGC
1 CCACCAGC
46831 ACCAGCTCCA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
36 68 0.99
37 1 0.01
ACGTcount: A:0.22, C:0.45, G:0.07, T:0.26
Consensus pattern (35 bp):
CCACCAGCTCCATTATTCCAAATCCATTTCAGCCT
Found at i:46835 original size:42 final size:42
Alignment explanation
Indices: 46752--46966 Score: 205
Period size: 45 Copynumber: 5.1 Consensus size: 42
46742 TTTCAACCTC
* *
46752 CACCAGCTCCACTAATTCCAAACCCCTTTCAG---CCT-C--
1 CACCAGCTCCACTTATTCCAAACCCCTTCCAGCCTCCTCCAG
* * *
46788 CACCAGCTCCACTTATTCCAAATCCATTTCAGCCTCCTCCAG
1 CACCAGCTCCACTTATTCCAAACCCCTTCCAGCCTCCTCCAG
*
46830 CACCAGCTCCA-TTAATTCCAAACCCCTTCCAGCCTCCTCCGG
1 CACCAGCTCCACTT-ATTCCAAACCCCTTCCAGCCTCCTCCAG
*
46872 CACCGCCAGCTCCA-TTAATTCCGAACCCCTTCCAGCCTCCTCCAG
1 CA---CCAGCTCCACTT-ATTCCAAACCCCTTCCAGCCTCCTCCAG
* *
46917 CACCTCCTGCACCAC-TATTTCCAAACCCCTTCCAGCCTCCTCCAG
1 CA---CCAGCTCCACTTA-TTCCAAACCCCTTCCAGCCTCCTCCAG
46962 CACCA
1 CACCA
46967 CCTGCACCAC
Statistics
Matches: 153, Mismatches: 14, Indels: 18
0.83 0.08 0.10
Matches are distributed among these distances:
36 29 0.19
39 3 0.02
40 1 0.01
41 2 0.01
42 39 0.25
44 1 0.01
45 78 0.51
ACGTcount: A:0.22, C:0.48, G:0.08, T:0.22
Consensus pattern (42 bp):
CACCAGCTCCACTTATTCCAAACCCCTTCCAGCCTCCTCCAG
Found at i:46884 original size:45 final size:44
Alignment explanation
Indices: 46790--46965 Score: 223
Period size: 45 Copynumber: 4.0 Consensus size: 44
46780 TCAGCCTCCA
* * *
46790 CCAGCTCCACTT-ATTCCAAATCCATTTCAGCCTCCTCCAGCA--
1 CCAGCTCCA-TTAATTCCAAACCCCTTCCAGCCTCCTCCAGCACC
*
46832 CCAGCTCCATTAATTCCAAACCCCTTCCAGCCTCCTCCGGCACC
1 CCAGCTCCATTAATTCCAAACCCCTTCCAGCCTCCTCCAGCACC
*
46876 GCCAGCTCCATTAATTCCGAACCCCTTCCAGCCTCCTCCAGCACC
1 -CCAGCTCCATTAATTCCAAACCCCTTCCAGCCTCCTCCAGCACC
* * * *
46921 TCCTGCACCACTATTTCCAAACCCCTTCCAGCCTCCTCCAGCACC
1 -CCAGCTCCATTAATTCCAAACCCCTTCCAGCCTCCTCCAGCACC
46966 ACCTGCACCA
Statistics
Matches: 118, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.02
42 35 0.30
45 81 0.69
ACGTcount: A:0.21, C:0.48, G:0.09, T:0.22
Consensus pattern (44 bp):
CCAGCTCCATTAATTCCAAACCCCTTCCAGCCTCCTCCAGCACC
Found at i:55555 original size:15 final size:17
Alignment explanation
Indices: 55537--55568 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
55527 CCTATTCTCA
55537 AAATAA-AATAA-ATAG
1 AAATAAGAATAATATAG
55552 AAATAAGAATAATATAG
1 AAATAAGAATAATATAG
55569 TGAAGAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (17 bp):
AAATAAGAATAATATAG
Found at i:57397 original size:23 final size:23
Alignment explanation
Indices: 57334--57399 Score: 80
Period size: 24 Copynumber: 2.9 Consensus size: 23
57324 ATGAAACAAC
* *
57334 ATTTTTTTCTTTTTCTT-ATTCG
1 ATTTTTTTCTTTTTTTTCTTTCG
*
57356 ATTTTTTTCTTTCTCTTTCTTTCG
1 ATTTTTTTCTTT-TTTTTCTTTCG
*
57380 ATTTTTTCCTTTTTTTTCTT
1 ATTTTTTTCTTTTTTTTCTT
57400 CCCAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.32
23 10 0.27
24 15 0.41
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.74
Consensus pattern (23 bp):
ATTTTTTTCTTTTTTTTCTTTCG
Found at i:64559 original size:17 final size:18
Alignment explanation
Indices: 64512--64552 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
64502 TCTTGAGAAA
64512 ACCTAAAGAAAATAAAAT
1 ACCTAAAGAAAATAAAAT
*
64530 ACCTAAAGAAAATAGAAT
1 ACCTAAAGAAAATAAAAT
64548 -CCTAA
1 ACCTAA
64553 TAAAAATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.61, C:0.15, G:0.07, T:0.17
Consensus pattern (18 bp):
ACCTAAAGAAAATAAAAT
Found at i:67599 original size:52 final size:52
Alignment explanation
Indices: 67521--67619 Score: 189
Period size: 52 Copynumber: 1.9 Consensus size: 52
67511 TCAATGCCTA
67521 CAAAATAGATGGAAAAAATTAGATTGATAAGGCATCAAATTTAAATTGCTTG
1 CAAAATAGATGGAAAAAATTAGATTGATAAGGCATCAAATTTAAATTGCTTG
*
67573 CAAAATAGATGGAAAAAATTAGATTGATAAGGCTTCAAATTTAAATT
1 CAAAATAGATGGAAAAAATTAGATTGATAAGGCATCAAATTTAAATT
67620 CTTACTTAGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.29
Consensus pattern (52 bp):
CAAAATAGATGGAAAAAATTAGATTGATAAGGCATCAAATTTAAATTGCTTG
Found at i:72672 original size:21 final size:21
Alignment explanation
Indices: 72646--72701 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
72636 CTAGTTACCA
* * *
72646 GCGATGGTCGTAATAGCGTCC
1 GCGATGGCCGGAATAGCGTAC
72667 GCGATGGCCGGAATAGCGTAC
1 GCGATGGCCGGAATAGCGTAC
**
72688 GCGGCGGCCGGAAT
1 GCGATGGCCGGAAT
72702 CATGATAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.39, T:0.16
Consensus pattern (21 bp):
GCGATGGCCGGAATAGCGTAC
Done.