Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007288.1 Hibiscus syriacus cultivar Beakdansim tig00019358_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: 66614
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7670 original size:23 final size:23
Alignment explanation
Indices: 7635--7682 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
7625 ATCAAGTACA
* *
7635 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* *
7658 ATAATGTAATAGGTAACGTTTAT
1 ATAATATAATAGGTAACGCTTAT
7681 AT
1 AT
7683 TGACTTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:8646 original size:182 final size:182
Alignment explanation
Indices: 8346--8776 Score: 646
Period size: 182 Copynumber: 2.4 Consensus size: 182
8336 TTCAATATCA
8346 ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
1 ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* *
8411 TTATTGGCGCTATAACTTATTTTCTTTTAAATTCCAAAAGTGTCGAAACTTATAATAAAATATCG
66 TTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGAAACTTATAATAAAATATCG
* * * ** * *
8476 ACACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCG
131 ACACTATCAACATATCCAGTAGCGATTTACAGGTTTTATCATTTAGAGACCG
* * * * *
8528 ATTTTGTCATATTTTTATCTGTTATATTGTTATAGATCGATGCATTTTTATAAAGTATCGATATT
1 ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * *
8593 TTATTAGCGCTATAATTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATCG
66 TTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGAAACTTATAATAAAATATCG
* * * *
8658 ACACTATCAACATATCTAGTAGCGATTTACATGTTTTGTCATTTATAGACCG
131 ACACTATCAACATATCCAGTAGCGATTTACAGGTTTTATCATTTAGAGACCG
* * *
8710 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATTAAGTATCGACACT
1 ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
8775 TT
66 TT
8777 CAATATATTA
Statistics
Matches: 220, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
182 220 1.00
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (182 bp):
ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGAAACTTATAATAAAATATCG
ACACTATCAACATATCCAGTAGCGATTTACAGGTTTTATCATTTAGAGACCG
Found at i:8847 original size:112 final size:112
Alignment explanation
Indices: 8647--9223 Score: 870
Period size: 112 Copynumber: 5.1 Consensus size: 112
8637 GATACTTATA
* * * *
8647 ATAAAGTATCGACACTATCAACATATCTA-GTAGCGATTTACATGTTTTGTCATTTATAGACCGG
1 ATAAAGTATCGACACTTTCAATATAT-TAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
*
8711 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
65 TTTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
* *
8759 ATTAAGTATCGACACTTTCAATATATTAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATTAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
8824 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
** *
8871 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATTAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
8936 TTTGTCATTTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA--TTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
* ** *
8985 ATAAAGTATGGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATTAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
9050 TGTGTCATTTTTTTACATGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
* * * *
9097 ATAAAGTATCGATATTTTTAATATATCT-GGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGG
1 ATAAAGTATCGACACTTTCAATATAT-TAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
* ** *
9161 TTTTGTCATTTTTTTACATATTATATTGTTATGGATTAATATATTTTT
65 TTTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
9209 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
9224 AACCCGACAA
Statistics
Matches: 429, Mismatches: 32, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
111 2 0.00
112 320 0.75
114 107 0.25
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.47
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATTAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
Found at i:9039 original size:226 final size:224
Alignment explanation
Indices: 8647--9223 Score: 929
Period size: 226 Copynumber: 2.6 Consensus size: 224
8637 GATACTTATA
* * * * *
8647 ATAAAGTATCGACACTATCAACATATCTAGTAGCGATTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
*
8712 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATTAAGTATCGACACTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* *
8777 CAATATATTAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACAT
131 CAATATATCAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTGTGTCATTTTTTTACAT
*
8842 GTTATATTGTTATGGATCGATACATTTTT
196 GTTATATTGTTATGGATCAATACATTTTT
*
8871 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
*
8936 TTTGTCATTTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATGGACACT
66 TTTGTCA--TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * *
9001 TTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGTTGTGTCATTTTTTTAC
129 TTCAATATATCAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTGTGTCATTTTTTTAC
*
9066 ATGTTATATTGTTATGGATCAATATATTTTT
194 ATGTTATATTGTTATGGATCAATACATTTTT
* * *
9097 ATAAAGTATCGATATTTTTAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
* * ** *
9162 TTTGTCATTTTTTTACATATTATATTGTTATGGATTAATATATTTTTATAAAGTATCGACAC
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
9224 AACCCGACAA
Statistics
Matches: 326, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
224 115 0.35
226 211 0.65
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.47
Consensus pattern (224 bp):
ATAAAGTATCGACACTTTCAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
CAATATATCAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTGTGTCATTTTTTTACAT
GTTATATTGTTATGGATCAATACATTTTT
Found at i:12157 original size:57 final size:58
Alignment explanation
Indices: 12077--12188 Score: 156
Period size: 57 Copynumber: 1.9 Consensus size: 58
12067 ACAAATGATC
** *
12077 CCCTTGACTATAGGACATCTC-TT-TTGAATTTCTGAATATTAAAAGTTACAAAATAGT
1 CCCTTGACTATAGGACATCTCTTTGTTGAATCCCGGAATATT-AAAGTTACAAAATAGT
* *
12134 CCCTTGACTATAGGGCATTTCTTTGTTGAATCCCGGAATATTAAAGTTACAAAAT
1 CCCTTGACTATAGGACATCTCTTTGTTGAATCCCGGAATATTAAAGTTACAAAAT
12189 GGTTCCTCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 19 0.40
58 15 0.31
59 14 0.29
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (58 bp):
CCCTTGACTATAGGACATCTCTTTGTTGAATCCCGGAATATTAAAGTTACAAAATAGT
Found at i:14119 original size:2 final size:2
Alignment explanation
Indices: 14112--14144 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
14102 GGGATGGGTC
*
14112 AT AT AT AT AA 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
14145 GTACAGCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:17746 original size:3 final size:3
Alignment explanation
Indices: 17738--17781 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
17728 TTATCCATTA
17738 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
17782 AGTTAGAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:26378 original size:20 final size:21
Alignment explanation
Indices: 26355--26408 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
26345 GAACCGATTC
*
26355 GAGTCAAG-TCGAACTGACCT
1 GAGTCAAGCCCGAACTGACCT
26375 GAGTC-AGCCCGAACTGACCT
1 GAGTCAAGCCCGAACTGACCT
26395 GAGTCAA-CCCGAAC
1 GAGTCAAGCCCGAAC
26409 CGGTCTAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 2 0.06
20 28 0.90
21 1 0.03
ACGTcount: A:0.30, C:0.31, G:0.24, T:0.15
Consensus pattern (21 bp):
GAGTCAAGCCCGAACTGACCT
Found at i:27678 original size:18 final size:18
Alignment explanation
Indices: 27655--27737 Score: 76
Period size: 18 Copynumber: 4.2 Consensus size: 18
27645 ACCGGTCGCA
27655 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
27673 ACCCGACCTGACCCGTTTACCCG
1 ACCCGACCCGACCCG-TT----G
27696 ACCCGTTTACCCGACCCGTTG
1 ACCCG---ACCCGACCCGTTG
*
27717 AGCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
27735 ACC
1 ACC
27738 GTTGACCCGT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
18 29 0.55
19 2 0.04
21 5 0.09
23 6 0.11
25 2 0.04
26 9 0.17
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:27726 original size:31 final size:28
Alignment explanation
Indices: 27655--27737 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 28
27645 ACCGGTCGCA
27655 ACCCGACCCGACCCGTTGACCCGACCTG
1 ACCCGACCCGACCCGTTGACCCGACCTG
*
27683 ACCCGTTTACCCGACCCGTTTACCCGACCCGTTG
1 ACCCG---ACCCGACCCGTTGACCCGA-CC--TG
*
27717 AGCCGACCCGACCCGTTGACC
1 ACCCGACCCGACCCGTTGACC
27738 GTTGACCCGT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 5 0.11
31 33 0.72
32 2 0.04
34 6 0.13
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.16
Consensus pattern (28 bp):
ACCCGACCCGACCCGTTGACCCGACCTG
Found at i:27737 original size:13 final size:13
Alignment explanation
Indices: 27677--27726 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
27667 CCGTTGACCC
*
27677 GACCTGACCCGTT
1 GACCCGACCCGTT
*
27690 TACCCGACCCGTT
1 GACCCGACCCGTT
*
27703 TACCCGACCCGTT
1 GACCCGACCCGTT
*
27716 GAGCCGACCCG
1 GACCCGACCCG
27727 ACCCGTTGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:27741 original size:7 final size:7
Alignment explanation
Indices: 27729--27760 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
27719 CCGACCCGAC
27729 CCGTTGA
1 CCGTTGA
27736 CCGTTGA
1 CCGTTGA
27743 CCCGTTGA
1 -CCGTTGA
27751 CCGTTGA
1 CCGTTGA
27758 CCG
1 CCG
27761 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:27746 original size:15 final size:15
Alignment explanation
Indices: 27726--27759 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
27716 GAGCCGACCC
27726 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
27741 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
27756 GACC
1 GACC
27760 GGAGTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:32493 original size:18 final size:18
Alignment explanation
Indices: 32470--32552 Score: 76
Period size: 18 Copynumber: 4.2 Consensus size: 18
32460 ACCGGTCACA
32470 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
32488 ACCCGACCTGACCCGTTTACCCG
1 ACCCGACCCGACCCG-TT----G
32511 ACCCGTTTACCCGACCCGTTG
1 ACCCG---ACCCGACCCGTTG
*
