Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002282.1 Hibiscus syriacus cultivar Beakdansim tig00004646_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: 60384
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3446 original size:198 final size:199
Alignment explanation
Indices: 3052--3630 Score: 787
Period size: 198 Copynumber: 2.9 Consensus size: 199
3042 CCAATTATTT
* * * * *
3052 AAAAGTATCAACACAAAATAAAAAAGTGTCGCTACATGTTGTAGACCTAGTC-TCTTATAAAATC
1 AAAAGTATCGACACAATATTAAAAAGTGTCGATACATGTTGTAGACCTA-TCTTCTCATAAAATC
*
3116 GGTATATTTTATACCGGTTATATTAAAAAATTACCTA-TACATTATAATTATGGGTTTCGATGTT
65 GGTATA-TTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
* * * * *
3180 TTTGGGATCGACACTTTTTGAAAATGTATTGACACTTTGTGCATTCACCCTTTTTGGCATCCATT
129 TTTGGGATCGACAC-TTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGACATCAATT
3245 CTGGACA
193 CTGGACA
*
3252 TAAAGTATCGACACAATATTAAAAAGTGTCGATACATGTTGTAGACCTATCTATCATCATAAAAT
1 AAAAGTATCGACACAATATTAAAAAGTGTCGATACATGTTGTAGACCTATCT-TC-TCATAAAAT
3317 C-G-ATATTTATACCGG-TATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
64 CGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
*
3379 TTCGGGATCGACACTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGACATCAATTC
129 TTTGGGATCGACACTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGACATCAATTC
3444 TGGACA
194 TGGACA
* * * *
3450 AAAATTATCGACACAATATTAAGAAGTGTCGATACATGTTATAGACTTAT-TCTCTCATAAAA-C
1 AAAAGTATCGACACAATATTAAAAAGTGTCGATACATGTTGTAGACCTATCT-TCTCATAAAATC
* * * * *
3513 TGTATATGTATACTGGTTATATTACAAAATTATCTATTACATT-TAATTATGGGGTTTTGATGTT
65 GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTAT-GGGTTTCGATGTT
* * * *
3577 TTTGGGATCGACACTTTTAATAAATGTATCGAAACTTTAAGCGTGCAACCCTTT
129 TTTGGGATCGACACTTTTGA-AAATGTATCGACACTTTATGCGTTC-ACCCTTT
3631 AGATCGACAC
Statistics
Matches: 341, Mismatches: 28, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
195 1 0.00
196 9 0.03
197 21 0.06
198 170 0.50
199 74 0.22
200 54 0.16
201 3 0.01
202 9 0.03
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (199 bp):
AAAAGTATCGACACAATATTAAAAAGTGTCGATACATGTTGTAGACCTATCTTCTCATAAAATCG
GTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
TGGGATCGACACTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGACATCAATTCTG
GACA
Found at i:6493 original size:172 final size:174
Alignment explanation
Indices: 6172--6575 Score: 544
Period size: 172 Copynumber: 2.3 Consensus size: 174
6162 TTTATTACAC
* * * *
6172 ATACTTATGAAAGTATCGACACTTTCAATATATCTGGTAACGCTTTACTGGTTTTATCATTTCGA
1 ATACTTATAAAAGTATCGACACTTT-AATATATCTGGTAGCGCTTTACCGATTTTATCATTTCGA
* * *
6237 TACTGGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATAAATTTTTATAAAGTATCG
65 TACCGG---T-TCA-ATTTTTACATGTTATATCATTGTGGATCGATAAATTTTTATAAAGTATCG
*
6302 ACACTTTATAGGCGCTAAAACTGATTCTCTTTTAAATTTACAAAGTGTCG
125 ACACTTTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCG
**
6352 ATACTTATAAAAGTATCGACACTTTAATATATCCAGTAGCGCTTTACCGATTTTATCATTTCGAT
1 ATACTTATAAAAGTATCGACACTTTAATATATCTGGTAGCGCTTTACCGATTTTATCATTTCGAT
*
6417 ACCGAG-TC-ATTTTTACATGTTATATCATTGTGG-TCGATACATTTTTATAAAGTATCGACACT
66 ACCG-GTTCAATTTTTACATGTTATATCATTGTGGATCGATAAATTTTTATAAAGTATCGACACT
* * *
6479 TTATAGGTGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTTTCG
130 TTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCG
* * *
6524 ATCCTTATATTAAAGTATCGACACGTTCAATATATCTGGTAGGGCTTTACCG
1 ATACTTATA--AAAGTATCGACAC-TTTAATATATCTGGTAGCGCTTTACCG
6576 GTATTATCTT
Statistics
Matches: 201, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
172 77 0.38
