Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007986.1 Hibiscus syriacus cultivar Beakdansim tig00110431_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: 45923
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:783 original size:3 final size:3
Alignment explanation
Indices: 775--849 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
765 TGAAGCTGAC
* * * ** * *
775 GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
823 GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
850 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:2472 original size:22 final size:23
Alignment explanation
Indices: 2439--2481 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2429 AACCGGTATA
2439 AAAATGTGTCGATACCTTTTTAT
1 AAAATGTGTCGATACCTTTTTAT
*
2462 AAAA-GTGTCGATACTTTTTT
1 AAAATGTGTCGATACCTTTTT
2482 CACTGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (23 bp):
AAAATGTGTCGATACCTTTTTAT
Found at i:5624 original size:23 final size:23
Alignment explanation
Indices: 5598--5661 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
5588 AATAGGTAAC
*
5598 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
5621 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
5644 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5662 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:5668 original size:23 final size:23
Alignment explanation
Indices: 5598--5670 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
5588 AATAGGTAAC
* **
5598 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
5621 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
5644 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
5667 ATAT
1 ATAT
5671 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:6058 original size:23 final size:23
Alignment explanation
Indices: 6027--6090 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
6017 ATAGGTAAAC
*
6027 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
6050 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
6073 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
6091 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:6097 original size:23 final size:23
Alignment explanation
Indices: 6027--6099 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
6017 ATAGGTAAAC
* **
6027 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
6050 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
6073 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
6096 ATAT
1 ATAT
6100 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:6487 original size:23 final size:23
Alignment explanation
Indices: 6456--6519 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
6446 ATAGGTAAAC
*
6456 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
6479 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
6502 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
6520 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:6526 original size:23 final size:23
Alignment explanation
Indices: 6456--6528 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
6446 ATAGGTAAAC
* **
6456 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
6479 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
6502 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
6525 ATAT
1 ATAT
6529 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:6913 original size:23 final size:23
Alignment explanation
Indices: 6882--6945 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
6872 ATAGGTAAAC
*
6882 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
6905 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
6928 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
6946 TGGTTATATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:6952 original size:23 final size:23
Alignment explanation
Indices: 6882--6954 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
6872 ATAGGTAAAC
* **
6882 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
6905 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
6928 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
6951 ATAT
1 ATAT
6955 GTAAAGTGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:7149 original size:426 final size:429
Alignment explanation
Indices: 5500--7187 Score: 3205
Period size: 429 Copynumber: 3.9 Consensus size: 429
5490 AATTCGCAGT
5500 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
5565 AAAAGTATGGACACTTTCAATATAATAGGT-AACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
5629 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
*
5694 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCCTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
*
5759 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTCTTACGTTACGATATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACG--ATATATTATT
*
5824 ATTAAATTAAAAATTCTAAATATTATTTTATAAAATAT-AAAACAATCAAATAATTTTTTGTGCA
324 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
5888 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
