Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004032.1 Hibiscus syriacus cultivar Beakdansim tig00008810_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: 143968
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:364 original size:208 final size:207
Alignment explanation
Indices: 1--400 Score: 676
Period size: 208 Copynumber: 1.9 Consensus size: 207
*
1 AATCAGTTGATTACATAGCCAATAAAACCCCTTGCAGAGTCTAAATGGTAAGCTAGGAATTGGTA
1 AATCAGTTGATTACATAGCCAATAAAACCCCTTGCAGAGTCCAAATGGTAAGCTAGGAATTGGTA
* * * * *
66 AGACAAGCTTTCTTTGAGGGTTTAGGGACTCAACTCTTCCCATGTAAGGACTACATGATTGAACA
66 AGACAAGCTTTCTTTAAGGGTTTAGGGACTCAACCCCTCCCAGGTAAAGACTACATGATTGAACA
131 TTACATAGAATAGTTGTATTCAATTCTTGAAGAATTGTTCTTCATTGTATATAAGAATAGTTGGG
131 TTACATAGAATAGTTGTATTCAATTCTTGAAGAATTGTTCTTCATTGTATATAAGAATAGTTGGG
196 ATTATCCAGATT
196 ATTATCCAGATT
* *
208 AATCATGTTGATTGCATAGCCAATAAAACCCCTTGCAGGGTCCAAATGGTAAGCTAGGAATTGGT
1 AATCA-GTTGATTACATAGCCAATAAAACCCCTTGCAGAGTCCAAATGGTAAGCTAGGAATTGGT
* *
273 AAGACAAGTTTTTTTTAAGGGTTTAGGGACTCAACCCCTCCCAGGTAAAGACTGA-ATGATTGAA
65 AAGACAAGCTTTCTTTAAGGGTTTAGGGACTCAACCCCTCCCAGGTAAAGACT-ACATGATTGAA
*
337 CATTACATAGAATAGTTGTATTCAATTCTTGAAGAATTGTTCTTCATTGTATTTAAGAATAGTT
129 CATTACATAGAATAGTTGTATTCAATTCTTGAAGAATTGTTCTTCATTGTATATAAGAATAGTT
401 ATAATGATCT
Statistics
Matches: 180, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
207 5 0.03
208 174 0.97
209 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (207 bp):
AATCAGTTGATTACATAGCCAATAAAACCCCTTGCAGAGTCCAAATGGTAAGCTAGGAATTGGTA
AGACAAGCTTTCTTTAAGGGTTTAGGGACTCAACCCCTCCCAGGTAAAGACTACATGATTGAACA
TTACATAGAATAGTTGTATTCAATTCTTGAAGAATTGTTCTTCATTGTATATAAGAATAGTTGGG
ATTATCCAGATT
Found at i:499 original size:18 final size:17
Alignment explanation
Indices: 468--529 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 17
458 ACATTTCACG
468 GTTATCAGATATTTACA
1 GTTATCAGATATTTACA
* * *
485 ATTATCAGATGATTTTCG
1 GTTATCAGAT-ATTTACA
*
503 GTTATCAGATTTTTTACA
1 GTTATCAGA-TATTTACA
521 GTTATCAGA
1 GTTATCAGA
530 CGTATATTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 9 0.25
18 26 0.72
19 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (17 bp):
GTTATCAGATATTTACA
Found at i:2184 original size:21 final size:21
Alignment explanation
Indices: 2134--2184 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2124 ATATGTTCAC
* *
2134 TAATTTTTCAAATTGGCTATT
1 TAATTTTTTAAATTGACTATT
* *
2155 TAATATTTTAAATTGACTTTT
1 TAATTTTTTAAATTGACTATT
2176 TAATTTTTT
1 TAATTTTTT
2185 GAATGGACCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (21 bp):
TAATTTTTTAAATTGACTATT
Found at i:2851 original size:31 final size:33
Alignment explanation
Indices: 2813--2881 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
2803 ACCTTACAAC
*
2813 TCCCTAGTTTTT-C-GGGCTAAACTAGAACCTT
1 TCCCTAGTTTTTACAGGGATAAACTAGAACCTT
*
2844 TCCCTAGTTTTTACATGGGATAAGCTAGAACCTT
1 TCCCTAGTTTTTACA-GGGATAAACTAGAACCTT
2878 TCCC
1 TCCC
2882 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 12 0.36
32 1 0.03
34 20 0.61
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (33 bp):
TCCCTAGTTTTTACAGGGATAAACTAGAACCTT
Found at i:3244 original size:20 final size:20
Alignment explanation
Indices: 3215--3288 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
3205 GCAGCCTTCG
*
3215 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
**
3235 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-CAGGA
* *
3256 AGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
3276 TGCATCGATGCAC
1 TGCATCGATGCAC
3289 TAAGTGCATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:3378 original size:21 final size:21
Alignment explanation