173 23 0.11
174 13 0.06
175 25 0.12
179 38 0.19
180 25 0.12
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.40
Consensus pattern (174 bp):
ATACTTATAAAAGTATCGACACTTTAATATATCTGGTAGCGCTTTACCGATTTTATCATTTCGAT
ACCGGTTCAATTTTTACATGTTATATCATTGTGGATCGATAAATTTTTATAAAGTATCGACACTT
TATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCG
Found at i:13729 original size:16 final size:16
Alignment explanation
Indices: 13708--13746 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
13698 TTCAATATCA
13708 AAAATCAAATTTCCAT
1 AAAATCAAATTTCCAT
13724 AAAATCAAATTTCCAT
1 AAAATCAAATTTCCAT
13740 AAAATCA
1 AAAATCA
13747 TTTTACTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATCAAATTTCCAT
Found at i:14044 original size:33 final size:33
Alignment explanation
Indices: 14007--14073 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
13997 ACCGTAGTGC
14007 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
14040 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
14073 T
1 T
14074 CTGTACTAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTCGTGTCCACCA
Found at i:24095 original size:2 final size:2
Alignment explanation
Indices: 24088--24115 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24078 AATGAAGTAA
24088 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
24116 TAAACAAGAT
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:24326 original size:3 final size:3
Alignment explanation
Indices: 24318--24386 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
24308 AAAATAAAAT
* * *
24318 TAA TAA TAA TAA T-C TAT TAA TAA TAA TAA TAA T-A TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
24364 T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
24387 ATAAATAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
2 5 0.09
3 53 0.91
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:24378 original size:14 final size:14
Alignment explanation
Indices: 24337--24386 Score: 82
Period size: 14 Copynumber: 3.5 Consensus size: 14
24327 TAATCTATTA
24337 ATAATAATAATAAT
1 ATAATAATAATAAT
*
24351 ATAATAATACTAAT
1 ATAATAATAATAAT
24365 ATAATAATAATAAT
1 ATAATAATAATAAT
24379 AATAATAA
1 -ATAATAA
24387 ATAAATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
14 26 0.79
15 7 0.21
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:24382 original size:17 final size:17
Alignment explanation
Indices: 24310--24390 Score: 91
Period size: 17 Copynumber: 4.9 Consensus size: 17
24300 TTTCAAGAAA
24310 AATAA-AAT-TAATAAT
1 AATAATAATATAATAAT
*
24325 AATAAT-CTATTAATAAT
1 AATAATAATA-TAATAAT
24342 AATAATAATATAATAAT
1 AATAATAATATAATAAT
*
24359 ACTAAT-ATAATAATAAT
1 AATAATAAT-ATAATAAT
24376 AATAATAATA-AATAA
1 AATAATAATATAATAA
24391 ATAAAAAAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.11
16 7 0.12
17 39 0.70
18 4 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAATAATATAATAAT
Found at i:24394 original size:20 final size:19
Alignment explanation
Indices: 24309--24390 Score: 89
Period size: 20 Copynumber: 4.3 Consensus size: 19
24299 ATTTCAAGAA
24309 AAATAA-AATTAATAATAAT
1 AAATAATAA-TAATAATAAT
* *
24328 AATCTATTAATAATAATAAT
1 AA-ATAATAATAATAATAAT
*
24348 -AAT-ATAATAATACTAAT
1 AAATAATAATAATAATAAT
24365 ATAATAATAATAATAATAAT
1 A-AATAATAATAATAATAAT
24385 AAATAA
1 AAATAA
24391 ATAAAAAAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 12 0.23
18 1 0.02
19 11 0.21
20 26 0.50
21 2 0.04
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATAATAATAATAATAAT
Found at i:26232 original size:6 final size:6
Alignment explanation
Indices: 26221--26295 Score: 84