32532 AGCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
32550 ACC
1 ACC
32553 GTTGACCCGT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
18 29 0.55
19 2 0.04
21 5 0.09
23 6 0.11
25 2 0.04
26 9 0.17
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:32541 original size:31 final size:28
Alignment explanation
Indices: 32470--32552 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 28
32460 ACCGGTCACA
32470 ACCCGACCCGACCCGTTGACCCGACCTG
1 ACCCGACCCGACCCGTTGACCCGACCTG
*
32498 ACCCGTTTACCCGACCCGTTTACCCGACCCGTTG
1 ACCCG---ACCCGACCCGTTGACCCGA-CC--TG
*
32532 AGCCGACCCGACCCGTTGACC
1 ACCCGACCCGACCCGTTGACC
32553 GTTGACCCGT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 5 0.11
31 33 0.72
32 2 0.04
34 6 0.13
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.16
Consensus pattern (28 bp):
ACCCGACCCGACCCGTTGACCCGACCTG
Found at i:32552 original size:13 final size:13
Alignment explanation
Indices: 32492--32541 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
32482 CCGTTGACCC
*
32492 GACCTGACCCGTT
1 GACCCGACCCGTT
*
32505 TACCCGACCCGTT
1 GACCCGACCCGTT
*
32518 TACCCGACCCGTT
1 GACCCGACCCGTT
*
32531 GAGCCGACCCG
1 GACCCGACCCG
32542 ACCCGTTGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:32556 original size:7 final size:7
Alignment explanation
Indices: 32544--32575 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
32534 CCGACCCGAC
32544 CCGTTGA
1 CCGTTGA
32551 CCGTTGA
1 CCGTTGA
32558 CCCGTTGA
1 -CCGTTGA
32566 CCGTTGA
1 CCGTTGA
32573 CCG
1 CCG
32576 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:32561 original size:15 final size:15
Alignment explanation
Indices: 32541--32574 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
32531 GAGCCGACCC
32541 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
32556 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
32571 GACC
1 GACC
32575 GGAGTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:37306 original size:18 final size:18
Alignment explanation
Indices: 37283--37365 Score: 76
Period size: 18 Copynumber: 4.2 Consensus size: 18
37273 ACCGGTCACA
37283 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
37301 ACCCGACCTGACCCGTTTACCCG
1 ACCCGACCCGACCCG-TT----G
37324 ACCCGTTTACCCGACCCGTTG
1 ACCCG---ACCCGACCCGTTG
*
37345 AGCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
37363 ACC
1 ACC
37366 GTTGACCCGT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
18 29 0.55
19 2 0.04
21 5 0.09
23 6 0.11
25 2 0.04
26 9 0.17
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:37354 original size:31 final size:28
Alignment explanation
Indices: 37283--37365 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 28
37273 ACCGGTCACA
37283 ACCCGACCCGACCCGTTGACCCGACCTG
1 ACCCGACCCGACCCGTTGACCCGACCTG
*
37311 ACCCGTTTACCCGACCCGTTTACCCGACCCGTTG
1 ACCCG---ACCCGACCCGTTGACCCGA-CC--TG
*
37345 AGCCGACCCGACCCGTTGACC
1 ACCCGACCCGACCCGTTGACC
37366 GTTGACCCGT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 5 0.11
31 33 0.72
32 2 0.04
34 6 0.13
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.16
Consensus pattern (28 bp):
ACCCGACCCGACCCGTTGACCCGACCTG
Found at i:37365 original size:13 final size:13
Alignment explanation
Indices: 37305--37354 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
37295 CCGTTGACCC
*
37305 GACCTGACCCGTT
1 GACCCGACCCGTT
*
37318 TACCCGACCCGTT
1 GACCCGACCCGTT
*
37331 TACCCGACCCGTT
1 GACCCGACCCGTT
*
37344 GAGCCGACCCG
1 GACCCGACCCG
37355 ACCCGTTGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:37369 original size:7 final size:7
Alignment explanation
Indices: 37357--37388 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
37347 CCGACCCGAC
37357 CCGTTGA
1 CCGTTGA
37364 CCGTTGA
1 CCGTTGA
37371 CCCGTTGA
1 -CCGTTGA
37379 CCGTTGA
1 CCGTTGA
37386 CCG
1 CCG
37389 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:37374 original size:15 final size:15
Alignment explanation
Indices: 37354--37387 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
37344 GAGCCGACCC
37354 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
37369 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
37384 GACC
1 GACC
37388 GGAGTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:43557 original size:7 final size:7
Alignment explanation
Indices: 43545--43622 Score: 61
Period size: 7 Copynumber: 11.0 Consensus size: 7
43535 TTAATATAAA
43545 AAAATAT
1 AAAATAT
43552 AAAATAT
1 AAAATAT
* *
43559 TATATAT
1 AAAATAT
*
43566 ATAAT-T
1 AAAATAT
*
43572 AATATA-
1 AAAATAT
43578 AAAATAT
1 AAAATAT
43585 AAAATAT
1 AAAATAT
* *
43592 TATATAT
1 AAAATAT
43599 AATTAATAT
1 AA--AATAT
43608 AAAAATAT
1 -AAAATAT
43616 AAAATAT
1 AAAATAT
43623 TATATATATA
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
6 9 0.17
7 34 0.63
8 5 0.09
9 4 0.07
10 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AAAATAT
Found at i:43633 original size:35 final size:33
Alignment explanation
Indices: 43517--43632 Score: 200
Period size: 31 Copynumber: 3.5 Consensus size: 33
43507 CCCGAACTCA
43517 AAAATATTATATATATAATTAATATAAAAAAATAT