389 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
5929 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
5993 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
6058 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
6123 AAAAGTGTCCATACTTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTT
196 AAAAGTGTCCATAC-TTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTT
*
6188 TAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATA-TATTA
260 TAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATTATTA
6252 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAA
325 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAA
6317 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
390 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
6357 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
6422 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
6487 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
6552 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
* *
6617 AAGATATTAATTTAGTAATTATAGACGTCTAATGATTTATTTTTTACGTTACGGTATATTATTAT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATTATTAT
6682 TAAATT-AAAATTCTAAATAATATTTTAT-AAATATAAAAACAATCAAATAATTTTTTGTGCAAA
326 TAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAA
6745 TGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 TGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
6784 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
6848 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
6913 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATA-TGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
6977 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
*
7042 AAGATATTAATTTAGTAATTATAGGCGTATAATGATTTATTTTTTACGTTACGATATA-TATTAT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATTATTAT
* *
7106 TAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAA
326 TAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAA
7171 TGAAATTATTAAATCAA
391 TGAAATTATTAAATCAA
7188 ATAATTCAAA
Statistics
Matches: 1242, Mismatches: 10, Indels: 17
0.98 0.01 0.01
Matches are distributed among these distances:
424 12 0.01
425 164 0.13
426 213 0.17
427 123 0.10
428 295 0.24
429 333 0.27
430 102 0.08
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (429 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATTATTAT
TAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAA
TGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:7268 original size:24 final size:25
Alignment explanation
Indices: 7219--7268 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
7209 ACAACAAATC
*
7219 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
7244 AATTGAACATTGTTAT-GGTACATT
1 AATTAAACATTGTTATGGGTACATT
7268 A
1 A
7269 TTTGGATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:7537 original size:18 final size:18
Alignment explanation
Indices: 7516--7552 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7506 GTAATTGGAG
7516 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
7534 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
7552 T
1 T
7553 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:7560 original size:24 final size:24
Alignment explanation
Indices: 7508--7554 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
7498 TTTCATATGT
* *
7508 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
7532 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
7555 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:7858 original size:39 final size:39
Alignment explanation
Indices: 7814--7932 Score: 220
Period size: 39 Copynumber: 3.1 Consensus size: 39
7804 GATGCTCATC
* *
7814 AAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATCA
1 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATCA
7853 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATCA
1 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATCA
7892 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATCA
1 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATCA
7931 AA
1 AA
7933 TCTACAACTT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (39 bp):
AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATCA
Found at i:8382 original size:21 final size:23
Alignment explanation
Indices: 8332--8393 Score: 83
Period size: 21 Copynumber: 2.8 Consensus size: 23
8322 AATAGGTAAC
*
8332 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* *
8355 ATATAATGTAATAGGTA-TCGTT
1 ATATAATGTAATAGGTAGCCCTT
8377 -TATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
8394 TGGTTATATG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.46
22 3 0.09
23 16 0.46
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:8400 original size:21 final size:21
Alignment explanation
Indices: 8356--8406 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
8346 GTAGCCCTTA
*
8356 TATAATGTAATAGGTATCGTT
1 TATAATGTAATAGGTATCGGT
8377 TATAATGTAATAGGTAGT-GGT
1 TATAATGTAATAGGTA-TCGGT
8398 TAT-ATGTAA
1 TATAATGTAA
8407 AGTGTCTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 6 0.21