Period size: 6 Copynumber: 13.0 Consensus size: 6
26211 TAATTATTAT
*
26221 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA ATAATA TT--TA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
* * * *
26267 -TAATA ATAATA TTTATA ATAATA ATAATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA
26296 ATTTTAAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
3 1 0.02
4 2 0.03
5 2 0.03
6 55 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TTAATA
Found at i:26244 original size:18 final size:18
Alignment explanation
Indices: 26222--26295 Score: 100
Period size: 18 Copynumber: 4.3 Consensus size: 18
26212 AATTATTATT
*
26222 TAATATTAATATTAATAT
1 TAATATTAATATTAATAA
26240 TAATATTAATATTAATAA
1 TAATATTAATATTAATAA
26258 TAATATT--TA-TAATAA
1 TAATATTAATATTAATAA
* *
26273 TAATATTTATAATAATAA
1 TAATATTAATATTAATAA
26291 TAATA
1 TAATA
26296 ATTTTAAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
15 13 0.25
16 2 0.04
17 2 0.04
18 35 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATTAATATTAATAA
Found at i:26270 original size:15 final size:15
Alignment explanation
Indices: 26252--26292 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
26242 ATATTAATAT
26252 TAATAATAATATTTA
1 TAATAATAATATTTA
26267 TAATAATAATATTTA
1 TAATAATAATATTTA
26282 TAATAATAATA
1 TAATAATAATA
26293 ATAATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATAATAATATTTA
Found at i:26296 original size:12 final size:12
Alignment explanation
Indices: 26222--26308 Score: 93
Period size: 12 Copynumber: 7.2 Consensus size: 12
26212 AATTATTATT
*
26222 TAATATTAATAT
1 TAATATTAATAA
*
26234 TAATATTAATAT
1 TAATATTAATAA
26246 TAATATTAATAA
1 TAATATTAATAA
*
26258 TAATATTTATAA
1 TAATATTAATAA
* * *
26270 TAATAATATTTA
1 TAATATTAATAA
*
26282 TAATAATAATAA
1 TAATATTAATAA
* *
26294 TAATTTTAAAAA
1 TAATATTAATAA
26306 TAA
1 TAA
26309 AATGAAAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 64 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:26307 original size:18 final size:18
Alignment explanation
Indices: 26222--26308 Score: 88
Period size: 18 Copynumber: 4.8 Consensus size: 18
26212 AATTATTATT
* * *
26222 TAATATTAATATTAATAT
1 TAATTTTAATAATAATAA
* *
26240 TAATATTAATATTAATAA
1 TAATTTTAATAATAATAA
26258 TAATATTT-ATAATAATAA
1 TAAT-TTTAATAATAATAA
26276 T-ATTTATAATAATAATAA
1 TAATTT-TAATAATAATAA
*
26294 TAATTTTAAAAATAA
1 TAATTTTAATAATAA
26309 AATGAAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
16 2 0.03
17 3 0.05
18 50 0.82
19 6 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATTTTAATAATAATAA
Found at i:26706 original size:48 final size:45
Alignment explanation
Indices: 26500--27043 Score: 730
Period size: 45 Copynumber: 11.8 Consensus size: 45
26490 TAAAATATCA
* * * **
26500 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * *
26545 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCAAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
26590 TTTGAAAACATTATGCACTGAAGGTCTTACAGATGACCCGAAGGCTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG--T
* * *
26637 TTTGAAAACATCATGCACTGAAGGTCTTACGGATGACCTGAAGGCTTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG---T
* * *
26685 TTTGAAAACATCCTGCACTGAAGGTCTTACA-AGTGACTCGAAGGCTTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGA-TGACCCGAAGG---T
* * *
26733 TTTGAAAACATCCTGAACTGAAGGTCTTACAGATGACCCGAAGGTTTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG---T
*
26781 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG---T
*
26829 TTTGAAAACATCATGCACTGAAGGGCATACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