1 AAAATATTATATATATAATTAATAT--AAAAATAT
43552 AAAATATTATATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAATAT
43585 AAAATA-T-TATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAATAT
43616 AAAATATTATATATATA
1 AAAATATTATATATATA
43633 TATATATAAT
Statistics
Matches: 79, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
31 30 0.38
32 2 0.03
33 22 0.28
35 25 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATATAAAAATAT
Found at i:50285 original size:43 final size:43
Alignment explanation
Indices: 50226--50589 Score: 279
Period size: 43 Copynumber: 8.6 Consensus size: 43
50216 TTTTTTATTC
* * * *
50226 TCACTTTATACATTTATAATTGAGACTCATAAGTTTTTCAATA
1 TCACTTTTTACTTTTATAATTGAGACTCCTAATTTTTTCAATA
* * *
50269 TCACTTTCTACTTTTATGATTGA-AGCTCCTAATTTTTT-TAT-
1 TCACTTTTTACTTTTATAATTGAGA-CTCCTAATTTTTTCAATA
*
50310 TCACTTTTTA-TCTTTATAATTGAGAC-CCTAATTTTTTCAATC
1 TCACTTTTTACT-TTTATAATTGAGACTCCTAATTTTTTCAATA
* * * *
50352 TAACTTTTTATTTTTATAATTGATG-C-CCATACTTTTTTCAATC
1 TCACTTTTTACTTTTATAATTGA-GACTCC-TAATTTTTTCAATA
* *
50395 TCACATTTTAGC-TTTATAATTGA-AGTCTCTAATTTTTT-AATA
1 TCACTTTTTA-CTTTTATAATTGAGACTC-CTAATTTTTTCAATA
* * ** *
50437 TCACTTTTTACCTTTATAAATGAGGTTCTTAATTCTTTT-AATA
1 TCACTTTTTACTTTTATAATTGAGACTCCTAATT-TTTTCAATA
* * * *
50480 TCATTTTTTA-TCTTTATAATTGAGGCCCCTAATTTTTTCAATC
1 TCACTTTTTACT-TTTATAATTGAGACTCCTAATTTTTTCAATA
* * ** * *
50523 TCACTTTCTAAC-TTTACAAATAAAGCCT-CTAATTTTTTTAATA
1 TCACTTT-TTACTTTTA-TAATTGAGACTCCTAATTTTTTCAATA
50566 TCACTTTTTACTTTTATAATTGAG
1 TCACTTTTTACTTTTATAATTGAG
50590 GCTTTCAATA
Statistics
Matches: 258, Mismatches: 42, Indels: 43
0.75 0.12 0.13
Matches are distributed among these distances:
40 12 0.05
41 23 0.09
42 66 0.26
43 148 0.57
44 9 0.03
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (43 bp):
TCACTTTTTACTTTTATAATTGAGACTCCTAATTTTTTCAATA
Found at i:50333 original size:128 final size:126
Alignment explanation
Indices: 50164--50589 Score: 409
Period size: 128 Copynumber: 3.3 Consensus size: 126
50154 TGGGTGCACG
* * * * *
50164 TCTCTAATTTTTATA-ATCTCATTATTTACCTTCATAATTGAGACCTTTAGTTTTTTTTATTCTC
1 TCTCTAATTTTTTTATATCAC-TT-TTTACCTTTATAATTGAGACCTTTA-ATTTTTTTAATCTC
* * * * *
50228 ACTTTATACATTTATAATTGAGACTCATAAGTTTTTCAATATCACTTTCTACTTTTATGATTGAA
63 ACTTTTTAC-TTTATAATTGAG-CCCATAATTTTTTCAATCTCACTTTCTAC-TTTATAATTGAA
50293 GC
125 GC
* * * *
50295 TC-CTAATTTTTTTAT-TCACTTTTTATCTTTATAATTGAGACC-CTAATTTTTTCAATCTAACT
1 TCTCTAATTTTTTTATATCACTTTTTACCTTTATAATTGAGACCTTTAATTTTTTTAATCTCACT
* *
50357 TTTTATTTTTATAATTGATGCCCATACTTTTTTCAATCTCACATTT-TAGCTTTATAATTGAAG-
66 TTTTA-CTTTATAATTGA-GCCCATAATTTTTTCAATCTCAC-TTTCTA-CTTTATAATTGAAGC
* * ** * * *
50420 TCTCTAATTTTTTAATATCACTTTTTACCTTTATAAATGAG-GTTCTTAATTCTTTTAATATCAT
1 TCTCTAATTTTTTTATATCACTTTTTACCTTTATAATTGAGACCT-TTAATTTTTTTAATCTCAC
* * * *
50484 TTTTTATCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTCTAACTTTACAAATAAAGC
65 TTTTTA-CTTTATAATTGA-GCCCATAATTTTTTCAATCTCACTTTCT-ACTTTATAATTGAAGC
*
50549 -CTCTAATTTTTTTAATATCACTTTTTACTTTTATAATTGAG
1 TCTCTAATTTTTTT-ATATCACTTTTTACCTTTATAATTGAG
50590 GCTTTCAATA
Statistics
Matches: 245, Mismatches: 37, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
125 2 0.01
126 72 0.29
127 32 0.13
128 95 0.39
129 28 0.11
130 14 0.06
131 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (126 bp):
TCTCTAATTTTTTTATATCACTTTTTACCTTTATAATTGAGACCTTTAATTTTTTTAATCTCACT
TTTTACTTTATAATTGAGCCCATAATTTTTTCAATCTCACTTTCTACTTTATAATTGAAGC
Found at i:50489 original size:85 final size:85
Alignment explanation
Indices: 50216--50703 Score: 341
Period size: 85 Copynumber: 5.8 Consensus size: 85
50206 ACCTTTAGTT
* * * * *
50216 TTTTTTATTCTCACTTTATA-CATTTATAATTG-AGACTCATAAGTTTTTCAATATCACTTTCTA
1 TTTTTTAATATCACTTTTTATC-TTTATAATTGAAGAC-CCTAATTTTTTCAATATCACTTTCTA
* * *
50279 CTTTTATGATTGAAGCTCC-TAA
64 CCTTTATAAATGAAGC-CCTTAA
* * * * **
50301 TTTTTTTAT-TCACTTTTTATCTTTATAATTG-AGACCCTAATTTTTTCAATCTAACTTTTTATT
1 TTTTTTAATATCACTTTTTATCTTTATAATTGAAGACCCTAATTTTTTCAATATCACTTTCTACC
* * * *
50364 TTTATAATTGATGCCCATAC
66 TTTATAAATGAAGCCCTTAA
* * * * * *
50384 TTTTTTCAATCTCACATTTTAGCTTTATAATTGAAGTCTCTAATTTTTT-AATATCACTTTTTAC
1 TTTTTT-AATATCACTTTTTATCTTTATAATTGAAGACCCTAATTTTTTCAATATCACTTTCTAC
* **
50448 CTTTATAAATGAGGTTCTTAA
65 CTTTATAAATGAAGCCCTTAA
* * * * *
50469 TTCTTTTAATATCATTTTTTATCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTCTAA
1 TT-TTTTAATATCACTTTTTATCTTTATAATTGAAGACCCTAATTTTTTCAATATCACTTTCTAC
* *
50534 CTTTACAAATAAAG-CCTCTAA
65 CTTTATAAATGAAGCCCT-TAA
*
50555 TTTTTTTAATATCACTTTTTA-CTTTTATAATTG-AG--GC------TTTCAATATCACCTTT-T
1 -TTTTTTAATATCACTTTTTATC-TTTATAATTGAAGACCCTAATTTTTTCAATATCA-CTTTCT
* *
50609 ACCTTTATAATTGAAGTCCC-TAT
63 ACCTTTATAAATGAAG-CCCTTAA
* * * * * *
50632 TTTTTTAATCTCACTTTTTATATTTATAATTG-AGACCCTTAATTTTTTTAATTTTACTTTTTAC
1 TTTTTTAATATCACTTTTTATCTTTATAATTGAAGACCC-TAATTTTTTCAATATCACTTTCTAC
*
50696 ATTTATAA
65 CTTTATAA
50704 TTTTTCCCTA
Statistics
Matches: 322, Mismatches: 57, Indels: 48
0.75 0.13 0.11
Matches are distributed among these distances:
76 31 0.10
77 25 0.08
78 5 0.02
79 2 0.01
82 2 0.01
83 43 0.13
84 29 0.09
85 113 0.35
86 70 0.22
87 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (85 bp):
TTTTTTAATATCACTTTTTATCTTTATAATTGAAGACCCTAATTTTTTCAATATCACTTTCTACC
TTTATAAATGAAGCCCTTAA
Found at i:50615 original size:77 final size:76
Alignment explanation
Indices: 50515--50665 Score: 191
Period size: 76 Copynumber: 2.0 Consensus size: 76
50505 CCCCTAATTT
*
50515 TTTCAATCTCACTTTCTAACTTTACAAATAAAG-CCTCTAATTTTTTTAATATCACTTTTTACT-
1 TTTCAATATCACTTTCTAACTTTACAAATAAAGTCC-CT-ATTTTTTTAATATCACTTTTTA-TA
50578 TTTATAATTGAGGC
63 TTTATAATTGAGGC
* * * * *
50592 TTTCAATATCACCTTT-TACCTTTATAATTGAAGTCCCTATTTTTTTAATCTCACTTTTTATATT
1 TTTCAATATCA-CTTTCTAACTTTACAAATAAAGTCCCTATTTTTTTAATATCACTTTTTATATT
50656 TATAATTGAG
65 TATAATTGAG
50666 ACCCTTAATT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
75 1 0.02
76 33 0.51
77 25 0.38
78 6 0.09
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.49
Consensus pattern (76 bp):
TTTCAATATCACTTTCTAACTTTACAAATAAAGTCCCTATTTTTTTAATATCACTTTTTATATTT
ATAATTGAGGC
Found at i:50662 original size:42 final size:41
Alignment explanation
Indices: 50600--50775 Score: 151
Period size: 42 Copynumber: 4.2 Consensus size: 41
50590 GCTTTCAATA
* *
50600 TCACCTTTTACCTTTATAATTGAAGTCCCTATTTTTTTAATC
1 TCACTTTTTACATTTATAATTG-AGTCCCTATTTTTTTAATC
* * *
50642 TCACTTTTTATATTTATAATTGAGACCCTTAATTTTTTTAATT
1 TCACTTTTTACATTTATAATTGAGTCCC-T-ATTTTTTTAATC
* ** *
50685 TTACTTTTTACATTTATAATT-TTTCCCTATTTTTTTAAAC
1 TCACTTTTTACATTTATAATTGAGTCCCTATTTTTTTAATC
* * * * *
50725 TTATTTTTTAGC-TTTATAGTTGAGGTCCCCAATTTTTTAATC
1 TCACTTTTTA-CATTTATAATTGA-GTCCCTATTTTTTTAATC
*
50767 -CAATTTTTA
1 TCACTTTTTA
50776 GTTTCATAAT
Statistics
Matches: 108, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
40 27 0.25
41 14 0.13
42 37 0.34
43 30 0.28
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.55
Consensus pattern (41 bp):
TCACTTTTTACATTTATAATTGAGTCCCTATTTTTTTAATC
Found at i:50691 original size:43 final size:42
Alignment explanation
Indices: 50600--50705 Score: 133
Period size: 43 Copynumber: 2.5 Consensus size: 42
50590 GCTTTCAATA
* * *
50600 TCACCTTTTACCTTTATAATTGAAGTCCCTATTTTTTTAATC
1 TCACTTTTTACATTTATAATTGAAGACCCTATTTTTTTAATC
* *
50642 TCACTTTTTATATTTATAATTG-AGACCCTTAATTTTTTTAATT
1 TCACTTTTTACATTTATAATTGAAGACCC-T-ATTTTTTTAATC
*
50685 TTACTTTTTACATTTATAATT
1 TCACTTTTTACATTTATAATT
50706 TTTCCCTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
41 5 0.09
42 20 0.36
43 30 0.55
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.55
Consensus pattern (42 bp):
TCACTTTTTACATTTATAATTGAAGACCCTATTTTTTTAATC
Found at i:50701 original size:119 final size:120
Alignment explanation
Indices: 50471--50705 Score: 296
Period size: 119 Copynumber: 2.0 Consensus size: 120
50461 GTTCTTAATT
* ** * *
50471 CTTTTAATATCATTTTTTATCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTCTAACT
1 CTTTCAATATCACCTTTTACCTTTATAATTGAAGCCCCTAATTTTTTCAATCTCACTTTCTAACT
* *
50536 TTACAAATAAAGCCTCTAATTTTTTTAATATCACTTTTTACTTTTATAATTGAGG
66 TTACAAATAAACCCTCTAATTTTTTTAATATCACTTTTTACATTTATAATTGAGG
* * *
50591 CTTTCAATATCACCTTTTACCTTTATAATTGAAGTCCCT-ATTTTTTTAATCTCACTTTTTATA-
1 CTTTCAATATCACCTTTTACCTTTATAATTGAAGCCCCTAATTTTTTCAATCTCACTTTCTA-AC
* * * * *
50654 TTTATAATTGAGACCCT-TAATTTTTTTAATTTTACTTTTTACATTTATAATT
65 TTTACAAAT-AAACCCTCTAATTTTTTTAATATCACTTTTTACATTTATAATT
50706 TTTCCCTATT
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
119 59 0.60
120 39 0.40
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (120 bp):
CTTTCAATATCACCTTTTACCTTTATAATTGAAGCCCCTAATTTTTTCAATCTCACTTTCTAACT
TTACAAATAAACCCTCTAATTTTTTTAATATCACTTTTTACATTTATAATTGAGG
Found at i:56478 original size:29 final size:30
Alignment explanation
Indices: 56436--56494 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
56426 AACTCGTACC
*
56436 TAAGGTTA-TTTTTTAGATTTGACTTAAAA
1 TAAGGTTATTTTTTTAGATTTAACTTAAAA
*
56465 TAAGGTTATTTTTTTATATTTAACTTAAAA
1 TAAGGTTATTTTTTTAGATTTAACTTAAAA
56495 ATAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (30 bp):
TAAGGTTATTTTTTTAGATTTAACTTAAAA
Found at i:61197 original size:81 final size:81
Alignment explanation
Indices: 61098--61482 Score: 448
Period size: 81 Copynumber: 4.8 Consensus size: 81
61088 AAATTATTTA
* * *
61098 AAATAAATCAATCTATATTTTAAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCA
1 AAATAAATCAATCCATATTTT-AAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCA
61163 ATCTATAC-AACTACAA-T
65 ATCTATACTAA-TA-AATT
61180 -AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTT-AAA-AAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAA
61242 TCTATACTAATAAATTTTT
66 TCTATACTAATAAA---TT
* * *
61261 AAAATAAATCGATTCATATTTT-AAATAAATCAATCCATACTAAT-AATTATTT-AAATAAATCA
1 -AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCA
61323 ATCTATAC-AACTACAA-T
65 ATCTATACTAA-TA-AATT
61340 -AAT-AATCAATCCATATTTTAAAATAAATCAATCCATACAAAT---TTATTTAAAAT-AATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAA
*