21 21 0.75
22 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (21 bp):
TATAATGTAATAGGTATCGGT
Found at i:8439 original size:19 final size:19
Alignment explanation
Indices: 8404--8440 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8394 TGGTTATATG
* *
8404 TAAAGTGTCTATCCTTTTA
1 TAAAGTGTCCATACTTTTA
8423 TAAAGTGTCCATACTTTT
1 TAAAGTGTCCATACTTTT
8441 TTCACTGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (19 bp):
TAAAGTGTCCATACTTTTA
Found at i:11622 original size:16 final size:17
Alignment explanation
Indices: 11588--11625 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
11578 AAGGTTCATT
11588 TTTTATATATAATTATA
1 TTTTATATATAATTATA
11605 TTTTATA-A-AATATATA
1 TTTTATATATAAT-TATA
11621 TTTTA
1 TTTTA
11626 GATAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 10 0.50
17 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATATATAATTATA
Found at i:11632 original size:16 final size:16
Alignment explanation
Indices: 11596--11633 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
11586 TTTTTTATAT
*
11596 ATAAT-TATATTTTAT
1 ATAATATATATTTTAG
*
11611 AAAATATATATTTTAG
1 ATAATATATATTTTAG
11627 ATAATAT
1 ATAATAT
11634 TAATAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATAATATATATTTTAG
Found at i:13183 original size:23 final size:23
Alignment explanation
Indices: 13153--13203 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
13143 AATATCGTCC
13153 AATATTCATAGTGAATCTATTCA
1 AATATTCATAGTGAATCTATTCA
13176 AATATTCATAGTGAATCTATTCA
1 AATATTCATAGTGAATCTATTCA
13199 AATAT
1 AATAT
13204 CCAATTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (23 bp):
AATATTCATAGTGAATCTATTCA
Found at i:25498 original size:2 final size:2
Alignment explanation
Indices: 25491--25518 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25481 TAATAAATTC
25491 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
25519 TTTGTTCGGA
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:30950 original size:29 final size:29
Alignment explanation
Indices: 30904--30988 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 29
30894 TAGTTTTCTG
* *
30904 GAAA-TTGAATTTTAAAAAATGAATTACT
1 GAAATTTGAATTATGAAAAATGAATTACT
30932 GAAATTTGAATTATGAAAAATGAATTACT
1 GAAATTTGAATTATGAAAAATGAATTACT
* *
30961 GAAATTTGAATTCTGGAAAATGAATTAC
1 GAAATTTGAATTATGAAAAATGAATTAC
30989 ATTTATGGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 4 0.08
29 48 0.92
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (29 bp):
GAAATTTGAATTATGAAAAATGAATTACT
Found at i:30955 original size:14 final size:15
Alignment explanation
Indices: 30918--30988 Score: 83
Period size: 14 Copynumber: 4.9 Consensus size: 15
30908 TTGAATTTTA
30918 AAAAATGAATTACTG
1 AAAAATGAATTACTG
**
30933 AAATTTGAATTA-TG
1 AAAAATGAATTACTG
30947 AAAAATGAATTACTG
1 AAAAATGAATTACTG
**
30962 AAATTTGAATT-CTG
1 AAAAATGAATTACTG
*
30976 GAAAATGAATTAC
1 AAAAATGAATTAC
30989 ATTTATGGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
14 23 0.51
15 22 0.49
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.32
Consensus pattern (15 bp):
AAAAATGAATTACTG
Found at i:30979 original size:15 final size:15
Alignment explanation
Indices: 30923--30972 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
30913 TTTTAAAAAA
30923 TGAATTACTGAAATT
1 TGAATTACTGAAATT
**
30938 TGAATTA-TGAAAAA
1 TGAATTACTGAAATT
30952 TGAATTACTGAAATT
1 TGAATTACTGAAATT
30967 TGAATT
1 TGAATT
30973 CTGGAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:31015 original size:34 final size:34
Alignment explanation
Indices: 30977--31060 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
30967 TGAATTCTGG
30977 AAAATGAATTACATTTATGGAAAACGTTTTCCGT
1 AAAATGAATTACATTTATGGAAAACGTTTTCCGT
31011 AAAATGAATTACATTTATGGAAAACGTTTTCCGT
1 AAAATGAATTACATTTATGGAAAACGTTTTCCGT
*
31045 AGAATGAATTACATTT
1 AAAATGAATTACATTT
31061 TTCTGGAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (34 bp):
AAAATGAATTACATTTATGGAAAACGTTTTCCGT
Found at i:31323 original size:31 final size:29
Alignment explanation
Indices: 31255--31386 Score: 81
Period size: 31 Copynumber: 4.4 Consensus size: 29
31245 AATATTATTT
*
31255 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
31285 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
* * * * * *
31318 TTATATTAATTATTTATTAAAGTAATAGT-G
1 TTATATT--TTATTAATAAAAATATTAATAA
* *
31348 TTATATTTTATT-TTAAAAATATTAATTA
1 TTATATTTTATTAATAAAAATATTAATAA
*
31376 GTATATTTTAT
1 TTATATTTTAT
31387 ATATCCTTAT
Statistics
Matches: 79, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
27 9 0.11
28 15 0.19
30 8 0.10
31 22 0.28
32 6 0.08
33 19 0.24
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:31372 original size:91 final size:87
Alignment explanation
Indices: 31216--31386 Score: 211
Period size: 89 Copynumber: 1.9 Consensus size: 87
31206 TATTATTTTT
* * * *
31216 AAAATATTAAAATAATTTATTTATTATTAAATATTATTTTTATAATTTTATTAATAAAAATATTA
1 AAAATATTAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTTTATTAATAAAAATATT-
*
31281 ATATTGGTATATTTTATTGAAATA