Indices: 3310--3407 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
3300 GGTGTTTGAG
*
3310 TGCATGGATGCACTGCATGG-
1 TGCATGGATGCACTGCAGGGA
* *
3330 TGCATCGATGCACT--AGTGCA
1 TGCATGGATGCACTGCAG-GGA
3350 TGTGCATGGATGCACTGCAGGGA
1 --TGCATGGATGCACTGCAGGGA
*
3373 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
3394 TGCATGGATGCACT
1 TGCATGGATGCACT
3408 TTGCCCTTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 13 0.20
21 34 0.52
22 13 0.20
23 2 0.03
24 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.23
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:3389 original size:13 final size:14
Alignment explanation
Indices: 3310--3377 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 14
3300 GGTGTTTGAG
3310 TGCATGGATGCA-C
1 TGCATGGATGCATC
3323 TGCATGG-TGCATC
1 TGCATGGATGCATC
* *
3336 GATGCACTAG-TGCATG
1 --TGCA-TGGATGCATC
3352 TGCATGGATGCA-C
1 TGCATGGATGCATC
*
3365 TGCAGGGATGCAT
1 TGCATGGATGCAT
3378 GGATGCACTG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
12 4 0.09
13 21 0.48
14 8 0.18
15 4 0.09
16 7 0.16
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.25
Consensus pattern (14 bp):
TGCATGGATGCATC
Found at i:3480 original size:30 final size:30
Alignment explanation
Indices: 3446--3515 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
3436 GAATTTAATG
3446 GACTTTGAATTATTTTTGAAACCTTTTAAA
1 GACTTTGAATTATTTTTGAAACCTTTTAAA
3476 GACTTTGAATTATTTTTGAAACCTTTTAAA
1 GACTTTGAATTATTTTTGAAACCTTTTAAA
*
3506 AACTTTGAAT
1 GACTTTGAAT
3516 AAATTCAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (30 bp):
GACTTTGAATTATTTTTGAAACCTTTTAAA
Found at i:4896 original size:88 final size:88
Alignment explanation
Indices: 4787--4963 Score: 336
Period size: 88 Copynumber: 2.0 Consensus size: 88
4777 TTCTAAATCA
*
4787 TTTTTCAAAATTTCATTTTGGCTTTCAAAATCTATTTTTGTGTTCAAAAGAAAATCGTTTTCGAT
1 TTTTTCAAAATTTCATTTTGGCTTTCAAAATCTATTTTTATGTTCAAAAGAAAATCGTTTTCGAT
4852 TTTAAATTTTGAAATCATTTTCT
66 TTTAAATTTTGAAATCATTTTCT
*
4875 TTTTTCAAAATTTCATTTTGGCTTTCAAAATCTATTTTTATTTTCAAAAGAAAATCGTTTTCGAT
1 TTTTTCAAAATTTCATTTTGGCTTTCAAAATCTATTTTTATGTTCAAAAGAAAATCGTTTTCGAT
4940 TTTAAATTTTGAAATCATTTTCT
66 TTTAAATTTTGAAATCATTTTCT
4963 T
1 T
4964 ATATTTGGAG
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (88 bp):
TTTTTCAAAATTTCATTTTGGCTTTCAAAATCTATTTTTATGTTCAAAAGAAAATCGTTTTCGAT
TTTAAATTTTGAAATCATTTTCT
Found at i:6242 original size:20 final size:20
Alignment explanation
Indices: 6213--6346 Score: 187
Period size: 20 Copynumber: 6.7 Consensus size: 20
6203 GTAGCCTTCG
* *
6213 TGCATGGATGCACAGTAGGA
1 TGCATCGATGCACAGAAGGA
***
6233 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-AAGGA
*
6254 TGCATCGATGCACAGAATGA
1 TGCATCGATGCACAGAAGGA
*
6274 TGCATCGATGCACATAAGGA
1 TGCATCGATGCACAGAAGGA
*
6294 TGCATCGATGCACAGAAAGA
1 TGCATCGATGCACAGAAGGA
6314 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGAAGGA
6334 TGCATCGATGCAC
1 TGCATCGATGCAC
6347 TAAGTGCATT
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
20 85 0.83
21 17 0.17
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGAAGGA
Found at i:6414 original size:22 final size:23
Alignment explanation
Indices: 6381--6423 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
6371 ATGGATGCAC
6381 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
6404 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
6424 GCAGGGGTGC
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:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:7338 original size:2 final size:2
Alignment explanation
Indices: 7331--7389 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
7321 AGAATTTTCT
