Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002264.1 Hibiscus syriacus cultivar Beakdansim tig00004605_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: 113934
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:2253 original size:30 final size:29
Alignment explanation
Indices: 2219--2330 Score: 122
Period size: 30 Copynumber: 3.8 Consensus size: 29
2209 CATAAGAGCT
* *
2219 AAAAAACAAGAAGAAGAAGAAAAAGAAGA
1 AAAAAAAAAGAAAAAGAAGAAAAAGAAGA
*
2248 AAAAAAAAGAAAAAAAGAAGAAAAAAGAAG-
1 AAAAAAAA-AGAAAAAGAAG-AAAAAGAAGA
*
2278 AAAAAAGAAGAAAAAAGAAGAAAAAAGAA-A
1 AAAAAAAAAG-AAAAAGAAG-AAAAAGAAGA
*
2308 AGAAAAAAAGAAAAAGAA-AAAAA
1 AAAAAAAAAGAAAAAGAAGAAAAA
2331 TCAAAAAAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
27 5 0.07
29 16 0.22
30 42 0.58
31 9 0.12
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAGAAAAAGAAGAAAAAGAAGA
Found at i:2257 original size:10 final size:10
Alignment explanation
Indices: 2232--2358 Score: 110
Period size: 11 Copynumber: 11.8 Consensus size: 10
2222 AAACAAGAAG
2232 AAGAAGAAAAA
1 AAGAA-AAAAA
2243 GAAGAAAAAAA
1 -AAGAAAAAAA
2254 AAGAAAAAAA
1 AAGAAAAAAA
*
2264 GAAGAAAAAAG
1 -AAGAAAAAAA
*
2275 AAGAAAAAAG
1 AAGAAAAAAA
*
2285 AAGAAAAAAG
1 AAGAAAAAAA
2295 AAGAAAAAAGAA
1 AAG-AAAAA-AA
2307 AAGAAAAAAA
1 AAGAAAAAAA
*
2317 GAAAAAGAAAAA
1 -AAGAA-AAAAA
* *
2329 AATCAAAAAAG
1 AA-GAAAAAAA
2340 AAGAAGAAAAA
1 AAGAA-AAAAA
*
2351 ATGAAAAA
1 AAGAAAAA
2359 TTAAAAAAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
10 40 0.40
11 44 0.44
12 16 0.16
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.02
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:2336 original size:14 final size:14
Alignment explanation
Indices: 2219--2370 Score: 99
Period size: 14 Copynumber: 10.0 Consensus size: 14
2209 CATAAGAGCT
* *
2219 AAAAAACAAGAAGA
1 AAAAAAAAAAAAGA
* *
2233 AGAAGAAAAAGAAGA
1 A-AAAAAAAAAAAGA
2248 AAAAAAAAGAAAA-A
1 AAAAAAAA-AAAAGA
2262 AAGAAGAAAAAAGAAGAA
1 AA-AA-AAAAAA-AAG-A
2280 AAAAGAAGAAAAAAGA
1 AAAA-AA-AAAAAAGA
*
2296 AGAAAAAAGAAAAGA
1 A-AAAAAAAAAAAGA
*
2311 AAAAAAGAAAAAGA
1 AAAAAAAAAAAAGA
2325 AAAAAATCAAAAAAGA
1 AAAAAA--AAAAAAGA
* * *
2341 AGAAGAAAAAATGA
1 AAAAAAAAAAAAGA
2355 AAAATTAAAAAAAAGA
1 AAAA--AAAAAAAAGA
2371 TGAGAGATGT
Statistics
Matches: 111, Mismatches: 14, Indels: 24
0.74 0.09 0.16
Matches are distributed among these distances:
14 37 0.33
15 27 0.24
16 29 0.26
17 11 0.10
18 7 0.06
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:2336 original size:20 final size:20
Alignment explanation
Indices: 2238--2351 Score: 137
Period size: 20 Copynumber: 5.8 Consensus size: 20
2228 GAAGAAGAAG
2238 AAAAAGAAGAAAAAAAAAGAA
1 AAAAAGAAGAAAAAAAAAG-A
*
2259 AAAAAGAAGAAAAAAGAAGA
1 AAAAAGAAGAAAAAAAAAGA
*
2279 AAAAAGAAGAAAAAAGAAGA
1 AAAAAGAAGAAAAAAAAAGA
2299 AAAAAGAA-AAGAAAAAAAG-
1 AAAAAGAAGAA-AAAAAAAGA
*
2318 AAAAAGAA-AAAAATCAAA-A
1 AAAAAGAAGAAAAA-AAAAGA
*
2337 AAGAAGAAGAAAAAA
1 AAAAAGAAGAAAAAA
2352 TGAAAAATTA
Statistics
Matches: 84, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.04
19 22 0.26
20 41 0.49
21 18 0.21
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.01
Consensus pattern (20 bp):
AAAAAGAAGAAAAAAAAAGA
Found at i:2350 original size:1 final size:1
Alignment explanation
Indices: 2247--2330 Score: 51
Period size: 1 Copynumber: 84.0 Consensus size: 1
2237 GAAAAAGAAG
* * * * * * * * * * *
2247 AAAAAAAAAGAAAAAAAGAAGAAAAAAGAAGAAAAAAGAAGAAAAAAGAAGAAAAAAGAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2312 AAAAAGAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAA
2331 TCAAAAAAGA
Statistics
Matches: 57, Mismatches: 26, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (1 bp):
A
Found at i:2357 original size:20 final size:19
