Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003859.1 Hibiscus syriacus cultivar Beakdansim tig00008296_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: 90230
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:253 original size:13 final size:13
Alignment explanation
Indices: 195--242 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
185 TGACCGGTCA
195 TGACCCGACCC--
1 TGACCCGACCCGT
206 -GACCCGACCCGT
1 TGACCCGACCCGT
* *
218 TTACCCGACCAGT
1 TGACCCGACCCGT
231 TGACCCGACCCG
1 TGACCCGACCCG
243 ACCCGTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.19, C:0.48, G:0.21, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:2593 original size:23 final size:24
Alignment explanation
Indices: 2546--2636 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
2536 TCAAATTTGA
* * *
2546 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
2570 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATCTGATACTTGACCTGG
*
2593 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
2617 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
2637 TTGAATTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:2615 original size:47 final size:48
Alignment explanation
Indices: 2546--2636 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
2536 TCAAATTTGA
* * *
2546 ATTCTGTTATGATACCTGACCTGGATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
*
2593 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
2637 TTGAATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:5032 original size:23 final size:24
Alignment explanation
Indices: 4985--5070 Score: 129
Period size: 24 Copynumber: 3.6 Consensus size: 24
4975 TCAAATTTGA
*
4985 ATTCTGTTATGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* * *
5009 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGG
5032 ATTCTGATATGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
5056 ATTCTGATATGATAC
1 ATTCTGATATGATAC
5071 TTAACTTGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 20 0.37
24 34 0.63
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACATGACCTGG
Found at i:9705 original size:3 final size:3
Alignment explanation
Indices: 9697--9749 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
9687 TTTTATATGC
9697 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9745 ATA AT
1 ATA AT
9750 GAGAGAGCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12288 original size:21 final size:21
Alignment explanation
Indices: 12232--12281 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
12222 TTTAATGGTC
*
12232 TGATACATCACTGAATTGAGG
1 TGATATATCACTGAATTGAGG
*
12253 TGATATATCACTGAATTGAGT
1 TGATATATCACTGAATTGAGG
12274 TGATATAT
1 TGATATAT
12282 TGTTGAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (21 bp):
TGATATATCACTGAATTGAGG
Found at i:18441 original size:20 final size:18
Alignment explanation
Indices: 18399--18437 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
18389 TTCCGCCTGG
18399 GGTATTGGGAAAAAATTC
1 GGTATTGGGAAAAAATTC
18417 GGTATTGGGAAAAAATTC
1 GGTATTGGGAAAAAATTC
18435 GGT
1 GGT
18438 GTATGTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.28
Consensus pattern (18 bp):
GGTATTGGGAAAAAATTC
Found at i:20503 original size:5 final size:5
Alignment explanation
Indices: 20493--20520 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
20483 TTCAACTGGA
20493 ATTTT ATTTT ATTTT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATT
20521 CCTAGGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:20704 original size:22 final size:21
Alignment explanation
Indices: 20665--20723 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
20655 TGATTTTTTA
* *
20665 TTAAAAATATAATTTTTTAAG
1 TTAAAAAAATAATATTTTAAG
20686 TTAAACAAAATAATATTTTATA-
1 TTAAA-AAAATAATATTTTA-AG
20708 TTAAAATAAA-AATATT
1 TTAAAA-AAATAATATT
20724 ATATTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 12 0.36
22 20 0.61
23 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAAAAAAATAATATTTTAAG
Found at i:26160 original size:2 final size:2
Alignment explanation
Indices: 26153--26190 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
26143 TACAAGGATA