7331 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7373 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
7390 TCATAGTCAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9284 original size:56 final size:55
Alignment explanation
Indices: 9194--9389 Score: 241
Period size: 56 Copynumber: 3.5 Consensus size: 55
9184 CGGGGTCCCA
* * * *
9194 AAAAATAGGAGTCCCGAAATCGAATATATCTATCAGTTGTTCCCATTAATAAACAT
1 AAAAATAGG-GCCCCGAAATCGAATATATATATCAGTTGTTACCATTAAGAAACAT
* * *
9250 AAAAATAGGAGCCCCGAAATCGAGTATATATATCAGTTGTTATCATTAAGAAATAT
1 AAAAATAGG-GCCCCGAAATCGAATATATATATCAGTTGTTACCATTAAGAAACAT
* * * * *
9306 AAAAATTAGGGCTCCGAAATCGAGTATATTTATCAGTTGTTGCCATTAAGAAGCAT
1 AAAAA-TAGGGCCCCGAAATCGAATATATATATCAGTTGTTACCATTAAGAAACAT
9362 AAAAATAGGGCCCCCGAAAT-GAATATAT
1 AAAAATAGGG-CCCCGAAATCGAATATAT
9390 CTAAAAAATA
Statistics
Matches: 123, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
55 12 0.10
56 107 0.87
57 4 0.03
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (55 bp):
AAAAATAGGGCCCCGAAATCGAATATATATATCAGTTGTTACCATTAAGAAACAT
Found at i:13619 original size:23 final size:22
Alignment explanation
Indices: 13593--13635 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
13583 ATTTTTGAAG
*
13593 ATAAATAAATAAATTGTATAACC
1 ATAAATAAAGAAATTG-ATAACC
*
13616 ATAAATTAAGAAATTGATAA
1 ATAAATAAAGAAATTGATAA
13636 ATGAATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (22 bp):
ATAAATAAAGAAATTGATAACC
Found at i:20081 original size:13 final size:13
Alignment explanation
Indices: 20063--20089 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20053 TATTTCTTTT
20063 ATGTAGCTCGATG
1 ATGTAGCTCGATG
20076 ATGTAGCTCGATG
1 ATGTAGCTCGATG
20089 A
1 A
20090 ATGAGCAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (13 bp):
ATGTAGCTCGATG
Found at i:22785 original size:19 final size:19
Alignment explanation
Indices: 22752--22796 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
22742 TAGGTCTCCA
*
22752 GGAGCACACGACGACTTAT
1 GGAGCACACGACGACCTAT
22771 GGAGCACAC-AGCGACCTAT
1 GGAGCACACGA-CGACCTAT
*
22790 GTAGCAC
1 GGAGCAC
22797 TTGGCGACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.31, C:0.29, G:0.27, T:0.13
Consensus pattern (19 bp):
GGAGCACACGACGACCTAT
Found at i:23064 original size:12 final size:12
Alignment explanation
Indices: 23037--23095 Score: 61
Period size: 11 Copynumber: 5.2 Consensus size: 12
23027 AAATTAATCA
*
23037 TTAATTA-AAAT
1 TTAATTATAATT
*
23048 TTAATTATACTT
1 TTAATTATAATT
23060 TTAA-TATAATT
1 TTAATTATAATT
*
23071 TTAATTCTAA-T
1 TTAATTATAATT
*
23082 TTAATTTTAATT
1 TTAATTATAATT
23094 TT
1 TT
23096 TTTATTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 27 0.68
12 13 0.32
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TTAATTATAATT
Found at i:23081 original size:17 final size:17
Alignment explanation
Indices: 23061--23093 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23051 ATTATACTTT
23061 TAATATAATTTTAATTC
1 TAATATAATTTTAATTC
*
23078 TAATTTAATTTTAATT
1 TAATATAATTTTAATT
23094 TTTTTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATATAATTTTAATTC
Found at i:24297 original size:24 final size:23
Alignment explanation
Indices: 24256--24306 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
24246 AATTTCAAGT
*
24256 TTAAATTAAAAATGTTAATATCAA
1 TTAAATTAAAAATATTAAT-TCAA
*
24280 TTAAATATAAAAA-ATTAATTCAC
1 TTAAAT-TAAAAATATTAATTCAA
24303 TTAA
1 TTAA
24307 TAACTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 11 0.46
25 6 0.25
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (23 bp):
TTAAATTAAAAATATTAATTCAA
Found at i:27274 original size:31 final size:31
Alignment explanation