26874 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
26919 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
26964 TTTGAAAATATCATGCACTGAAGGGATTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
27009 TTTGAAAAAATCATGCACTGAAGGGCTTACAGATG
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
27044 TGGGAAATAG
Statistics
Matches: 465, Mismatches: 29, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
45 248 0.53
47 43 0.09
48 173 0.37
49 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
Found at i:27790 original size:22 final size:22
Alignment explanation
Indices: 27713--27791 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 22
27703 AATAAGGCTT
* * *
27713 TCATATTTGAAAAGAGATTCAA
1 TCATATTTGAAGAGAGAATCTA
* *
27735 TCATCTTTAAAGAGAGAATCTA
1 TCATATTTGAAGAGAGAATCTA
*
27757 CCATATTTGAAGAGAGAATCTA
1 TCATATTTGAAGAGAGAATCTA
*
27779 TCATCTTTGAAGA
1 TCATATTTGAAGA
27792 ATGTAGATGT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (22 bp):
TCATATTTGAAGAGAGAATCTA
Found at i:29219 original size:75 final size:75
Alignment explanation
Indices: 29063--29311 Score: 253
Period size: 75 Copynumber: 3.4 Consensus size: 75
29053 CATAATGATG
* * * * * * *
29063 TGGGCCTTCAGCATGCCTCAGCATTTACTGATATGAACATTCAAAATG-----TTATTCTAATTT
1 TGGGCTTTCAGCATACCCCAGCATTTGCTGACATGAACATTCAAAATGCACCAATATTCCAATTT
29123 CTGATTGAAA
66 CTGATTGAAA
* *
29133 TGGGCTTTCAGCATGCCCCAGCATTTGCTGATACA-G-ACGTTCAAAATGCACCAATATTCCAAT
1 TGGGCTTTCAGCATACCCCAGCATTTGCTG--ACATGAACATTCAAAATGCACCAATATTCCAAT
29196 TTCTGATTGAAA
64 TTCTGATTGAAA
* * * ** * *
29208 TGGGCTTTCAGCATACCCCAGTATTTGTTGACATGAACATTCAATATGCGTCGATATTCCTGA-T
1 TGGGCTTTCAGCATACCCCAGCATTTGCTGACATGAACATTCAAAATGCACCAATATTCC-AATT
*
29272 TATGATTGAAA
65 TCTGATTGAAA
*
29283 TGGGCTTTCAGCATACCCCATCATTTGCT
1 TGGGCTTTCAGCATACCCCAGCATTTGCT
29312 TCTTGTTGAT
Statistics
Matches: 149, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
70 38 0.26
71 1 0.01
72 2 0.01
73 3 0.02
74 1 0.01
75 103 0.69
76 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (75 bp):
TGGGCTTTCAGCATACCCCAGCATTTGCTGACATGAACATTCAAAATGCACCAATATTCCAATTT
CTGATTGAAA
Found at i:32436 original size:72 final size:72
Alignment explanation
Indices: 32317--32452 Score: 236
Period size: 72 Copynumber: 1.9 Consensus size: 72
32307 GTATAATAAG
32317 TTAGCTGAATATTATCCATAAAGCCAGGGCAATTAACCAATTACTTTAGGGGGATAACTCAAGCA
1 TTAGCTGAATATTATCCATAAAGCCAGGGCAATTAACCAATTACTTTAGGGGGATAACTCAAGCA
32382 TAACAGA
66 TAACAGA
* * * *
32389 TTAGCTGAATATTATCCATAAAGTCGGGGCTATTAACCAATTGCTTTAGGGGGATAACTCAAGC
1 TTAGCTGAATATTATCCATAAAGCCAGGGCAATTAACCAATTACTTTAGGGGGATAACTCAAGC
32453 TTTATTTTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (72 bp):
TTAGCTGAATATTATCCATAAAGCCAGGGCAATTAACCAATTACTTTAGGGGGATAACTCAAGCA
TAACAGA
Found at i:37470 original size:2 final size:2
Alignment explanation
Indices: 37465--37599 Score: 207
Period size: 2 Copynumber: 67.5 Consensus size: 2
37455 CATATGCGTG
* *
37465 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
37507 TA TA TA TA TG TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
37549 CA TG TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37591 TA TA TA TA T
1 TA TA TA TA T
37600 GTGTGTGTGT
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 119 1.00
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:37838 original size:3 final size:3
Alignment explanation
Indices: 37832--37886 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
37822 AAAACAAAAT
* *
37832 TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAC TAA T-A TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