26153 AT AT AT AT AT 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 AT AT AT AT AT
26191 GATAATGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32152 original size:21 final size:21
Alignment explanation
Indices: 32128--32181 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
32118 CTCGGAGGGA
32128 ACCGATTCCCCCCCAGGGGGT
1 ACCGATTCCCCCCCAGGGGGT
32149 ACCGATTCCCCCCCAGGGGGT
1 ACCGATTCCCCCCCAGGGGGT
32170 ACCGATTCCCCC
1 ACCGATTCCCCC
32182 TTGTATGACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.15, C:0.46, G:0.24, T:0.15
Consensus pattern (21 bp):
ACCGATTCCCCCCCAGGGGGT
Found at i:36565 original size:23 final size:21
Alignment explanation
Indices: 36513--36574 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
36503 TTTTGGTGCA
*
36513 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
36533 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
36554 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
36575 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:36600 original size:20 final size:20
Alignment explanation
Indices: 36515--36600 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
36505 TTGGTGCAGA
* *
36515 GGGAATCGA-TCCCCCCTTG
1 GGGAACCGATTCCCCCCTAG
*
36534 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATTCCCCC-CT--AG
*
36558 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCC-TAG
* *
36579 GGGAATCGATACCCCCCTAG
1 GGGAACCGATTCCCCCCTAG
36599 GG
1 GG
36601 TTCTGGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.23
21 23 0.43
22 1 0.02
23 16 0.30
24 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCTAG
Found at i:42427 original size:23 final size:23
Alignment explanation
Indices: 42400--42443 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42390 AGAATACCAA
*
42400 AAAGACATAAGAAAACATGTCGT
1 AAAGACAGAAGAAAACATGTCGT
* *
42423 AAAGACAGATGAAAACGTGTC
1 AAAGACAGAAGAAAACATGTC
42444 ATACATACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.14, G:0.20, T:0.16
Consensus pattern (23 bp):
AAAGACAGAAGAAAACATGTCGT
Found at i:51334 original size:87 final size:88
Alignment explanation
Indices: 51174--51336 Score: 256
Period size: 90 Copynumber: 1.8 Consensus size: 88
51164 TATTTAATTT
* * *
51174 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGATTAGGGTAACT
1 CAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCC--ATATGACTAGGGTAACT
51239 TAGATATAAAAATATTATTATATTC
64 TAGATATAAAAATATTATTATATTC
*
51264 CAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCC-TATGACTAGGGTAACTTG
1 CAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCATATGACTAGGGTAACTTA
*
51328 GCTATAAAA
66 GATATAAAA
51337 GGGTATGTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
87 24 0.35
90 44 0.65
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (88 bp):
CAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCATATGACTAGGGTAACTTA
GATATAAAAATATTATTATATTC
Found at i:54601 original size:75 final size:74
Alignment explanation
Indices: 54450--54632 Score: 181
Period size: 75 Copynumber: 2.4 Consensus size: 74
54440 CTCAGATATA
* * *
54450 AAAAGGTTTAACCATGGAAGACAAGGAATCAACCCCAGAGGTTGCTTTAAAACAAAAGGTCTAAA
1 AAAAGG-TTAATCATGGAAGATAATGAATCAACCCCAGAGGTTGCTTTAAAACAAAAGGTCT-AA
54515 TTTCTGATGTT
64 TTTCTGATGTT
* * * * * * *
54526 AGAAGGTTAATCATGGAAGATAATGAATCAATCCCAGAGGTTGGTTTGAACCAGAAGGTCT-CTT
1 AAAAGGTTAATCATGGAAGATAATGAATCAACCCCAGAGGTTGCTTTAAAACAAAAGGTCTAATT
*
54590 TCGTTGGTGTT
66 TC--TGATGTT
** *
54601 AAAAGCATAATCATGG-AGCATAATGAGTCAAC
1 AAAAGGTTAATCATGGAAG-ATAATGAATCAAC
54633 TCGACAGCTC
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
73 4 0.05
74 2 0.02
75 77 0.88
76 5 0.06
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (74 bp):
AAAAGGTTAATCATGGAAGATAATGAATCAACCCCAGAGGTTGCTTTAAAACAAAAGGTCTAATT
TCTGATGTT
Found at i:56210 original size:118 final size:118
Alignment explanation
Indices: 56002--56231 Score: 433
Period size: 118 Copynumber: 1.9 Consensus size: 118
55992 AGAGGAAAAC
*
56002 CCTCCATGCCTAATGCTTTGGTGCCTGTGAAACAACCTGTGTCAACAACAGTCCTTGAAAAGCGA
1 CCTCCATGCCTAATGCTTTGGTGCCTGTGAAACAACCAGTGTCAACAACAGTCCTTGAAAAGCGA
* *
56067 TCTTCCTTGAATTGGCAGACAGAAATGGACATGGCCAGTGAATCATGGACGAA