Indices: 27238--27297 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
27228 AACTTAAAAA
* *
27238 AGTTTTGCAATACTGATATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
27269 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
27298 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:27835 original size:31 final size:32
Alignment explanation
Indices: 27775--27835 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
27765 ATCAAAATAA
* *
27775 ATATAAAATTTTAATAATATATAAAATAATTT
1 ATATAAAAATTAAATAATATATAAAATAATTT
* *
27807 ATATAAAAATTAAAT-ATCTATAATATAAT
1 ATATAAAAATTAAATAATATATAAAATAAT
27836 ATTAAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (32 bp):
ATATAAAAATTAAATAATATATAAAATAATTT
Found at i:27864 original size:23 final size:24
Alignment explanation
Indices: 27800--27880 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 24
27790 AATATATAAA
*
27800 ATAATTTATATAAAAATTAAATATCT
1 ATAATTTATTTAAAAATT-AATAT-T
* *
27826 ATAATATAATATTAAAAAATAATATT
1 ATAAT-TTAT-TTAAAAATTAATATT
27852 -TAATTTATTTAAAAATTAATATT
1 ATAATTTATTTAAAAATTAATATT
*
27875 AAAATT
1 ATAATT
27881 AATATCTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 14 0.30
24 7 0.15
25 4 0.09
26 6 0.13
27 8 0.17
28 7 0.15
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATTTATTTAAAAATTAATATT
Found at i:27886 original size:62 final size:63
Alignment explanation
Indices: 27802--27963 Score: 219
Period size: 62 Copynumber: 2.6 Consensus size: 63
27792 TATATAAAAT
* *
27802 AATTTATATAAAAATTAAATATCTATAATATAATATTAAAAAA-TAATATTTAATTTATTTAAA
1 AATTAATATTAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAA
*
27865 AATTAATATTAAAATTAATATCTAT-A-ATAATATTAAAAAATTAATATTTACTTTATTTAAA
1 AATTAATATTAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAA
* *
27926 ATTTTAATATTAAAATTAAAATC-A-AATATAATA-TAAAA
1 A-ATTAATATTAAAATTAATATCTATAATATAATATTAAAA
27964 TTAAATATAA
Statistics
Matches: 90, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
60 14 0.16
61 28 0.31
62 34 0.38
63 14 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (63 bp):
AATTAATATTAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAA
Found at i:27910 original size:38 final size:36
Alignment explanation
Indices: 27832--27912 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 36
27822 ATCTATAATA
* *
27832 TAATATTAAAAAATAATATTTAATTTATTTAAAAAT
1 TAATATTAAAAAATAATATTTAATATATTAAAAAAT
*
27868 TAATATT-AAAATTAATATCTATAATAATATTAAAAAAT
1 TAATATTAAAAAATAATAT-T-TAAT-ATATTAAAAAAT
27906 TAATATT
1 TAATATT
27913 TACTTTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 10 0.26
36 8 0.21
37 4 0.10
38 17 0.44
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (36 bp):
TAATATTAAAAAATAATATTTAATATATTAAAAAAT
Found at i:32260 original size:163 final size:163
Alignment explanation
Indices: 31990--32315 Score: 636
Period size: 163 Copynumber: 2.0 Consensus size: 163
31980 ATCAAAAAGA
31990 TTTCTTTAAAATAAAGAAAGCAATGGCAAAACGCTAAAAACTAAAAAGCAGCAGCTGTTTGTAAT
1 TTTCTTTAAAATAAAGAAAGCAATGGCAAAACGCTAAAAACTAAAAAGCAGCAGCTGTTTGTAAT
32055 GTTGACCACCCTCTTCTTTTGCCTTTATATCTCTTAATGCCTAAAATGCCCCCTCAATCTGAATG
66 GTTGACCACCCTCTTCTTTTGCCTTTATATCTCTTAATGCCTAAAATGCCCCCTCAATCTGAATG
32120 TATCATAGCTTTTACTATATAAAAATTTTGGCT
131 TATCATAGCTTTTACTATATAAAAATTTTGGCT
32153 TTTCTTTAAAAT-AAGAAAGCAATGGCAAAACGCTAAAAAACTAAAAAGCAGCAGCTGTTTGTAA
1 TTTCTTTAAAATAAAGAAAGCAATGGCAAAACGCT-AAAAACTAAAAAGCAGCAGCTGTTTGTAA
32217 TGTTGACCACCCTCTTCTTTTGCCTTTATATCTCTTAATGCCTAAAATGCCCCCTCAATCTGAAT
65 TGTTGACCACCCTCTTCTTTTGCCTTTATATCTCTTAATGCCTAAAATGCCCCCTCAATCTGAAT
32282 GTATCATAGCTTTTACTATATAAAAATTTTGGCT
130 GTATCATAGCTTTTACTATATAAAAATTTTGGCT