61399 TCCATACTAATAATTATTT
66 TCTATACTAATAA--A-TT
*
61418 AAAATAAATCAATCC--ATTTT-AAATAAATCAATTCATACAAATAAATTATTTAAAATAAATCA
1 -AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCA
61480 ATC
65 ATC
61483 CATATTTTAA
Statistics
Matches: 268, Mismatches: 11, Indels: 48
0.82 0.03 0.15
Matches are distributed among these distances:
74 1 0.00
75 20 0.07
76 21 0.08
77 26 0.10
78 38 0.14
79 11 0.04
80 33 0.12
81 53 0.20
82 45 0.17
83 20 0.07
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (81 bp):
AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAA
TCTATACTAATAAATT
Found at i:61298 original size:82 final size:83
Alignment explanation
Indices: 61084--61482 Score: 407
Period size: 82 Copynumber: 4.9 Consensus size: 83
61074 ACAACTACAA
* * *
61084 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAAATAAATCAATACATACTAATAAATTA
1 TAATAAATT-TTTAAAATAAATCATTC-ATATTTT-AAAATAAATCAATCCATACAAATAAATTA
61149 TTTAAAATAAATCAATCTATAC
63 TTT-AAATAAATCAATCTATAC
*
61171 -AACTACAA----T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTA
1 TAA-TA-AATTTTTAAAATAAATC-ATTCATATTTTAAAATAAATCAATCCATACAAATAAATTA
61229 TTTAAA-AAATCAATCTATAC
63 TTTAAATAAATCAATCTATAC
*
61249 TAATAAATTTTTAAAATAAATCGATTCATATTTT-AAATAAATCAATCCATACTAAT-AATTATT
1 TAATAAATTTTTAAAATAAATC-ATTCATATTTTAAAATAAATCAATCCATACAAATAAATTATT
61312 TAAATAAATCAATCTATAC
65 TAAATAAATCAATCTATAC
*
61331 -AACTACAA----T--AAT-AATCAATCCATATTTTAAAATAAATCAATCCATACAAAT---TTA
1 TAA-TA-AATTTTTAAAATAAATC-ATTCATATTTTAAAATAAATCAATCCATACAAATAAATTA
*
61385 TTTAAA-ATAATCAATCCATAC
63 TTTAAATA-AATCAATCTATAC
* * *
61406 TAAT-AATTATTTAAAATAAATCAATC-CATTTT-AAATAAATCAATTCATACAAATAAATTATT
1 TAATAAATT-TTTAAAATAAATCATTCATATTTTAAAATAAATCAATCCATACAAATAAATTATT
61468 TAAAATAAATCAATC
65 T-AAATAAATCAATC
61483 CATATTTTAA
Statistics
Matches: 268, Mismatches: 15, Indels: 63
0.77 0.04 0.18
Matches are distributed among these distances:
73 2 0.01
74 1 0.00
75 22 0.08
76 16 0.06
77 26 0.10
78 38 0.14
79 11 0.04
80 35 0.13
81 39 0.15
82 50 0.19
83 22 0.08
86 2 0.01
87 2 0.01
88 2 0.01
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (83 bp):
TAATAAATTTTTAAAATAAATCATTCATATTTTAAAATAAATCAATCCATACAAATAAATTATTT
AAATAAATCAATCTATAC
Found at i:61299 original size:21 final size:22
Alignment explanation
Indices: 61257--61299 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
61247 ACTAATAAAT
* *
61257 TTTTAAAATAAATCGATTCATA
1 TTTTAAAATAAATCAATCCATA
61279 TTTT-AAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
61300 CTAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:61314 original size:30 final size:30
Alignment explanation
Indices: 61201--61694 Score: 166
Period size: 30 Copynumber: 18.3 Consensus size: 30
61191 CCATATTTTA
*
61201 AAATAAATCAATCCATACAAATAAATTATTT
1 AAATAAATCAATCCATACTAAT-AATTATTT
*
61232 AAA-AAATCAATCTATACTAATAAATT-TTT
1 AAATAAATCAATCCATACTAAT-AATTATTT
*
61261 AAAATAAATCGAT---T-C--AT-A-T-TTT
1 -AAATAAATCAATCCATACTAATAATTATTT
61283 AAATAAATCAATCCATACTAATAATTATTT
1 AAATAAATCAATCCATACTAATAATTATTT
*
61313 AAATAAATCAATCTATAC-AACTACA--A--T
1 AAATAAATCAATCCATACTAA-TA-ATTATTT
61340 -AAT-AATCAATCCATA-T--T--TTA---
1 AAATAAATCAATCCATACTAATAATTATTT
*
61360 AAATAAATCAATCCATAC-AA-ATTTATTT
1 AAATAAATCAATCCATACTAATAATTATTT
61388 AAA-ATAATCAATCCATACTAATAATTATTT
1 AAATA-AATCAATCCATACTAATAATTATTT
*
61418 AAAATAAATCAATCCAT--T-TTAA--A--T
1 -AAATAAATCAATCCATACTAATAATTATTT
* * *
61442 AAATCAATTC-ATACA-AAT-A-AATTATTT
1 AAAT-AAATCAATCCATACTAATAATTATTT
61469 AAAATAAATCAATCCATA-T--T--TTA---
1 -AAATAAATCAATCCATACTAATAATTATTT
61492 AAATAAATCAATCCATACTAATAAATTATTT
1 AAATAAATCAATCCATACTAAT-AATTATTT
61523 AAAATAAATCAATCCATAC-AACTACA--A--T
1 -AAATAAATCAATCCATACTAA-TA-ATTATTT
61551 -AATAAATCAATCCATA-T--T--TTA---
1 AAATAAATCAATCCATACTAATAATTATTT
*
61572 AAATAAATTAATCCATACTAAT-ATTATTT
1 AAATAAATCAATCCATACTAATAATTATTT
*
61601 AAAATAAATC-AT-C-TAC-AACTCCA--A--T
1 -AAATAAATCAATCCATACTAA-T-AATTATTT
*
61626 -AATAAATC-ATCCAACTAAT-A-AATTATTT
1 AAATAAATCAATCC-A-TACTAATAATTATTT
61654 AAAATAAATCAATCCATACTAATAAATTATTT
1 -AAATAAATCAATCCATACTAAT-AATTATTT
61686 AAAATAAAT
1 -AAATAAAT
61695 TATTTTAAAA
Statistics
Matches: 361, Mismatches: 18, Indels: 167
0.66 0.03 0.31
Matches are distributed among these distances:
21 15 0.04
22 50 0.14
23 24 0.07
24 9 0.02
25 21 0.06
26 29 0.08
27 18 0.05
28 36 0.10
29 17 0.05
30 72 0.20
31 32 0.09
32 38 0.11
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (30 bp):
AAATAAATCAATCCATACTAATAATTATTT
Found at i:61321 original size:51 final size:52
Alignment explanation
Indices: 61084--61533 Score: 279
Period size: 52 Copynumber: 8.5 Consensus size: 52
61074 ACAACTACAA
* *
61084 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAAATAAATCAATACATAC
1 TAATAAATTATTTAAAATAAATCATTC-ATATTTT--AAATAAATCAATCCATAC
* ***
61139 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCATTC-AT---A-TTTTA-AATAAATCAATCCATAC
** * * * * *
61196 TTTTAAA--A--T-AAATCAATCCATACAAATAAATTATTTAAAAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAAT-CATTC--AT--ATT-TTAAATAAATCAATCCATAC