66 TCTTCCATGAATTGGCAAACAGAAATGGACATGGCCAGTGAATCATGGACGAA
56120 CCTCCATGCCTAATGCTTTGGTGCCTGTGAAACAACCAGTGTCAACAACAGTCCTTGAAAAGCGA
1 CCTCCATGCCTAATGCTTTGGTGCCTGTGAAACAACCAGTGTCAACAACAGTCCTTGAAAAGCGA
56185 TCTTCCATGAATTGGCAAACAGAAATGGACATGGCCAGTGAATCATG
66 TCTTCCATGAATTGGCAAACAGAAATGGACATGGCCAGTGAATCATG
56232 CCCTTCGTCC
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 109 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.23
Consensus pattern (118 bp):
CCTCCATGCCTAATGCTTTGGTGCCTGTGAAACAACCAGTGTCAACAACAGTCCTTGAAAAGCGA
TCTTCCATGAATTGGCAAACAGAAATGGACATGGCCAGTGAATCATGGACGAA
Found at i:57863 original size:17 final size:17
Alignment explanation
Indices: 57843--57875 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
57833 TTAAGGAATC
57843 TAAAATAAA-AATATAAT
1 TAAAA-AAATAATATAAT
57860 TAAAAAAATAATATAA
1 TAAAAAAATAATATAA
57876 ATTTGTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAAAATAATATAAT
Found at i:58974 original size:19 final size:19
Alignment explanation
Indices: 58947--58995 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
58937 GACCTAGTGT
*
58947 ATCGGTACACTCCAGGTGC
1 ATCGATACACTCCAGGTGC
*
58966 ATCGATACACTCTAGGTGC
1 ATCGATACACTCCAGGTGC
58985 ATCGATACACT
1 ATCGATACACT
58996 AATTGCATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (19 bp):
ATCGATACACTCCAGGTGC
Found at i:61360 original size:21 final size:22
Alignment explanation
Indices: 61327--61374 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
61317 AATATAAGTT
61327 CAAATTAAAAAATTAATC-AAAC
1 CAAATTAAAAAA-TAATCAAAAC
61349 CAAATT-AAAAATAATCAAAAC
1 CAAATTAAAAAATAATCAAAAC
61370 CAAAT
1 CAAAT
61375 ATATATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 5 0.20
21 14 0.56
22 6 0.24
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (22 bp):
CAAATTAAAAAATAATCAAAAC
Found at i:63347 original size:20 final size:21
Alignment explanation
Indices: 63322--63378 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 21
63312 ACCCGACCAG
*
63322 TGTATCGGTACACTC-CTGAA
1 TGTATCGGTACACTCAATGAA
*
63342 TGTATCGATACACATTCAATGAA
1 TGTATCGGTACAC--TCAATGAA
*
63365 TGCATCGGTACACT
1 TGTATCGGTACACT
63379 ATCATAGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 12 0.40
21 1 0.03
22 2 0.07
23 15 0.50
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (21 bp):
TGTATCGGTACACTCAATGAA
Found at i:64187 original size:12 final size:12
Alignment explanation
Indices: 64170--64197 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
64160 TAATTGCGAA
64170 AAAATAAAAATT
1 AAAATAAAAATT
64182 AAAATAAAAATT
1 AAAATAAAAATT
64194 AAAA
1 AAAA
64198 AATTCAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:64320 original size:8 final size:8
Alignment explanation
Indices: 64298--64338 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 8
64288 AATTAATTAT
64298 ATAATAATA
1 ATAATAA-A
64307 ATAATAAA
1 ATAATAAA
*
64315 AAAATAAA
1 ATAATAAA
64323 ATAATAGAA
1 ATAATA-AA
64332 ATAATAA
1 ATAATAA
64339 TACTAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (8 bp):
ATAATAAA
Found at i:66771 original size:84 final size:84
Alignment explanation
Indices: 66645--67118 Score: 441
Period size: 84 Copynumber: 5.7 Consensus size: 84
66635 CTGAATGAAA
* * * * * * * * *
66645 TCGAACTCGAATG-CATTTGTTGACAGATAACCCCTATAGCCTTGAGTTATGTTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGT
* *
66709 GCCTTGGATCTGAACGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * *
66728 TCGACCTCGAAGGTCTTTTGTTGGCGGATAGCCCTTCTCGCCTTGAGCTATGCTACAGATGTTGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGT
* * * *
66793 GCCTTTGAGCTGTGTGTAA
66 GCCTTGGAGCTGAGCGTAG
* * *
66812 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATAATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGT
* * *
66877 GCCTTAGAACTGAGCATAG
66 GCCTTGGAGCTGAGCGTAG
* ** * * * * ** *
66896 TTGAACTTTAAGGTCTTTTGTTGGCAAATGACCCTTCTTGCCTTAAGCTATATTACAAATGAAT-
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATG-ATG
*
66960 TGCCTTGGAGCTGAGTGTAG
65 TGCCTTGGAGCTGAGCGTAG
* * * * *
66980 TTGATCTCGAATGTCTTTTGTTGGCAGATAACCCTTTTCGCCTTGAGCTATGCTGCAAATGTTGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGT
* * *