Alignment explanation
Indices: 2220--2358 Score: 126
Period size: 18 Copynumber: 7.3 Consensus size: 19
2210 ATAAGAGCTA
* *
2220 AAAAACAAGAAG-AAGAAG
1 AAAAAGAAGAAGAAAAAAG
*
2238 AAAAAGAAGAAAAAAAAAG
1 AAAAAGAAGAAGAAAAAAG
2257 AAAAA-AAGAAGAAAAAAG
1 AAAAAGAAGAAGAAAAAAG
*
2275 AAGAAAAAAGAAGAAAAAAG
1 AA-AAAGAAGAAGAAAAAAG
*
2295 AAGAA-AA-AAGAAAAGAA-
1 AAAAAGAAGAAGAAAA-AAG
* *
2312 AAAAAGAAAAAGAAAAAAATCA
1 AAAAAGAAGAAG-AAAAAA--G
2334 AAAAAGAAGAAGAAAAAATG
1 AAAAAGAAGAAGAAAAAA-G
2354 AAAAA
1 AAAAA
2359 TTAAAAAAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
17 11 0.11
18 30 0.29
19 20 0.20
20 24 0.24
21 6 0.06
22 11 0.11
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (19 bp):
AAAAAGAAGAAGAAAAAAG
Found at i:5269 original size:24 final size:24
Alignment explanation
Indices: 5242--5290 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5232 TGCATGACAT
5242 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
5266 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
5290 T
1 T
5291 TAGGAAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:9696 original size:2 final size:2
Alignment explanation
Indices: 9691--9721 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9681 ACAGTGTGTG
9691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9722 GTTTATCGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11952 original size:3 final size:3
Alignment explanation
Indices: 11938--11971 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
11928 TTAGTTTTAG
11938 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
11972 ATCATCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:14806 original size:15 final size:15
Alignment explanation
Indices: 14786--14819 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
14776 AATATATATC
14786 ATTTAAAAACCTTTA
1 ATTTAAAAACCTTTA
*
14801 ATTTAAAAACCTTTC
1 ATTTAAAAACCTTTA
14816 ATTT
1 ATTT
14820 CAGTTATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTAAAAACCTTTA
Found at i:19129 original size:19 final size:20
Alignment explanation
Indices: 19084--19126 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
19074 TTTTTTCATG
19084 AAAACAACATAATTAAATCA
1 AAAACAACATAATTAAATCA
*
19104 AAAACAACA-ATTTAGAATCA
1 AAAACAACATAATTA-AATCA
19124 AAA
1 AAA
19127 CAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAACAACATAATTAAATCA
Found at i:19552 original size:21 final size:19
Alignment explanation
Indices: 19524--19567 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 19
19514 TAAAAACCAG
19524 ACCCCATGGAGGGTATCGGT
1 ACCCCAT-GAGGGTATCGGT
19544 ACCCTCATGAGGGTATCGGT
1 ACCC-CATGAGGGTATCGGT
19564 ACCC
1 ACCC
19568 ACTCAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (19 bp):
ACCCCATGAGGGTATCGGT
Found at i:19606 original size:22 final size:21
Alignment explanation
Indices: 19534--19611 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 21
19524 ACCCCATGGA
* *
19534 GGGTATCGGTA-CCCTCATGA
1 GGGTATCGGTACCCCTCAAGG
19554 GGGTATCGGTACCCACTCAAAAGG
1 GGGTATCGGTACCC-CTC--AAGG
19578 GGG-ATCGGTACCCCTTCAAGG
1 GGGTATCGGTACCCC-TCAAGG
*
19599 GGGTATCGATACC
1 GGGTATCGGTACC
19612 TCCTGCACTA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
20 11 0.22
21 9 0.18
22 12 0.24
23 12 0.24
24 5 0.10
ACGTcount: A:0.23, C:0.26, G:0.31, T:0.21
Consensus pattern (21 bp):
GGGTATCGGTACCCCTCAAGG
Found at i:23437 original size:22 final size:21
Alignment explanation
Indices: 23395--23434 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23385 AAGGCCATTT
23395 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
23416 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