61249 TAATAAATT-TTTAAAATAAATCGATTCATATTTTAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATC-ATTCATATTTTAAATAAATCAATCCATAC
* ***
61301 TAAT-AATTATTT-AAATAAATCAATCTATACAACTACAATAATAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCATTC-ATA-TTTTA-AAT-A-AATCAATCCATAC
** * * *
61355 TTTTAAA--A--T-AAATCAATCCATACAAATTTATTTAAA-ATAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-CATTC--ATAT-TTTAAATA-AATCAATCCATAC
* * *
61406 TAAT-AATTATTTAAAATAAATCAATC-CATTTTAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCATTCATATTTTAAATAAATCAATCCATAC
* *
61456 AAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATC-ATTCATATTTT-AAATAAATCAATCCATAC
61510 TAATAAATTATTTAAAATAAATCA
1 TAATAAATTATTTAAAATAAATCA
61534 ATCCATACAA
Statistics
Matches: 307, Mismatches: 52, Indels: 74
0.71 0.12 0.17
Matches are distributed among these distances:
50 40 0.13
51 46 0.15
52 56 0.18
53 28 0.09
54 48 0.16
55 54 0.18
56 2 0.01
57 16 0.05
58 16 0.05
59 1 0.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (52 bp):
TAATAAATTATTTAAAATAAATCATTCATATTTTAAATAAATCAATCCATAC
Found at i:61474 original size:32 final size:32
Alignment explanation
Indices: 61433--61543 Score: 125
Period size: 32 Copynumber: 3.8 Consensus size: 32
61423 AAATCAATCC
* *
61433 ATTTTAAATAAATCAATTCATACAAATAAATT
1 ATTTAAAATAAATCAATCCATACAAATAAATT
61465 ATTTAAAATAAATCAAT-C---C--AT--A-T
1 ATTTAAAATAAATCAATCCATACAAATAAATT
*
61488 -TTTAAAATAAATCAATCCATACTAATAAATT
1 ATTTAAAATAAATCAATCCATACAAATAAATT
61519 ATTTAAAATAAATCAATCCATACAA
1 ATTTAAAATAAATCAATCCATACAA
61544 CTACAATAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 20
0.75 0.02 0.22
Matches are distributed among these distances:
22 16 0.24
23 2 0.03
24 1 0.01
26 3 0.04
28 3 0.04
30 1 0.01
31 2 0.03
32 39 0.58
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
ATTTAAAATAAATCAATCCATACAAATAAATT
Found at i:61492 original size:22 final size:22
Alignment explanation
Indices: 61466--61508 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
61456 AAATAAATTA
61466 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
61488 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
61509 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:61501 original size:132 final size:136
Alignment explanation
Indices: 61343--61743 Score: 479
Period size: 132 Copynumber: 3.0 Consensus size: 136
61333 CTACAATAAT
*
61343 AATCAATCCATATTTTAAAATAAATCAATCCATAC-A-AATTTATTTAAAAT-AATCAATCCATA
1 AATCAATCCATATTTTAAAATAAATCAATCCATACAATAAATTATTTAAAATAAATCAATCCATA
*
61405 CTAATAATTATTTAAAATAAATCAATCCATTTT-AAATAAATCAATTCATACAAATAAATTATTT
66 CTAATAATTATTTAAAATAAATCAATCCATTTTAAAATAAATCAATTCATACTAATAAATTATTT
61469 AAAATA
131 AAAATA
61475 AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT
1 AATCAATCCATATTTTAAAATAAATCAATCCATAC-AATAAATTATTTAAAATAAATCAATCCAT
* *
61540 AC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATTAATCCATACTAAT--AT
65 ACTAA-TA-ATTATTTAAAATAAATCAATCC--ATTTTAAAATAAATCAATTCATACTAATAAAT
61596 TATTTAAAATA
126 TATTTAAAATA
* **
61607 AATC-ATCTACA-ACTCCAATAATAAATC-ATCCA-ACTAATAAATTATTTAAAATAAATCAATC
1 AATCAATC--CATATTTTAA-AATAAATCAATCCATAC-AATAAATTATTTAAAATAAATCAATC
61668 CATACTAATAAATTATTTAAAATAAAT---T--ATTTTAAAATAAATCAA-TCAATACTAATAAA
62 CATACTAAT-AATTATTTAAAATAAATCAATCCATTTTAAAATAAATCAATTC-ATACTAATAAA
61727 TTATTTAAAATA
125 TTATTTAAAATA
61739 AATCA
1 AATCA
61744 TTTTAAAATA
Statistics
Matches: 236, Mismatches: 9, Indels: 47
0.81 0.03 0.16
Matches are distributed among these distances:
129 1 0.00
130 24 0.10
131 52 0.22
132 81 0.34
133 17 0.07
134 21 0.09
135 17 0.07
136 15 0.06
137 8 0.03
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (136 bp):
AATCAATCCATATTTTAAAATAAATCAATCCATACAATAAATTATTTAAAATAAATCAATCCATA
CTAATAATTATTTAAAATAAATCAATCCATTTTAAAATAAATCAATTCATACTAATAAATTATTT
AAAATA
Found at i:61517 original size:22 final size:22
Alignment explanation
Indices: 61468--61516 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
61458 ATAAATTATT
**
61468 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
61490 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
61513 TAAA
1 TAAA
61517 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:61661 original size:14 final size:14
Alignment explanation
Indices: 61642--61756 Score: 77
Period size: 15 Copynumber: 7.5 Consensus size: 14
61632 TCATCCAACT
61642 AATAAATTATTTAA
1 AATAAATTATTTAA
* * *
61656 AATAAATCAATCCATACT
1 AATAAAT-TAT--TTA-A
61674 AATAAATTATTTAA
1 AATAAATTATTTAA
61688 AATAAATTATTTTAA
1 AATAAATTA-TTTAA
* * *
61703 AATAAATCAATCAATACT
1 AATAAAT-TAT--TTA-A
61721 AATAAATTATTTAA
1 AATAAATTATTTAA
*
61735 AATAAATCATTTTAA
1 AATAAATTA-TTTAA
61750 AATAAAT
1 AATAAAT
61757 CAATCCATTT
Statistics
Matches: 78, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
14 24 0.31
15 31 0.40
16 1 0.01
17 8 0.10
18 14 0.18
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:61675 original size:32 final size:30
Alignment explanation