65 A-ATTAGTATATTTTATTGAAATA
* *
31305 AAAATATTATAAATTATATTAATTATTTATTAAAGTAATAGTGTTAT-ATTTTATT-TTAAAAAT
1 AAAATATTA-AAATAAT-TTAATTA-TTATTAAA-TAATAGTGTTATAATTTTATTAATAAAAAT
31368 ATTAATTAGTATATTTTAT
62 ATTAATTAGTATATTTTAT
31387 ATATCCTTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
89 23 0.32
90 7 0.10
91 16 0.23
92 16 0.23
93 9 0.13
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (87 bp):
AAAATATTAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTTTATTAATAAAAATATTA
ATTAGTATATTTTATTGAAATA
Found at i:31461 original size:19 final size:19
Alignment explanation
Indices: 31393--31461 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
31383 TTATATATCC
31393 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
31412 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
31431 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
31451 TTATTAATAAT
1 TTATTAATAAT
31462 TTAATAATAC
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 8 0.20
19 18 0.44
20 8 0.20
22 7 0.17
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:31626 original size:23 final size:24
Alignment explanation
Indices: 31582--31639 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
31572 TTACTTTATT
31582 ATAATATTATTAAAAATATTAATAA
1 ATAATATT-TTAAAAATATTAATAA
* *
31607 AT-ATATTTTAAATATTTTAATAA
1 ATAATATTTTAAAAATATTAATAA
*
31630 TTAATATTTT
1 ATAATATTTT
31640 GATTAAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.52
24 12 0.41
25 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATAATATTTTAAAAATATTAATAA
Found at i:32372 original size:24 final size:25
Alignment explanation
Indices: 32339--32387 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
32329 TTTTATTTTA
*
32339 TTAATTTAATATTAAT-AAAATATT
1 TTAATATAATATTAATCAAAATATT
*
32363 TTAATATAATTTTAATCAAAATATT
1 TTAATATAATATTAATCAAAATATT
32388 AATTATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAATATAATATTAATCAAAATATT
Found at i:32452 original size:20 final size:19
Alignment explanation
Indices: 32397--32456 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
32387 TAATTATTAA
* *
32397 AATATTTAAATATT-TATT
1 AATATTTTAATATTATAAT
*
32415 AATATTTCTAATAATATAAT
1 AATATTT-TAATATTATAAT
32435 ATATATTTTAATATTATAAT
1 A-ATATTTTAATATTATAAT
32455 AA
1 AA
32457 AATAATAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 7 0.20
19 6 0.17
20 16 0.46
21 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTTTAATATTATAAT
Found at i:32471 original size:23 final size:23
Alignment explanation
Indices: 32445--32518 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
32435 ATATATTTTA
32445 ATATTATAATAAAATAATAAATT
1 ATATTATAATAAAATAATAAATT
32468 ATATTATAATAAAATAATAAATT
1 ATATTATAATAAAATAATAAATT
* * *
32491 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAATAAATT
32514 ATATT
1 ATATT
32519 TTTATTTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
ATATTATAATAAAATAATAAATT
Found at i:32471 original size:31 final size:33
Alignment explanation
Indices: 32424--32506 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 33
32414 TAATATTTCT
* **
32424 AATAATATAATATATATTTTAATATTATAATAA
1 AATAATATAATATATATTATAATAAAATAATAA
32457 AATAATA-AAT-TATATTATAATAAAATAATAA
1 AATAATATAATATATATTATAATAAAATAATAA
*
32488 ATTATATTATAATAATATA
1 A--ATAATATAAT-ATATA
32507 AGATATTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 19 0.46
32 3 0.07
33 12 0.29
34 3 0.07
36 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
AATAATATAATATATATTATAATAAAATAATAA
Found at i:32650 original size:14 final size:13
Alignment explanation
Indices: 32605--32651 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
32595 TATATTTAAT
32605 ATTAATATA-ATA
1 ATTAATATATATA
32617 ATCTAATA-ATATA
1 AT-TAATATATATA
*
32630 TTTAATATATACTA
1 ATTAATATATA-TA
32644 ATTAATAT
1 ATTAATAT
32652 TTTTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 8 0.28
13 12 0.41
14 9 0.31
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTAATATATATA
Found at i:32656 original size:23 final size:22
Alignment explanation
Indices: 32581--32663 Score: 68
Period size: 23 Copynumber: 3.9 Consensus size: 22
32571 ATTTAATAGA
*
32581 AATAATATTATTT-ATATAT-TT
1 AATAATA-TATTTAATATATACT
* *
32602 AATATTA-ATATAATA-AT-CT
1 AATAATATATTTAATATATACT
32621 AATAATATATTTAATATATACT
1 AATAATATATTTAATATATACT
* *
32643 AATTAATATTTTTAAAATATA
1 AA-TAATATATTTAATATATA
32664 ATATAACACT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 12 0.24
20 10 0.20
21 8 0.16
22 4 0.08
23 16 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATATATTTAATATATACT
Found at i:32853 original size:22 final size:23
Alignment explanation
Indices: 32795--32855 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
32785 AATTATTTTA
*
32795 ATATTTTA-AAAATAATAATATT
1 ATATTTTATTAAATAATAATATT
* *
32817 AAATTTTATGATAAATAATATTATT
1 ATATTTTAT--TAAATAATAATATT
32842 -TATTTTATTAAATA
1 ATATTTTATTAAATA
32856 TTTATAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 13 0.41
24 7 0.22
25 12 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTATTAAATAATAATATT
Done.