23435 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:25114 original size:20 final size:20
Alignment explanation
Indices: 25089--25127 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25079 CATTATAAGA
*
25089 TGGGGGTATCGGTACCCTCT
1 TGGGGGTATCAGTACCCTCT
25109 TGGGGGTATCAGTACCCTC
1 TGGGGGTATCAGTACCCTC
25128 CGAGCAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.33, T:0.28
Consensus pattern (20 bp):
TGGGGGTATCAGTACCCTCT
Found at i:26176 original size:39 final size:39
Alignment explanation
Indices: 26143--26258 Score: 178
Period size: 39 Copynumber: 3.0 Consensus size: 39
26133 GAGGAGTTTG
*
26143 CAGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTA
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTA
* * *
26182 CAATAAAGACTTACCCTGAGCACAAAGCCGAGGAACCTA
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTA
* *
26221 CGGTAAGGACTTACCCTGAACACAAAGCCGAGGAGCCT
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCT
26259 GCGAAAAGTG
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.35, C:0.28, G:0.23, T:0.14
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTA
Found at i:33114 original size:12 final size:12
Alignment explanation
Indices: 33097--33128 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
33087 TCCAGAACCA
33097 TACACCCACCTG
1 TACACCCACCTG
33109 TACACCCACCTG
1 TACACCCACCTG
33121 TACACCCA
1 TACACCCA
33129 GTAAGGGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.50, G:0.06, T:0.16
Consensus pattern (12 bp):
TACACCCACCTG
Found at i:33298 original size:39 final size:39
Alignment explanation
Indices: 33127--33321 Score: 178
Period size: 39 Copynumber: 5.0 Consensus size: 39
33117 CCTGTACACC
* * *
33127 CAGTAAGGGCTTACCCT-ATGCACAAAG-CAGAAGAGCCTG
1 CAGTAAGGACTTACCCTGA-GCACAAAGTC-GAGGAACCTG
* * * * * ** * *
33166 CAGTAAGGTCTTATCATGTGCATAAAGGAGAGGAGCCTA
1 CAGTAAGGACTTACCCTGAGCACAAAGTCGAGGAACCTG
* * * * *
33205 TAGTAAGGACTTACTCTGAGCACAATGTCGAGGAGCCTT
1 CAGTAAGGACTTACCCTGAGCACAAAGTCGAGGAACCTG
* *
33244 CAGTAAGGACTTACCCTGAGCACAAAGCCGAAGAACCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGTCGAGGAACCTG
*
33283 CGGTAAGGACTTACCCTGAGCACAAAGTCGAGGAACCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGTCGAGGAACCTG
33322 AAAAAAAACA
Statistics
Matches: 125, Mismatches: 29, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
39 125 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.18
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGAGCACAAAGTCGAGGAACCTG
Found at i:37839 original size:21 final size:21
Alignment explanation
Indices: 37807--37846 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
37797 AATTGCACAT
*
37807 TACAGAGGGTATCGATACTCC
1 TACAGAGGGTATCAATACTCC
37828 TACAG-GGAGTATCAATACT
1 TACAGAGG-GTATCAATACT
37847 ACCTTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (21 bp):
TACAGAGGGTATCAATACTCC
Found at i:42303 original size:31 final size:29
Alignment explanation
Indices: 42268--42327 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
42258 TCTTTGATCA
*
42268 AATTTTTAAAATATATAAAGATTAAAATATT
1 AATTTTTAAAATACAT-AA-ATTAAAATATT
* *
42299 AATTTTTATAATACATGAATTAAAATATT
1 AATTTTTAAAATACATAAATTAAAATATT
42328 TTTTTAGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 11 0.42
30 1 0.04
31 14 0.54
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (29 bp):
AATTTTTAAAATACATAAATTAAAATATT
Found at i:45657 original size:15 final size:16
Alignment explanation
Indices: 45632--45661 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
45622 AAATATAAAA
45632 TTATATTTTTTATTTT
1 TTATATTTTTTATTTT
45648 TTAT-TTTTTTATTT
1 TTATATTTTTTATTT
45662 CCTTTCGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTATATTTTTTATTTT
Found at i:53944 original size:19 final size:19