32316 AAATATCAAG
Statistics
Matches: 162, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
162 22 0.14
163 140 0.86
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (163 bp):
TTTCTTTAAAATAAAGAAAGCAATGGCAAAACGCTAAAAACTAAAAAGCAGCAGCTGTTTGTAAT
GTTGACCACCCTCTTCTTTTGCCTTTATATCTCTTAATGCCTAAAATGCCCCCTCAATCTGAATG
TATCATAGCTTTTACTATATAAAAATTTTGGCT
Found at i:36142 original size:56 final size:56
Alignment explanation
Indices: 36054--36168 Score: 185
Period size: 56 Copynumber: 2.1 Consensus size: 56
36044 TTGAAATAGA
* * * *
36054 CTTGATGAAATAAACATTGTAAGTGTGGAAAACTAGTAACCTTTCATGAAGGATGT
1 CTTGATGAAATAAACAATGTAAGCGTGAAAAACTAGTAACCTTCCATGAAGGATGT
*
36110 CTTGATGAAATAAACAATGTAAGCGTGAAAAACTAGTCACCTTCCATGAAGGATGT
1 CTTGATGAAATAAACAATGTAAGCGTGAAAAACTAGTAACCTTCCATGAAGGATGT
36166 CTT
1 CTT
36169 TTTAGGATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (56 bp):
CTTGATGAAATAAACAATGTAAGCGTGAAAAACTAGTAACCTTCCATGAAGGATGT
Found at i:37458 original size:19 final size:20
Alignment explanation
Indices: 37426--37463 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
37416 TTTTTGTTTG
*
37426 GCCGCCGATGAACGACGGCC
1 GCCGCCGATCAACGACGGCC
*
37446 GCCG-CGATCAACGGCGGC
1 GCCGCCGATCAACGACGGC
37464 GGTGAGGCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.18, C:0.39, G:0.37, T:0.05
Consensus pattern (20 bp):
GCCGCCGATCAACGACGGCC
Found at i:49267 original size:105 final size:105
Alignment explanation
Indices: 49085--49752 Score: 1104
Period size: 105 Copynumber: 6.3 Consensus size: 105
49075 AGGTTTTACC
*
49085 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
49150 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTT
*
49190 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
49255 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTT
* *
49295 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
49360 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTT
* *
49400 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGCAAGTTCGACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
49465 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTT
*
49505 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
49570 AAGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAA-AATTTCTCAATTT
* *
49611 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
49676 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTC-CAAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAA-AATTTCTC-AATTT
* *
49717 CGGAACCAATTTCAACTTCACAACGAAGGATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
49753 CCTCGGAACA
Statistics
Matches: 528, Mismatches: 33, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
105 385 0.73
106 143 0.27
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTT
Found at i:51170 original size:20 final size:20
Alignment explanation
Indices: 51145--51183 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
51135 TTTTTGTTTG
*
51145 GCCGCCGATGAACGACGGCC
1 GCCGCCGATCAACGACGGCC
*
51165 GCCGCCGATCAACGGCGGC
1 GCCGCCGATCAACGACGGC
51184 GGTGAGGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.36, T:0.05
Consensus pattern (20 bp):
GCCGCCGATCAACGACGGCC
Found at i:53596 original size:29 final size:29
Alignment explanation
Indices: 53539--53598 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
53529 TGATGCATTT
* *
53539 CTGATTTTGCATAGGATTATATCCCCGTC
1 CTGATTCTGCATAGGATTATATCACCGTC
*
53568 CTGATTCTGCAT-GAGATTATATCATCGTC
1 CTGATTCTGCATAG-GATTATATCACCGTC
53597 CT
1 CT
53599 TATAATGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (29 bp):
CTGATTCTGCATAGGATTATATCACCGTC