67045 GCCTTTGAGCTGAGGGTAA
66 GCCTTGGAGCTGAGCGTAG
* *** * * *
67064 TCTAACTCGAAGGTC-TTCACTGACAGATAACCTTTCTCGCCTTGAGTTATGCTGC
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGC
67119 CAATACTTTC
Statistics
Matches: 309, Mismatches: 79, Indels: 6
0.78 0.20 0.02
Matches are distributed among these distances:
83 45 0.15
84 262 0.85
85 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:66911 original size:168 final size:168
Alignment explanation
Indices: 66625--67080 Score: 495
Period size: 168 Copynumber: 2.7 Consensus size: 168
66615 AAATTTGACA
* * * * * *
66625 TGCCCTTGAGCTGAATGAAATCGAACTCGAATG-CATTTGTTGACAGATAACCCCTATAGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTTGTTGGCAGATAACCCTTATAGCCTTG
* * * * * * * *
66689 AGTTATGTTGTAAATGATGTGCCTTGGATCTGAACGTAGTCGACCTCGAAGGTCTTTTGTTGGCG
66 AGTTATGCTGCAAATGATGTGCCTTAGAACTGAGCATAGTCGAACTCGAAGGTCTTTTGTTGGCA
* * * * *
66754 GAT-AGCCCTTCTCGCCTTGAGCTATGCTACAGATG-TT
131 AATGA-CCCTTCTCGCCTTAAGCTATACTACAAATGAAT
* * *
66791 GTGCCTTTGAGCTGTGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
1 -TGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTTGTTGGCAGATAACCCTTATAGCCTT
* * **
66856 GAGTTATGCTGCAAATAATGTGCCTTAGAACTGAGCATAGTTGAACTTTAAGGTCTTTTGTTGGC
65 GAGTTATGCTGCAAATGATGTGCCTTAGAACTGAGCATAGTCGAACTCGAAGGTCTTTTGTTGGC
* *
66921 AAATGACCCTTCTTGCCTTAAGCTATATTACAAATGAAT
130 AAATGACCCTTCTCGCCTTAAGCTATACTACAAATGAAT
* * * * * *
66960 TGCCTTGGAGCTGAGTGTAGTTGATCTCGAATGTCTTTTGTTGGCAGATAACCCTTTTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTTGTTGGCAGATAACCCTTATAGCCTTG
* * * * ** * *
67025 AGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGGGTAATCTAACTCGAAGGTCTT
66 AGTTATGCTGCAAATGATGTGCCTTAGAACTGAGCATAGTCGAACTCGAAGGTCTT
67081 CACTGACAGA
Statistics
Matches: 238, Mismatches: 48, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
167 28 0.12
168 208 0.87
169 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (168 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTTGTTGGCAGATAACCCTTATAGCCTTG
AGTTATGCTGCAAATGATGTGCCTTAGAACTGAGCATAGTCGAACTCGAAGGTCTTTTGTTGGCA
AATGACCCTTCTCGCCTTAAGCTATACTACAAATGAAT
Found at i:67645 original size:19 final size:19
Alignment explanation
Indices: 67621--67659 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
67611 GCTGATCTGG
67621 CCCTTGGAATCAATCATGC
1 CCCTTGGAATCAATCATGC
*
67640 CCCTTGGAATCGATCATGC
1 CCCTTGGAATCAATCATGC
67659 C
1 C
67660 TCATTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (19 bp):
CCCTTGGAATCAATCATGC
Found at i:68437 original size:95 final size:95
Alignment explanation
Indices: 68239--68496 Score: 344
Period size: 94 Copynumber: 2.7 Consensus size: 95
68229 GGTTATCTGG
* * * *
68239 ATCCATAAAGCCTGTGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATCATTGTATAG-AT
1 ATCCATAAAGCCTGGGCATTTAACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TATTGTAT
68303 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
68337 ATCCATAAA-CCTGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATT
1 ATCCATAAAGCCT-GGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATT
* *
68401 ATAATCACCTTTATGAGGCTAGCTGAATCTT
65 ATAATCACCTTTATCAGGCTAGCTGAATATT
* * * * *
68432 ATCCATAAAGCC-GGGCCTTTAACCAATTGTTTTAGAGGGACAATTGAAGCTTTATTGTAT-TTA
1 ATCCATAAAGCCTGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
68495 TA
66 TA
68497 TAATATTATA
Statistics
Matches: 146, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
93 5 0.03
94 47 0.32
95 45 0.31
96 4 0.03
97 4 0.03
98 41 0.28
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGCCTGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:68499 original size:95 final size:96
Alignment explanation
Indices: 68239--68500 Score: 345
Period size: 95 Copynumber: 2.7 Consensus size: 96
68229 GGTTATCTGG
* * *
68239 ATCCATAAAGCCTGTGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA--TATCATTGTATAGA
1 ATCCATAAAGCCTGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCT-TTATTGTAT--A
68302 TATTATAATCACCTTTATCAGGCTAGCTGAATATT
63 TA-TATAATCACCTTTATCAGGCTAGCTGAATATT
68337 ATCCATAAA-CCTGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-
1 ATCCATAAAGCCT-GGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATA
* *
68400 TATAATCACCTTTATGAGGCTAGCTGAATCTT
65 TATAATCACCTTTATCAGGCTAGCTGAATATT
* * * * * *
68432 ATCCATAAAGCC-GGGCCTTTAACCAATTGTTTTAGAGGGACAATTGAAGCTTTATTGTATTTAT
1 ATCCATAAAGCCTGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATAT
68496 ATAAT
66 ATAAT
68501 ATTATAATAT
Statistics
Matches: 148, Mismatches: 11, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
94 44 0.30
95 45 0.30
96 2 0.01
97 5 0.03
98 43 0.29
99 8 0.05
100 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (96 bp):
ATCCATAAAGCCTGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATAT
ATAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:74150 original size:95 final size:98
Alignment explanation
Indices: 73972--74157 Score: 281
Period size: 95 Copynumber: 1.9 Consensus size: 98
73962 AAGCCGAGGC
* *
73972 GTTTAACCAATTACTCTAGAGGGATAACTCAATATCATTATATAGATATTATAATCACCTTTATC
1 GTTTAACCAATTACTCTAGAGGGACAACTCAATAGCATTATATAGATATTATAATCACCTTTATC
74037 AGGCTAGCTGAATATTATCCATAAAGACAGAGT
66 AGGCTAGCTGAATATTATCCATAAAGACAGAGT
* *
74070 GTTTAACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TATTGTATATTATAATCACCTTTAT
1 GTTTAACCAATTACTCTAGAGGGACAACTCAATAGCATTATATAG-ATATTATAATCACCTTTAT
* *
74131 CTGGCTAGCTGAATCTTATCCATAAAG
65 CAGGCTAGCTGAATATTATCCATAAAG
74158 CTATGGCATT
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
94 4 0.05
95 46 0.57
96 2 0.02
97 1 0.01
98 28 0.35
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (98 bp):
GTTTAACCAATTACTCTAGAGGGACAACTCAATAGCATTATATAGATATTATAATCACCTTTATC
AGGCTAGCTGAATATTATCCATAAAGACAGAGT
Found at i:74170 original size:95 final size:94
Alignment explanation
Indices: 73973--74204 Score: 279
Period size: 95 Copynumber: 2.4 Consensus size: 94
73963 AGCCGAGGCG
* * *
73973 TTTAACCAATTACTCTAGAGGGATAACTCAATATCATTATATAGATATTATAATCACCTTTATCA
1 TTTAACCAATTGCTCTAGAGGGATAACTC-A-AGC-TT-TATTGATATTATAATCACCTTTATCA
**
74038 GGCTAGCTGAATATTATCCATAAAGACAGAGTG
62 GGCTAGCTGAATATTATCCATAAAGACAGAGCA
* *
74071 TTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTATCTGGC
1 TTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTG-ATATTATAATCACCTTTATCAGGC
*
74136 TAGCTGAATCTTATCCATAAAG-CTATG-GCA
65 TAGCTGAATATTATCCATAAAGAC-A-GAGCA
* * * *
74166 TTTAACCAATTGATTTAGAGGGATATCTGAAGCTTTATT
1 TTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATT
74205 ATTTTTATAT
Statistics
Matches: 118, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
94 5 0.04
95 82 0.69
96 3 0.03
97 1 0.01
98 27 0.23
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (94 bp):
TTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGATATTATAATCACCTTTATCAGGCT
AGCTGAATATTATCCATAAAGACAGAGCA
Found at i:78306 original size:20 final size:21
Alignment explanation
Indices: 78254--78307 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
78244 GATGAGAAAA
*
78254 ATATGTATGTGATATATGTTAT
1 ATAT-TATGTAATATATGTTAT
78276 ATAATTA--TAATATATG-TAT
1 AT-ATTATGTAATATATGTTAT
78295 ATATTATGTAATA
1 ATATTATGTAATA
78308 CATATATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 4 0.14
19 5 0.18
20 13 0.46
22 4 0.14
23 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (21 bp):
ATATTATGTAATATATGTTAT
Found at i:79510 original size:84 final size:84
Alignment explanation
Indices: 79219--79785 Score: 649
Period size: 84 Copynumber: 6.8 Consensus size: 84
79209 CAAATAGCCT
* * * * * *
79219 TTCTTCCCTTGAGCTACGCTTCAAATGATGTACCTTTGAGCTGAGTGTAATCGAACTTGAAGGTC
1 TTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTC
79284 ---T-TTGGTAGATAACCC
66 TTTTGTTGGTAGATAACCC
* * *
79299 TTCTTGCCATGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTATTCGAACTCGAAGATC
1 TTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTC
79364 -TTTGTTGGTAGATAACCC
66 TTTTGTTGGTAGATAACCC
* * * * * *
79382 TTCTAGCATTGAGTTATGTTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
1 TTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTC
* *
79447 TTTTGTTGGAAGATAGCCC
66 TTTTGTTGGTAGATAACCC
* * * * * *
79466 TTCTTGCCTTGAGCTATGCTGTAGATGTTGTCCCTTTGAACTGAGTGTAATCGAACTCGAAGGTC
1 TTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTC
* *
79531 TTTTGTTGGCATATAACCC