Alignment explanation
Indices: 53891--53946 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
53881 TTTAGGCCGA
*
53891 GTCAAAGTCAACAGGTTGG
1 GTCAAAGTCAACAGGTCGG
* * *
53910 GTAAAAGTGAATAGGTCGG
1 GTCAAAGTCAACAGGTCGG
53929 GTCAAAGTCAACAGGTCG
1 GTCAAAGTCAACAGGTCG
53947 AGTTAGGTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (19 bp):
GTCAAAGTCAACAGGTCGG
Found at i:56787 original size:117 final size:117
Alignment explanation
Indices: 56581--56827 Score: 361
Period size: 117 Copynumber: 2.1 Consensus size: 117
56571 GGATAAACCA
* * * * *
56581 ATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGCGGAAAGTTCATAACGAGAAGAACTCATCCGACGAGGAAGAAGAAGTTCAT
* * * *
56646 AATGAGAAGAACTTGTTCAACCTTGGTTTGATTCCATCACAGAA-GGAGGTGG
66 AATGAGAAAAACTGGTTCAACCTTGGCTCGATTCCATCACA-AAGGGAGGTGG
* * *
56698 ATCAACATTTCTAGTGGAAAGTTCATAACGAGAAGAATTCATCCGACGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGCGGAAAGTTCATAACGAGAAGAACTCATCCGACGAGGAAGAAGAAGTTCAT
56763 AATGAGAAAAACTGGTTCAACCTTGGCTCGATTCCATCACAAAGGGAGGTGG
66 AATGAGAAAAACTGGTTCAACCTTGGCTCGATTCCATCACAAAGGGAGGTGG
*
56815 ATCAATATTTCCA
1 ATCAACATTTCCA
56828 TCATAGAGGA
Statistics
Matches: 115, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
116 2 0.02
117 113 0.98
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (117 bp):
ATCAACATTTCCAGCGGAAAGTTCATAACGAGAAGAACTCATCCGACGAGGAAGAAGAAGTTCAT
AATGAGAAAAACTGGTTCAACCTTGGCTCGATTCCATCACAAAGGGAGGTGG
Found at i:57262 original size:4 final size:4
Alignment explanation
Indices: 57253--57286 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
57243 TTCGAACATA
*
57253 AAAT AAAT AATT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
57287 CAAGTTAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:58250 original size:4 final size:4
Alignment explanation
Indices: 58241--58267 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
58231 CGAAAATAAG
58241 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
58268 AATTGCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:58537 original size:2 final size:2
Alignment explanation
Indices: 58532--58564 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
58522 GTAATTAATA
58532 AT AT AT AT AT AT AT AT AT AT 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
58565 GGGGTGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59892 original size:21 final size:21
Alignment explanation
Indices: 59866--59944 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 21
59856 AGGGTGTCAA
*
59866 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATACACCCCTGC
*
59887 AGTGCATCCATACACCCTTGC
1 AGTGCATCCATACACCCCTGC
*
59908 AGTGTATCCATACACCCCTGC
1 AGTGCATCCATACACCCCTGC
* *
59929 ATTGCATCCATGCACC
1 AGTGCATCCATACACC
59945 TGCACTAGTG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.23, C:0.39, G:0.15, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATACACCCCTGC
Found at i:59963 original size:22 final size:24
Alignment explanation
Indices: 59931--59974 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
59921 ACCCCTGCAT
59931 TGCATCCATGCA-CC-TGCACTAG
1 TGCATCCATGCATCCATGCACTAG
*
59953 TGCATCGATGCATCCATGCACT
1 TGCATCCATGCATCCATGCACT
59975 CAAACACCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (24 bp):
TGCATCCATGCATCCATGCACTAG
Found at i:63985 original size:18 final size:18
Alignment explanation
Indices: 63962--64027 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
63952 ATTTCTATAC
63962 ATTTTAATTTAGTCCATA
1 ATTTTAATTTAGTCCATA
* **
63980 ATTTTAATTGA-TTTATTTA
1 ATTTTAATTTAGTCCA--TA
*
63999 ATTATAATTTAGTCCATA
1 ATTTTAATTTAGTCCATA
*
64017 ATTTTATTTTA
1 ATTTTAATTTA
64028 TTTTAGTCCT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