Found at i:54518 original size:20 final size:20
Alignment explanation
Indices: 54495--54547 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
54485 TAGAACCTGA
54495 ATTTTTAAGTTACAAACCAG
1 ATTTTTAAGTTACAAACCAG
* *
54515 A-TTTTAGGTTGCAAACCAG
1 ATTTTTAAGTTACAAACCAG
*
54534 ATTTTTAAATTACA
1 ATTTTTAAGTTACA
54548 GACAAAGTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (20 bp):
ATTTTTAAGTTACAAACCAG
Found at i:54609 original size:40 final size:40
Alignment explanation
Indices: 54554--54679 Score: 114
Period size: 40 Copynumber: 3.1 Consensus size: 40
54544 TACAGACAAA
*
54554 GTGATGTATCGTACGAGGTACACACCTAAACATGAAAATG
1 GTGATATATCGTACGAGGTACACACCTAAACATGAAAATG
* * * * *
54594 GTGATATATTGTACGAGATACACA-TTCAATTACAAG-GAAT-
1 GTGATATATCGTACGAGGTACACACCT-AA--ACATGAAAATG
* * *
54634 GTGATATATCGTATGAGGTACACACCTAAATATAAAAAGTG
1 GTGATATATCGTACGAGGTACACACCTAAACATGAAAA-TG
54675 GTGAT
1 GTGAT
54680 GTATTGTATG
Statistics
Matches: 65, Mismatches: 14, Indels: 13
0.71 0.15 0.14
Matches are distributed among these distances:
38 2 0.03
39 3 0.05
40 47 0.72
41 9 0.14
42 4 0.06
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (40 bp):
GTGATATATCGTACGAGGTACACACCTAAACATGAAAATG
Found at i:54762 original size:126 final size:127
Alignment explanation
Indices: 54620--54865 Score: 347
Period size: 127 Copynumber: 1.9 Consensus size: 127
54610 GATACACATT
* *
54620 CAATTACAAGGAATGTGATATATCGTA-TGAGGTACACACCTAAATATAAAAAGTGGTGATGTAT
1 CAATTACAAGGAATGTGATATATCGTACAG-GGTACACACCTAAACATAAAAA-TGGTGATGTAT
* * *
54684 TGTATG-G-GATACACCTAATATGGTACTTTAAGGAAGATTAGAAATTTTGAATGATATACAAG
64 TGTACGAGAGATACAACTAATATGATACTTTAAGGAAGATTAGAAATTTTGAATGATATACAAG
* * *
54746 CAATTACAAGCG-ATGTGATGTATCGTACAGGGTATACACCTAAACATGAAAATGGTGATGTATT
1 CAATTACAAG-GAATGTGATATATCGTACAGGGTACACACCTAAACATAAAAATGGTGATGTATT
* *
54810 GTACGAGATATACAACTAATATGATACTTTAATGAAGATTAGAAATTTTGAATGAT
65 GTACGAGAGATACAACTAATATGATACTTTAAGGAAGATTAGAAATTTTGAATGAT
54866 GTTTATAACT
Statistics
Matches: 106, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
125 16 0.15
126 44 0.42
127 46 0.43
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.30
Consensus pattern (127 bp):
CAATTACAAGGAATGTGATATATCGTACAGGGTACACACCTAAACATAAAAATGGTGATGTATTG
TACGAGAGATACAACTAATATGATACTTTAAGGAAGATTAGAAATTTTGAATGATATACAAG
Found at i:58756 original size:29 final size:29
Alignment explanation
Indices: 58664--58818 Score: 186
Period size: 29 Copynumber: 5.4 Consensus size: 29
58654 GCTACAATCA
* * *
58664 TGATTCTGTATTAGATTATATCCCCGTCT
1 TGATTCTGCATGAGATTATATCCCCGTCC
* * * *
58693 TAATTTTGCATGGGATTATAT-CCCGTCT
1 TGATTCTGCATGAGATTATATCCCCGTCC
58721 TGATTCTGCATGAGATTATATCCCCGTCC
1 TGATTCTGCATGAGATTATATCCCCGTCC
* *
58750 TGGTTCTGCATGAGATTATATCTCCGTCC
1 TGATTCTGCATGAGATTATATCCCCGTCC
* ***
58779 TGGTTCTGCATGAGATTATATCTTTGTCC
1 TGATTCTGCATGAGATTATATCCCCGTCC
58808 TGATTCTGCAT
1 TGATTCTGCAT
58819 AGGATCCTCT
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
28 25 0.23
29 86 0.77
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.41
Consensus pattern (29 bp):
TGATTCTGCATGAGATTATATCCCCGTCC
Found at i:58760 original size:57 final size:58
Alignment explanation
Indices: 58664--58823 Score: 196
Period size: 57 Copynumber: 2.8 Consensus size: 58
58654 GCTACAATCA
* * * * * *
58664 TGATTCTGTATTAGATTATATCCCCGTCTTAATTTTGCATGGGATTATATC-CCGTCT
1 TGATTCTGCATGAGATTATATCCCCGTCCTGATTCTGCATGGGATTATATCTCCGTCC
* *
58721 TGATTCTGCATGAGATTATATCCCCGTCCTGGTTCTGCATGAGATTATATCTCCGTCC
1 TGATTCTGCATGAGATTATATCCCCGTCCTGATTCTGCATGGGATTATATCTCCGTCC
* *** *
58779 TGGTTCTGCATGAGATTATATCTTTGTCCTGATTCTGCATAGGAT
1 TGATTCTGCATGAGATTATATCCCCGTCCTGATTCTGCATGGGAT