66 TTTTGTTGGTAGATAACCC
* * * * * * * **
79550 TTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTAGAGCTGAGCATAGTTGAACTTTAAGGTC
1 TTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTC
* *
79615 TTTTGTTGGAAAATAACCC
66 TTTTGTTGGTAGATAACCC
** * * * *
79634 TTCTTGCCTTGAGCTATATTGCAAAATGATGTTCCTTGGAGCTGAGCGTAGTCGAACTCGAATGT
1 TTCTTGCCTTGAGCTATGCTGC-AAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGT
*
79699 ATTTTGTTGGTAGATAACCC
65 CTTTTGTTGGTAGATAACCC
* * * * * *
79719 TTCTCGCCTTGAGCTATGCTACAAATGTTGTGCCTTTGAGCTGAGAGTAATCTAACTCAAAGGTC
1 TTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTC
79784 TT
66 TT
79786 GGCTGACAGA
Statistics
Matches: 406, Mismatches: 76, Indels: 6
0.83 0.16 0.01
Matches are distributed among these distances:
80 56 0.14
82 1 0.00
83 70 0.17
84 209 0.51
85 70 0.17
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (84 bp):
TTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTC
TTTTGTTGGTAGATAACCC
Found at i:79722 original size:253 final size:248
Alignment explanation
Indices: 79219--79785 Score: 690
Period size: 253 Copynumber: 2.3 Consensus size: 248
79209 CAAATAGCCT
* * * *
79219 TTCTTCCCTTGAGCTACGCTTCAAATGATGTACCTTTGAGCTGAGTGTAATCGAACTTGAAGGTC
1 TTCTTGCCTTGAGCTATGCTT-AAATGTTGTACCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
* * * *
79284 --TTTGGTAGATAACCCTTCTTGCCATGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGT
65 TTTTTGGCAGATAACCCTTCTAGCCATGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCAT
* * * *
79347 ATTCGAACTCGAAGATCTTTGTTGGTAGATAACCCTTCTAGCATTGAGTTATGTTACAAATGATG
130 ATTCGAACTCGAAGATCTTTGTTGGAAAATAACCCTTCTAGCATTGAGCTATATTACAAATGATG
* * * *
79412 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGAAGATAGCCC
195 TGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTATTTTGTTGGAAGATAACCC
* * *
79466 TTCTTGCCTTGAGCTATGCTGTAGATGTTGTCCCTTTGAACTGAGTGTAATCGAACTCGAAGGTC
1 TTCTTGCCTTGAGCTATGCT-TAAATGTTGTACCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
* * * *
79531 TTTTGTTGGCATATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTAGAGCTGAGC
65 -TTT-TTGGCAGATAACCCTTCTAGCCATGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGC
** * * * *
79596 ATAGTT-GAACTTTAAGGTCTTTTGTTGGAAAATAACCCTTCTTGCCTTGAGCTATATTGCAAAA
128 ATA-TTCGAACTCGAAGATC-TTTGTTGGAAAATAACCCTTCTAGCATTGAGCTATATTAC-AAA
* * * *
79660 TGATGTTCCTTGGAGCTGAGCGTAGTCGAACTCGAATGTATTTTGTTGGTAGATAACCC
190 TGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTATTTTGTTGGAAGATAACCC
* * * * * *
79719 TTCTCGCCTTGAGCTATGCTACAAATGTTGTGCCTTTGAGCTGAGAGTAATCTAACTCAAAGGTC
1 TTCTTGCCTTGAGCTATGCT-TAAATGTTGTACCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
79784 TT
65 TT
79786 GGCTGACAGA
Statistics
Matches: 270, Mismatches: 42, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
247 56 0.21
248 1 0.00
250 1 0.00
251 65 0.24
252 37 0.14
253 110 0.41
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (248 bp):
TTCTTGCCTTGAGCTATGCTTAAATGTTGTACCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
TTTTGGCAGATAACCCTTCTAGCCATGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCATA
TTCGAACTCGAAGATCTTTGTTGGAAAATAACCCTTCTAGCATTGAGCTATATTACAAATGATGT
GCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTATTTTGTTGGAAGATAACCC
Found at i:81132 original size:95 final size:95
Alignment explanation
Indices: 80923--81183 Score: 328
Period size: 95 Copynumber: 2.7 Consensus size: 95
80913 TGGCTAGCTG
* * *
80923 TATCCATAAAGCCGGGGCATTTAACCAATTGCTATAGAGGGACAACTCAATATCATTGTATAG-A
1 TATCCATAAAGACGGGGCATTTAACCAATTGCTATAGAGGGACAACTC-A-AGC-TT-TATTGTA
*
80987 TATTATAATCACCTTTATCAGGCTAGCTGAATAT
62 TATTATAATCACCTTTATCAGGCTAGATGAATAT
** * *
81021 TATCCATAAAGACGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTTTTGTATATT
1 TATCCATAAAGACGGGGCATTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTATTGTATATT
*
81086 ATAATCACCTTTATCAGGCTAGATGAATCT
66 ATAATCACCTTTATCAGGCTAGATGAATAT
* ** * * *
81116 TATCCATAAAGTCGGGGCATTTAATAAAATTGCTTTAGAGGGACAGCTAAAGCTTTATTGTAT-T
1 TATCCATAAAGACGGGGCATTTAA-CCAATTGCTATAGAGGGACAACTCAAGCTTTATTGTATAT
81180 TATA
65 TATA
81184 TAATACTATA
Statistics