Indices: 61626--61694 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 30
61616 CAACTCCAAT
61626 AATAAATCATCCAACTAATAAATTATTTAA
1 AATAAATCATCCAACTAATAAATTATTTAA
61656 AATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATC-ATCCA-ACTAATAAATTATTTAA
61688 AATAAAT
1 AATAAAT
61695 TATTTTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 8 0.22
31 5 0.14
32 24 0.65
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (30 bp):
AATAAATCATCCAACTAATAAATTATTTAA
Found at i:61703 original size:15 final size:15
Alignment explanation
Indices: 61674--61850 Score: 96
Period size: 15 Copynumber: 11.3 Consensus size: 15
61664 AATCCATACT
61674 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
61688 AATAAATTATTTTAA
1 AATAAATTATTTTAA
* ** *
61703 AATAAATCAATCAATACT
1 AATAAAT-TAT-TTTA-A
61721 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
*
61735 AATAAATCATTTTAA
1 AATAAATTATTTTAA
*
61750 AATAAATCAATCCATTTT-T
1 AATAAAT---T--ATTTTAA
* *
61769 TATAATTTATTTTAA
1 AATAAATTATTTTAA
*
61784 AATAAATCAATCCATTTTAT
1 AATAAAT---T--ATTTTAA
*
61804 AATAATTTATTTTAA
1 AATAAATTATTTTAA
61819 AAT-AATTATTTT-A
1 AATAAATTATTTTAA
*
61832 TA-AAATTATTTTAA
1 AATAAATTATTTTAA
61846 AATAA
1 AATAA
61851 TAACCTTATT
Statistics
Matches: 122, Mismatches: 22, Indels: 37
0.67 0.12 0.20
Matches are distributed among these distances:
13 11 0.09
14 32 0.26
15 42 0.34
16 3 0.02
17 4 0.03
18 8 0.07
19 5 0.04
20 17 0.14
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:61709 original size:47 final size:47
Alignment explanation
Indices: 61642--61764 Score: 221
Period size: 47 Copynumber: 2.6 Consensus size: 47
61632 TCATCCAACT
61642 AATAAATTA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
61688 AATAAATTATTTTAAAATAAATCAATCAATACTAATAAATTATTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
61735 AATAAATCATTTTAAAATAAATCAATCCAT
1 AATAAATTATTTTAAAATAAATCAATCCAT
61765 TTTTTATAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 9 0.12
47 64 0.88
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (47 bp):
AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:61765 original size:20 final size:20
Alignment explanation
Indices: 61742--61808 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
61732 TAAAATAAAT
61742 CATTTTAAAATAAATCAATC
1 CATTTTAAAATAAATCAATC
* *
61762 CATTTT----T-TAT-AATT
1 CATTTTAAAATAAATCAATC
*
61776 TATTTTAAAATAAATCAATC
1 CATTTTAAAATAAATCAATC
*
61796 CATTTTATAATAA
1 CATTTTAAAATAA
61809 TTTATTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 1 0.03
18 1 0.03
19 2 0.06
20 20 0.59
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (20 bp):
CATTTTAAAATAAATCAATC
Found at i:61786 original size:34 final size:35
Alignment explanation
Indices: 61743--61823 Score: 146
Period size: 34 Copynumber: 2.3 Consensus size: 35
61733 AAAATAAATC
*
61743 ATTTTAAAATAAATCAATCCATTTT-TTATAATTT
1 ATTTTAAAATAAATCAATCCATTTTATAATAATTT
61777 ATTTTAAAATAAATCAATCCATTTTATAATAATTT
1 ATTTTAAAATAAATCAATCCATTTTATAATAATTT
61812 ATTTTAAAATAA
1 ATTTTAAAATAA
61824 TTATTTTATA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 25 0.56
35 20 0.44
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (35 bp):
ATTTTAAAATAAATCAATCCATTTTATAATAATTT
Found at i:61840 original size:13 final size:14
Alignment explanation
Indices: 61797--61851 Score: 76
Period size: 14 Copynumber: 3.9 Consensus size: 14
61787 AAATCAATCC
61797 ATTTTATAATAATTT
1 ATTTTATAATAA-TT
*
61812 ATTTTAAAATAATT
1 ATTTTATAATAATT
61826 ATTTTATAA-AATT
1 ATTTTATAATAATT
*
61839 ATTTTAAAATAAT
1 ATTTTATAATAAT
61852 AACCTTATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.33
14 13 0.36
15 11 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTATAATAATT
Found at i:61845 original size:27 final size:27
Alignment explanation
Indices: 61797--61874 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
61787 AAATCAATCC
*
61797 ATTTTATAATAATTTATTTTAAAATAATT
1 ATTTTATAA-AA-TTATTTTAAAATAATA
61826 ATTTTATAAAATTATTTTAAAATAATA
1 ATTTTATAAAATTATTTTAAAATAATA
** *
61853 ACCTTATTAAATTA-TTTAAAAT
1 ATTTTATAAAATTATTTTAAAAT
61875 TATTTTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
26 8 0.18
27 26 0.58
28 2 0.04
29 9 0.20
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTTTATAAAATTATTTTAAAATAATA
Found at i:64651 original size:43 final size:44
Alignment explanation
Indices: 64510--64651 Score: 154
Period size: 43 Copynumber: 3.4 Consensus size: 44
64500 CTACAAATTC
* *
64510 GGTATATAGCGGCGTTTTTAGGATA-AAACGCAGATAAAGATAT
1 GGTATATAGCGGCGTTTTTAGGATACAAACGCCGATAAAGGTAT
* *
64553 GATATATAGCGGCGTTTTTAGGATACAAACGTCGAT----G-AT
1 GGTATATAGCGGCGTTTTTAGGATACAAACGCCGATAAAGGTAT
* ** * *
64592 GGTCTGGAGCGGCGTTTTTAGTATACAAACGCCGGTAAAGGT-T
1 GGTATATAGCGGCGTTTTTAGGATACAAACGCCGATAAAGGTAT
64635 GGTATATAGCGGCGTTT
1 GGTATATAGCGGCGTTT
64652 GTAACAAAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
39 31 0.39
43 40 0.51
44 8 0.10
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.30
Consensus pattern (44 bp):
GGTATATAGCGGCGTTTTTAGGATACAAACGCCGATAAAGGTAT
Done.