58824 CCTCTACAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
57 44 0.51
58 43 0.49
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (58 bp):
TGATTCTGCATGAGATTATATCCCCGTCCTGATTCTGCATGGGATTATATCTCCGTCC
Found at i:65789 original size:186 final size:183
Alignment explanation
Indices: 65247--65818 Score: 1006
Period size: 186 Copynumber: 3.1 Consensus size: 183
65237 TTTTCTAATT
* * * *
65247 TATATAA-A-ATTAAATATTTTTTAATTCAAACAA-AGTTTATAATTAATTTAAATAATAAATAA
1 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
** * *
65309 TTATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAAATTATAT-TATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65374 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTA
129 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTA
65429 TATATAATATATTTAATATTTTTTAATTAAAAAACAGTTTACAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTAAAAAACAGTTTACAATTAATTTAAATAATATATAAT
65494 TATAAAATAAAAAAATTATATTATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
66 TATAAAATAAAAAAATTATATTATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
65559 GATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTATA
131 GATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATG-T-TA
65614 TATATAATATATTTAATATTTTTTAATTAAAAAACAGTTTACAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTAAAAAACAGTTTACAATTAATTTAAATAATATATAAT
65679 TATAAAATAAAAAAAATTATATTATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAAT-AAAAAAATTATATTATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
65744 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTA
130 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTA
65798 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
65819 AATATTTAAT
Statistics
Matches: 376, Mismatches: 8, Indels: 10
0.95 0.02 0.03
Matches are distributed among these distances:
182 7 0.02
183 99 0.26
184 87 0.23
185 76 0.20
186 107 0.28
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAACAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAAAATTATATTATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
GATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTA
Found at i:66529 original size:31 final size:32
Alignment explanation
Indices: 66505--66599 Score: 99
Period size: 32 Copynumber: 3.1 Consensus size: 32
66495 TTAAGAGTCG
* *
66505 AATTGATATTTTATCTAAAGTTTAAAGGTAAA
1 AATTAATATTTTATCTAAAATTTAAAGGTAAA
*
66537 AATTAATATTTTATCTAAAATTTAAA---ATA
1 AATTAATATTTTATCTAAAATTTAAAGGTAAA
* * * *
66566 AATTATTATTCTATATAAAA-TTAAAGGTGAA
1 AATTAATATTTTATCTAAAATTTAAAGGTAAA
66597 AAT
1 AAT
66600 CAAAATTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 5 0.10
29 19 0.37
31 4 0.08
32 24 0.46
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.41
Consensus pattern (32 bp):
AATTAATATTTTATCTAAAATTTAAAGGTAAA
Found at i:69111 original size:6 final size:6
Alignment explanation
Indices: 69100--69163 Score: 128
Period size: 6 Copynumber: 10.7 Consensus size: 6
69090 GAACGTGGCC
69100 GGGACA GGGACA GGGACA GGGACA GGGACA GGGACA GGGACA GGGACA
1 GGGACA GGGACA GGGACA GGGACA GGGACA GGGACA GGGACA GGGACA
69148 GGGACA GGGACA GGGA
1 GGGACA GGGACA GGGA
69164 TCGTTATCGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.33, C:0.16, G:0.52, T:0.00
Consensus pattern (6 bp):
GGGACA
Found at i:76890 original size:198 final size:199
Alignment explanation
Indices: 76554--76951 Score: 741
Period size: 198 Copynumber: 2.0 Consensus size: 199
76544 GGAGTACTCG
76554 AACAGTATTCAGCTTCGCCACAGGTGCAAAAGTTCTGTGAAATCTATCCCATATGTTGTGTAAAG
1 AACAGTATTCAGCTTCGCCACAGGTGCAAAAGTTCTGTGAAATCTATCCCATATGTTGTGTAAAG