Matches: 143, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
94 3 0.02
95 61 0.43
96 34 0.24
97 1 0.01
98 44 0.31
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (95 bp):
TATCCATAAAGACGGGGCATTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTATTGTATATT
ATAATCACCTTTATCAGGCTAGATGAATAT
Found at i:82712 original size:17 final size:17
Alignment explanation
Indices: 82682--82715 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
82672 GCAGATGATA
82682 AAAATAAAATAAAAGAG
1 AAAATAAAATAAAAGAG
82699 AAAA-AAAATGAAAAGAG
1 AAAATAAAAT-AAAAGAG
82716 TTAGTCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (17 bp):
AAAATAAAATAAAAGAG
Found at i:83402 original size:95 final size:94
Alignment explanation
Indices: 83231--83486 Score: 320
Period size: 95 Copynumber: 2.7 Consensus size: 94
83221 GGCTAGCTGG
* * *
83231 ATCCATAAAGCTGAGGCGTTTAACCAATTGCTATAGATGGACAACTCAA--TATTATTGTATAGA
1 ATCCATAAAGC-GGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAAGCT-TTATTGTATA-T
* *
83294 TATTATAATCTTTATCAGGCTAGCTGAATATT
63 TATAATAACCTTTATCAGGCTAGCTGAATATT
* *
83326 ATCCATAAAGACGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAG-CGGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTATTGTATATTA
* *
83391 TAATCACCTTTATCAGGCTAGCTGAATCTT
65 TAATAACCTTTATCAGGCTAGCTGAATATT
* * * * *
83421 ATCCATAAAGTTGGGGCGTTTAACCAATTGCTTTAGAGGGCCAGCTGAAGCTTTATTGTAT-TTA
1 ATCCATAAAG-CGGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTATTGTATATTA
83485 TA
65 TA
83487 TAATATTATA
Statistics
Matches: 142, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
94 5 0.04
95 125 0.88
96 11 0.08
97 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (94 bp):
ATCCATAAAGCGGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTATTGTATATTAT
AATAACCTTTATCAGGCTAGCTGAATATT
Found at i:87553 original size:20 final size:21
Alignment explanation
Indices: 87501--87554 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
87491 AATGAGAAAA
*
87501 ATATGTATGTGATATATGTTAT
1 ATAT-TATGTAATATATGTTAT
87523 ATAATTA--TAATATATG-TAT
1 AT-ATTATGTAATATATGTTAT
87542 ATATTATGTAATA
1 ATATTATGTAATA
87555 CATATATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 4 0.14
19 5 0.18
20 13 0.46
22 4 0.14
23 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (21 bp):
ATATTATGTAATATATGTTAT
Found at i:87587 original size:19 final size:20
Alignment explanation
Indices: 87550--87589 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
87540 ATATATTATG
87550 TAATACATATATACTATAAA
1 TAATACATATATACTATAAA
87570 TAATAGCATATA-AC-ATAAA
1 TAATA-CATATATACTATAAA
87589 T
1 T
87590 TAACACGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 7 0.37
21 6 0.32
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (20 bp):
TAATACATATATACTATAAA
Found at i:88418 original size:164 final size:165
Alignment explanation
Indices: 88103--88757 Score: 800
Period size: 164 Copynumber: 4.0 Consensus size: 165
88093 GTATTGTTAA
* * * * *
88103 CAGATAGCCTTTCT-GCATTGAGCTATTCTTCAAATGATATGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTA-TGTTCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* ** *
88167 CTTGAAGGTC-T-TTGGCAGATTGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTG
65 CTCGAAGGTCTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTG
88230 AGCTGAGCGTATTCGAACTCGAAGGTC-TTTGTTGG
130 AGCTGAGCGTATTCGAACTCGAAGGTCTTTTGTTGG
* * *
88265 TAGATAACCCTTCTAGCATTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGTT-CAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * * *
88330 CTCGAAGGTCTTG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGG
65 CTCGAAGGTCTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTG
* *
88394 AACTGAGCGTAGTCGAACTCGAAGG-CTTTTGTTGG
130 AGCTGAGCGTATTCGAACTCGAAGGTCTTTTGTTGG
* * * *
88429 CAGATAACCCTTCTCGCCTTGAGCTATGCTTCAGATGTTGTGCCTTTGAGCTGAGTGTAATCAAA
1 CAGATAACCCTTCTAGCCTTGAGCTATG-TTCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* *
88494 CTCGAAGGTCTTTTGTTGGCATATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
65 CTCGAAGGTC--TTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTT
* * * **
88559 AGAGCTGAGCATATTTGAACTTTAAGGTCTTTTGTTGG