37878 TAA TAA TAA
1 TAA TAA TAA
37887 ATAAAAAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:37862 original size:23 final size:23
Alignment explanation
Indices: 37827--37886 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
37817 CAAAAAAAAC
*
37827 AAAATTAATAATAATAATATAAT
1 AAAAATAATAATAATAATATAAT
* *
37850 AATAATAATAATACTAATATAAT
1 AAAAATAATAATAATAATATAAT
37873 AAAAATAATAATAA
1 AAAAATAATAATAA
37887 ATAAAAAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAAATAATAATAATAATATAAT
Found at i:37893 original size:17 final size:17
Alignment explanation
Indices: 37836--37894 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 17
37826 CAAAATTAAT
37836 AATAATAATATAATAATAA
1 AATAATAATA-AATAA-AA
*
37855 TAATAATACTAATATAATAAA
1 -AATAATAATAA-AT-A-AAA
37876 AATAATAATAAATAAAA
1 AATAATAATAAATAAAA
37893 AA
1 AA
37895 GACAAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 5 0.15
18 1 0.03
19 3 0.09
20 21 0.62
21 3 0.09
22 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAATAATAAATAAAA
Found at i:38335 original size:14 final size:13
Alignment explanation
Indices: 38310--38374 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
38300 GGGTATAAAA
*
38310 AAAATACTAAATT
1 AAAATATTAAATT
38323 AAAATATTGAAA-T
1 AAAATATT-AAATT
38336 -AAA-ATT--ATT
1 AAAATATTAAATT
* *
38345 AAAGTACTAAATT
1 AAAATATTAAATT
38358 AAAATATTGAAATT
1 AAAATATT-AAATT
38372 AAA
1 AAA
38375 GGGGTAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 13
0.69 0.09 0.22
Matches are distributed among these distances:
8 1 0.03
9 1 0.03
10 2 0.05
11 5 0.12
12 3 0.08
13 17 0.43
14 11 0.28
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (13 bp):
AAAATATTAAATT
Found at i:39722 original size:3 final size:3
Alignment explanation
Indices: 39716--39773 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
39706 ATATTAAAAT
* * * *
39716 TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAT TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39764 TAA TAA TAA T
1 TAA TAA TAA T
39774 TTTAAAAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:40040 original size:45 final size:45
Alignment explanation
Indices: 39976--40662 Score: 836
Period size: 45 Copynumber: 14.8 Consensus size: 45
39966 TAAAATATCA
* * **
39976 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
* *
40021 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCAAAGGT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
*
40066 TTTGAAAACATTATGCACTGAAGGTCTTACAGATGACCCGAAGGCTT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGG--T
* * * * *
40113 TTTGAAAACATCCTACACTGAAGGTCTTACGGATGACCTGAAAGCTTT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCG-AAG--GT
* *
40161 TTTGAAAACATCCTGCACTGAAGGTCTTACA-AGTGACTCGAAGGCTTT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGA-TGACCCGAAGG---T
* * *
40209 TTTGAAAACATCCTGAACTGAAGGTCTTACAGATGACCCGAATGTTTTT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAA-G---GT
* * *
40258 TTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCAAAGGTTTT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGG---T
* *
40306 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGGAGGCTT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGG--T
* *
40353 TTTGAAAACATCATGCACTGAAGGTCTTACGGATGACCTGAAGGCTTT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGG---T
* *
40401 TTTGAAAACATCCTGCAGTGAAGGTCTTACAGATGACCCGAAGGTTTT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGG---T
*
40449 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