17 2 0.06
18 21 0.58
19 11 0.31
20 2 0.06
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (18 bp):
ATTTTAATTTAGTCCATA
Found at i:66734 original size:21 final size:21
Alignment explanation
Indices: 66702--66741 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
66692 AACTGCACAT
*
66702 TACAGAGGGTATTAATACTCC
1 TACAGAGGGTATCAATACTCC
66723 TACAG-GGAGTATCAATACT
1 TACAGAGG-GTATCAATACT
66742 ACTTTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (21 bp):
TACAGAGGGTATCAATACTCC
Found at i:71197 original size:31 final size:29
Alignment explanation
Indices: 71162--71221 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
71152 TCTTTGATCA
*
71162 AATTTTTAAAATATATAAAGATTAAAATATT
1 AATTTTTAAAATACAT-AA-ATTAAAATATT
* *
71193 AATTTTTATAATACATGAATTAAAATATT
1 AATTTTTAAAATACATAAATTAAAATATT
71222 TTTTTAGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 11 0.42
30 1 0.04
31 14 0.54
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (29 bp):
AATTTTTAAAATACATAAATTAAAATATT
Found at i:75041 original size:18 final size:18
Alignment explanation
Indices: 75018--75083 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
75008 ATTTCTATAC
75018 ATTTTAATTTAGTCCATA
1 ATTTTAATTTAGTCCATA
* **
75036 ATTTTAATTGA-TTTATTTA
1 ATTTTAATTTAGTCCA--TA
*
75055 ATTATAATTTAGTCCATA
1 ATTTTAATTTAGTCCATA
*
75073 ATTTTATTTTA
1 ATTTTAATTTA
75084 TTTTAGTCCT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
17 2 0.06
18 21 0.58
19 11 0.31
20 2 0.06
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (18 bp):
ATTTTAATTTAGTCCATA
Found at i:79306 original size:25 final size:23
Alignment explanation
Indices: 79275--79325 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
79265 GTTTATTACA
* *
79275 TTTTTATTCTATATT-TTTTATT
1 TTTTTATTATTTATTATTTTATT
*
79297 TTTTTATTATTTGTTATTTTATT
1 TTTTTATTATTTATTATTTTATT
79320 TTTTTA
1 TTTTTA
79326 AAATTCGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTTTATTATTTATTATTTTATT
Found at i:89384 original size:2 final size:2
Alignment explanation
Indices: 89377--89409 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
89367 TATTAAACCA
89377 AT AT AT AT AT AT AT AT AT AT 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
89410 ATGAAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89589 original size:15 final size:15
Alignment explanation
Indices: 89569--89598 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
89559 ATAATTATTA
89569 ATCAATGATTAAAAT
1 ATCAATGATTAAAAT
*
89584 ATCAATTATTAAAAT
1 ATCAATGATTAAAAT
89599 TAAGAAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (15 bp):
ATCAATGATTAAAAT
Found at i:90831 original size:3 final size:3
Alignment explanation
Indices: 90823--90897 Score: 80
Period size: 3 Copynumber: 25.0 Consensus size: 3
90813 TATATATATT
* * * *
90823 TAA TAA TAAA TAA TAA TAA TAA T-A TTA TAT TAA TAA TAA TAT TTA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
90868 TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
90898 ACTAAAAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:91339 original size:21 final size:21
Alignment explanation
Indices: 91313--91391 Score: 108
Period size: 21 Copynumber: 3.7 Consensus size: 21
91303 AGGGTGTCAA
91313 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
91334 AGTGCATCCATACACCCCTGC
1 AGTGCATCCATGCACCCCTGC
91355 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCACCCCTG--C
91376 TAGTGCATCCATGCAC
1 -AGTGCATCCATGCAC
91392 TCAAACACCG
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.08
21 34 0.65
22 14 0.27
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:92991 original size:14 final size:14
Alignment explanation