128 TGAGCTGAGCGTATTCGAACTCGAAGGTCTTTTGTTGG
* ** * * * *
88597 CAAATAACCCTTCTTTCCTTGAGCTATATTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGTT-CAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * * *
88662 CTCGAATGTATTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGTTGTGCCTT
65 CTCGAA-G-GTCTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTT
* * * *
88727 TGAGCTGAGGGTAATCTAACTCAAAGGTCTT
128 TGAGCTGAGCGTATTCGAACTCGAAGGTCTT
88758 GGCTGACAGA
Statistics
Matches: 423, Mismatches: 57, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
162 14 0.03
163 53 0.13
164 141 0.33
165 2 0.00
166 3 0.01
167 68 0.16
168 140 0.33
169 1 0.00
170 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (165 bp):
CAGATAACCCTTCTAGCCTTGAGCTATGTTCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
TCGAAGGTCTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGA
GCTGAGCGTATTCGAACTCGAAGGTCTTTTGTTGG
Found at i:88779 original size:84 final size:83
Alignment explanation
Indices: 88103--88796 Score: 763
Period size: 84 Copynumber: 8.4 Consensus size: 83
88093 GTATTGTTAA
* * * * * * *
88103 CAGATAGCCTTTCT-GCATTGAGCTATTCTTCAAATGATATGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAA
*
88167 CTTGAAGGTC--T-TTGG
66 CTCGAAGGTCTTTGTTGG
** * *
88182 CAGATTGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTATTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAA
88247 CTCGAAGGTCTTTGTTGG
66 CTCGAAGGTCTTTGTTGG
* * * * *
88265 TAGATAACCCTTCTAGCATTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAA
*
88330 CTCGAAGGTC-TTG-TGA
66 CTCGAAGGTCTTTGTTGG
* * * * *
88346 CAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGGAACTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAA
88411 CTCGAAGG-CTTTTGTTGG
66 CTCGAAGGTC-TTTGTTGG
* * * * * *
88429 CAGATAACCCTTCTCGCCTTGAGCTATGCTTCAGATGTTGTGCCTTTGAGCTGAGTGTAATCAAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAA
88494 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTC-TTTGTTGG
* * * * * *
88513 CATATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTAGAGCTGAGCATATTTGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAA
**
88578 CTTTAAGGTCTTTTGTTGG
66 CTCGAAGGTC-TTTGTTGG
* ** ** * * *
88597 CAAATAACCCTTCTTTCCTTGAGCTATATTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAA
* *
88662 CTCGAATGTATTTTGTTGG
66 CTCGAAGGT-CTTTGTTGG
* * * *
88681 CAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGGGTAATCTAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAA
* * * *
88746 CTCAAAGGTCTTGGCTGA
66 CTCGAAGGTCTTTGTTGG
* * * *
88764 CAGATAAAACTTTCTCGCCTTGAGTTATGCTGC
1 CAGAT-AACCCTTCTAGCCTTGAGCTATGCTGC
88797 CAATAGTTTC
Statistics
Matches: 518, Mismatches: 87, Indels: 15
0.84 0.14 0.02
Matches are distributed among these distances:
79 12 0.02
80 54 0.10
81 67 0.13
82 7 0.01
83 145 0.28
84 233 0.45
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (83 bp):
CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAA
CTCGAAGGTCTTTGTTGG
Found at i:90075 original size:92 final size:94
Alignment explanation
Indices: 89888--90137 Score: 314
Period size: 92 Copynumber: 2.7 Consensus size: 94
89878 AGTTGGATCT
* * *
89888 ATAAAGCCGGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAATATCATTGTATAG-ATATTA
1 ATAAAGACGGGGCGTTTAACCAATTGCTATAGAGGGACAACTC-A-AGCTTTGT-T-GTATATTA
89952 TAATCACCTTATCAGGCTAGCTGAATATTATCC
62 TAATCACCTTATCAGGCTAGCTGAATATTATCC
*
89985 ATAAAGACGGGGCGTTTAACCAATTG-TCTAGAGGGAC-ACTCAAGCTTTGTTGTATATTATAAT
1 ATAAAGACGGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTGTTGTATATTATAAT
* *
90048 CACTTTTATCA-GCTAGCTGAATCTTATCC
66 CAC-CTTATCAGGCTAGCTGAATATTATCC
* * * * *
90077 ATAAAGTCAGGGCG-TTAACCAATTGCTTTAGAGGGACAACTGAAGCTTTATTGTAT-TTATA
1 ATAAAGACGGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTGTTGTATATTATA
90138 TAATATTATA
Statistics
Matches: 138, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
91 12 0.09
92 58 0.42
93 28 0.20
94 1 0.01
95 4 0.03
96 10 0.07
97 25 0.18
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (94 bp):
ATAAAGACGGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTGTTGTATATTATAAT
CACCTTATCAGGCTAGCTGAATATTATCC
Done.