*
40494 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
* *
40539 TTTGAAAATATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
* * **
40584 TTTGAAAAAATCATGCACTGAAGGGCTTACAGATGACTTGAAGGT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
*
40629 TTTGAAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCATGCACTGAAGGTCTTACAGAT
40663 ATGGGAAATA
Statistics
Matches: 575, Mismatches: 49, Indels: 36
0.87 0.07 0.05
Matches are distributed among these distances:
45 247 0.43
47 82 0.14
48 206 0.36
49 40 0.07
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
Found at i:40392 original size:240 final size:234
Alignment explanation
Indices: 39976--40659 Score: 1004
Period size: 240 Copynumber: 2.9 Consensus size: 234
39966 TAAAATATCA
* ** *
39976 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCCTGCACTG
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTG
* * *
40041 AAGGTCTTACAGATGACCCAAAGGTTTTGAAAACATTATGCACTGAAGGTCTTACAGATGACCCG
66 AAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
* *
40106 AAGGCTTTTTGAAAACATCCTACACTGAAGGTCTTACGGATGACCTGAAAGCTTTTTTGAAAACA
131 AAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACGGATGACCTGAAAGCTTTTTTGAAAACA
*
40171 TCCTGCACTGAAGGTCTTACAAG-TGACTCGAAGGCTTT
196 TCCTGCACTGAAGGTCTTACAAGATGACCCGAAGGCTTT
* *
40209 TTTGAAAACATCCTGAACTGAAGGTCTTACAGATGACCCGAATGTTTTTTTTGAAAACATCATGC
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAA-G---GTTTTGAAAACATCATGC
*
40274 ATTGAAGGGCTTACAGATGACCCAAAGGTTTTTTTGAAAACATCATGCACTGAAGGGCTTACAGA
62 ACTGAAGGGCTTACAGATGACCCAAAGG---TTTTGAAAACATCATGCACTGAAGGGCTTACAGA
* *
40339 TGACCCGGAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACGGATGACCTGAAGGCTTTTTT
124 TGACCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACGGATGACCTGAAAGCTTTTTT
* *
40404 GAAAACATCCTGCAGTGAAGGTCTTAC-AGATGACCCGAAGGTTTT
189 GAAAACATCCTGCACTGAAGGTCTTACAAGATGACCCGAAGGCTTT
* *
40449 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTG
1 TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTG
* *
40514 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCATGCACTGAAGGGCTTACAGATGACCCG
66 AAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
* * * * *
40579 AAGG--TTTTGAAAAAATCATGCACTGAAGGGCTTACAGATGACTTG-AAG--GTTTTGAAAACA
131 AAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACGGATGACCTGAAAGCTTTTTTGAAAACA
* *
40639 TCATGCACTGAAGGGCTTACA
196 TCCTGCACTGAAGGTCTTACA
40660 GATATGGGAA
Statistics
Matches: 408, Mismatches: 34, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
228 28 0.07
230 2 0.00
231 37 0.09
233 81 0.20
234 1 0.00
236 43 0.11
237 42 0.10
239 3 0.01
240 171 0.42
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (234 bp):
TTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTG
AAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
AAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACGGATGACCTGAAAGCTTTTTTGAAAACA
TCCTGCACTGAAGGTCTTACAAGATGACCCGAAGGCTTT
Found at i:41392 original size:22 final size:22
Alignment explanation
Indices: 41334--41411 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 22
41324 AATAAGGCTT
* *
41334 TCATATTTGAAAAGAGAATCAA
1 TCATATTTGAAGAGAGAATCTA
* *
41356 TAAT-TTTAAAGAGAGAATCTA
1 TCATATTTGAAGAGAGAATCTA
*
41377 CCATATTTGAAGAGAGAATCTA
1 TCATATTTGAAGAGAGAATCTA
*
41399 TCATCTTTGAAGA
1 TCATATTTGAAGA
41412 ATGTAGATGT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
21 16 0.35
22 30 0.65
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (22 bp):
TCATATTTGAAGAGAGAATCTA
Found at i:42839 original size:75 final size:75