Indices: 92972--93017 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
92962 CGTTCGTGAA
92972 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
92986 CGTTCGTTTATGTT
1 CGTTCGATTATGTT
*
93000 CGTTCGGTTATGTT
1 CGTTCGATTATGTT
93014 CGTT
1 CGTT
93018 TATGTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.52
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:93004 original size:38 final size:39
Alignment explanation
Indices: 92947--93037 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 39
92937 AACATAGGTC
*
92947 TCGTTCGTTCAT-TTACGTTC-GTGAACGTTCGATTATGT
1 TCGTTCGTTTATGTTACGTTCGGT-AACGTTCGATTATGT
* * *
92985 TCGTTCGTTTATGTT-CGTTCGGTTATGTTCGTTTATGT
1 TCGTTCGTTTATGTTACGTTCGGTAACGTTCGATTATGT
* *
93023 TCATTCATTTATGTT
1 TCGTTCGTTTATGTT
93038 TAACCCAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 41 0.91
39 4 0.09
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (39 bp):
TCGTTCGTTTATGTTACGTTCGGTAACGTTCGATTATGT
Found at i:93034 original size:24 final size:24
Alignment explanation
Indices: 92987--93037 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
92977 GATTATGTTC
* *
92987 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
*
93011 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
93035 GTT
1 GTT
93038 TAACCCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCAGTTAT
Found at i:94114 original size:16 final size:16
Alignment explanation
Indices: 94089--94153 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
94079 CCAACGTTTA
*
94089 TGTTCGTTTATGTCCG
1 TGTTCGTTTATGTTCG
*
94105 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
94121 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
**
94137 TGCGCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
94153 T
1 T
94154 TTATTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.08, C:0.15, G:0.25, T:0.52
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:94243 original size:16 final size:16
Alignment explanation
Indices: 94222--94252 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
94212 AAAAAAAAAT
94222 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
94238 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
94253 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:95324 original size:25 final size:24
Alignment explanation
Indices: 95288--95338 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
95278 AAACCATAAG
* *
95288 AAACGTACCACAAGAATAGGAAAAA
1 AAACGTAACACAAAAATA-GAAAAA
*
95313 AAACGTAACACAAAAATATAAAAA
1 AAACGTAACACAAAAATAGAAAAA
95337 AA
1 AA
95339 CATGTCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.67, C:0.14, G:0.10, T:0.10
Consensus pattern (24 bp):
AAACGTAACACAAAAATAGAAAAA
Found at i:97242 original size:18 final size:18
Alignment explanation
Indices: 97219--97284 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
97209 ATTTCTATAC
97219 ATTTTAATTTAGTCCATA
1 ATTTTAATTTAGTCCATA
* **
97237 ATTTTAATTGA-TTTATTTA
1 ATTTTAATTTAGTCCA--TA
*
97256 ATTATAATTTAGTCCATA
1 ATTTTAATTTAGTCCATA
*
97274 ATTTTATTTTA
1 ATTTTAATTTA
97285 TTTTAGTCCT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
17 2 0.06
18 21 0.58
19 11 0.31
20 2 0.06
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (18 bp):
ATTTTAATTTAGTCCATA
Found at i:111500 original size:30 final size:30
Alignment explanation
Indices: 111459--111519 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
111449 ATGCCGAAGG
111459 ACCTATCCATATGTC-CTGAAGAACATAGGT
1 ACCTATCCATATGTCTC-GAAGAACATAGGT
* * *
111489 ACCTGTCCATATGTTTCGAAGGACATAGGT
1 ACCTATCCATATGTCTCGAAGAACATAGGT
111519 A
1 A
111520 ACCCTCGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (30 bp):
ACCTATCCATATGTCTCGAAGAACATAGGT
Done.