Alignment explanation
Indices: 42684--42932 Score: 235
Period size: 75 Copynumber: 3.4 Consensus size: 75
42674 CATAATGATG
* * ** * * *
42684 TGGGCCTTCAGCATGCCCCAGCTTTTATTGATATGAACATTCAAAATG-----TTATTCTAATTT
1 TGGGCTTTCAGCATGCCCCAGCATTTGCTGACATGAACATTCAAAATGCACCAATATTCCAATTT
42744 CTGATTGAAA
66 CTGATTGAAA
**
42754 TGGGCTTTCAGCATGCCCCAGCATTTGCTGATACA-G-ATGTTCAAAATGCACCAATATTCCAAT
1 TGGGCTTTCAGCATGCCCCAGCATTTGCTG--ACATGAACATTCAAAATGCACCAATATTCCAAT
*
42817 TTCTGATTGAAT
64 TTCTGATTGAAA
* * * ** * *
42829 TGGGCTTTCAGCATGCTCCAGTATTTGTTGACATGAACATTCAAAATGCGTCGATATTCCTGA-T
1 TGGGCTTTCAGCATGCCCCAGCATTTGCTGACATGAACATTCAAAATGCACCAATATTCC-AATT
*
42893 TATGATTGAAA
65 TCTGATTGAAA
* *
42904 TGGGCTTTCAGCATACCCCATCATTTGCT
1 TGGGCTTTCAGCATGCCCCAGCATTTGCT
42933 TCTTGTTGAT
Statistics
Matches: 143, Mismatches: 26, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
70 36 0.25
71 1 0.01
72 2 0.01
73 3 0.02
74 1 0.01
75 99 0.69
76 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (75 bp):
TGGGCTTTCAGCATGCCCCAGCATTTGCTGACATGAACATTCAAAATGCACCAATATTCCAATTT
CTGATTGAAA
Found at i:46024 original size:72 final size:72
Alignment explanation
Indices: 45938--46072 Score: 234
Period size: 72 Copynumber: 1.9 Consensus size: 72
45928 GTATAATAAG
45938 TTAGCTGAATATTATCCATAAAGCCAGGGCAATTAACCAATTACTTTAGGGGGATAACTCAAGAA
1 TTAGCTGAATATTATCCATAAAGCCAGGGCAATTAACCAATTACTTTAGGGGGATAACTCAAGAA
46003 TAACATA
66 TAACATA
* * * *
46010 TTAGCTGAATATTATCCATAAAGTCGGGGCTATTAACCAATTGCTTTAGGGGGATAACTCAAG
1 TTAGCTGAATATTATCCATAAAGCCAGGGCAATTAACCAATTACTTTAGGGGGATAACTCAAG
46073 CTTTATTTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28
Consensus pattern (72 bp):
TTAGCTGAATATTATCCATAAAGCCAGGGCAATTAACCAATTACTTTAGGGGGATAACTCAAGAA
TAACATA
Found at i:51491 original size:3 final size:3
Alignment explanation
Indices: 51483--51549 Score: 84
Period size: 3 Copynumber: 23.0 Consensus size: 3
51473 AAAACAAAAT
* * *
51483 TAA TAA TAA TAA T-C TAT TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
51530 T-A TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
51550 ATAAAAAAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 3 0.05
3 52 0.95
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:51524 original size:29 final size:29
Alignment explanation
Indices: 51478--51549 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
51468 CAAGAAAAAC
* *
51478 AAAATTAATAATAATAAT-CTATTAATAAT
1 AAAAATAATAATAATAATACTAAT-ATAAT
*
51507 AATAATAATAATAATAATACTAATATAAT
1 AAAAATAATAATAATAATACTAATATAAT
51536 AAAAATAATAATAA
1 AAAAATAATAATAA
51550 ATAAAAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 34 0.89
30 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAAATAATAATAATAATACTAATATAAT
Found at i:53361 original size:3 final size:3
Alignment explanation
Indices: 53355--53394 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
53345 AATTATTATT
* * *
53355 TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAG TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
53395 TTTAAAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:58686 original size:21 final size:23
Alignment explanation
Indices: 58661--58704 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
58651 ACATCTAATA
*
58661 AACAATAGCAAA-AGT-GGAAAT
1 AACAACAGCAAACAGTGGGAAAT
*
58682 AACAACAGTAAACAGTGGGAAAT
1 AACAACAGCAAACAGTGGGAAAT
58705 GGACAACTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 3 0.16
23 6 0.32
ACGTcount: A:0.55, C:0.11, G:0.20, T:0.14
Consensus pattern (23 bp):
AACAACAGCAAACAGTGGGAAAT
Done.