76619 CCTCTGGCCACTAGTCTCGCTTGTATCGTTTGATGCTACCATTTGAGTTATACTTTACAATAAAG
66 CCTCTGGCCACTAGTCTCGCTTGTATCGTTTGATGCTACCATTTGAGTTATACTTTACAATAAAG
76684 ATCCATTTACAGCCAAC-ACC-TTTTTCCTTGAGGAAGGTCCGTAACAGTCCAAGTAGCA-TTTT
131 ATCCATTTACAGCCAACAACCTTTTTTCCTTGAGGAAGGTCCGTAACAGTCCAAGTAGCATTTTT
76746 CTCC
196 CTCC
76750 AACAGTATTCAGCTTCGCCACAGGTGCAAAAGTTTCTGTGAAATCTATCCCATATGTTTGTGTAA
1 AACAGTATTCAGCTTCGCCACAGGTGCAAAAG-TTCTGTGAAATCTATCCCATATG-TTGTGTAA
76815 AGCCTCTGGCCACTAGTCTCGCTTTGTATCGTTTGATGCTACCATTTGAGTTATAC-TTACAATA
64 AGCCTCTGGCCACTAGTCTCGC-TTGTATCGTTTGATGCTACCATTTGAGTTATACTTTACAATA
76879 AAGATCCATTTACAGCCAACAACCTTTTTTCCTTGAGGAAGGTCCGTAACAGTCCAAGTAGCATT
128 AAGATCCATTTACAGCCAACAACCTTTTTTCCTTGAGGAAGGTCCGTAACAGTCCAAGTAGCATT
76944 TTTCTCC
193 TTTCTCC
76951 A
1 A
76952 GTGCACAAAT
Statistics
Matches: 196, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
196 32 0.16
197 23 0.12
198 58 0.30
199 36 0.18
200 38 0.19
201 9 0.05
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (199 bp):
AACAGTATTCAGCTTCGCCACAGGTGCAAAAGTTCTGTGAAATCTATCCCATATGTTGTGTAAAG
CCTCTGGCCACTAGTCTCGCTTGTATCGTTTGATGCTACCATTTGAGTTATACTTTACAATAAAG
ATCCATTTACAGCCAACAACCTTTTTTCCTTGAGGAAGGTCCGTAACAGTCCAAGTAGCATTTTT
CTCC
Found at i:79098 original size:27 final size:27
Alignment explanation
Indices: 79067--79135 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
79057 TCTATTTACA
*
79067 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAAGAATGGTAAC
79094 AAATCATATCTCTATAAGAATGGTAAC
1 AAATCATATCTCTATAAGAATGGTAAC
79121 AAATC--ATCTCTATAA
1 AAATCATATCTCTATAA
79136 TTCCTACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 10 0.24
27 31 0.76
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.30
Consensus pattern (27 bp):
AAATCATATCTCTATAAGAATGGTAAC
Found at i:80645 original size:271 final size:271
Alignment explanation
Indices: 80162--80702 Score: 1082
Period size: 271 Copynumber: 2.0 Consensus size: 271
80152 TTTAGGTAAT
80162 GGATATTGAAGGATTAATATCCAAACCCTTAGCGAATGGTAAATTTATTATCTGAATCTGTCATA
1 GGATATTGAAGGATTAATATCCAAACCCTTAGCGAATGGTAAATTTATTATCTGAATCTGTCATA
80227 TCTGAATAAACAAAAACAGTTCTTGTAGTCTTGGAATTGCCTTCCAGAGTGGTGATTATGAAAGG
66 TCTGAATAAACAAAAACAGTTCTTGTAGTCTTGGAATTGCCTTCCAGAGTGGTGATTATGAAAGG
80292 AAGTCTTATTCGGCATGTTGATGACAATAAAGGTTATAAAACTATTAAGGATAAACTACACAGAT
131 AAGTCTTATTCGGCATGTTGATGACAATAAAGGTTATAAAACTATTAAGGATAAACTACACAGAT
80357 GATCCCTCAATTATAGGATACTTTTTAGTTGGGTCATCTGAGTATAAAATGTTATAAATTGGTCA
196 GATCCCTCAATTATAGGATACTTTTTAGTTGGGTCATCTGAGTATAAAATGTTATAAATTGGTCA
80422 CTTGAGTTATA
261 CTTGAGTTATA
80433 GGATATTGAAGGATTAATATCCAAACCCTTAGCGAATGGTAAATTTATTATCTGAATCTGTCATA
1 GGATATTGAAGGATTAATATCCAAACCCTTAGCGAATGGTAAATTTATTATCTGAATCTGTCATA
80498 TCTGAATAAACAAAAACAGTTCTTGTAGTCTTGGAATTGCCTTCCAGAGTGGTGATTATGAAAGG
66 TCTGAATAAACAAAAACAGTTCTTGTAGTCTTGGAATTGCCTTCCAGAGTGGTGATTATGAAAGG
80563 AAGTCTTATTCGGCATGTTGATGACAATAAAGGTTATAAAACTATTAAGGATAAACTACACAGAT
131 AAGTCTTATTCGGCATGTTGATGACAATAAAGGTTATAAAACTATTAAGGATAAACTACACAGAT
80628 GATCCCTCAATTATAGGATACTTTTTAGTTGGGTCATCTGAGTATAAAATGTTATAAATTGGTCA
196 GATCCCTCAATTATAGGATACTTTTTAGTTGGGTCATCTGAGTATAAAATGTTATAAATTGGTCA
80693 CTTGAGTTAT
261 CTTGAGTTAT
80703 CGGAATTTAC
Statistics
Matches: 270, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
271 270 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.34
Consensus pattern (271 bp):
GGATATTGAAGGATTAATATCCAAACCCTTAGCGAATGGTAAATTTATTATCTGAATCTGTCATA
TCTGAATAAACAAAAACAGTTCTTGTAGTCTTGGAATTGCCTTCCAGAGTGGTGATTATGAAAGG
AAGTCTTATTCGGCATGTTGATGACAATAAAGGTTATAAAACTATTAAGGATAAACTACACAGAT
GATCCCTCAATTATAGGATACTTTTTAGTTGGGTCATCTGAGTATAAAATGTTATAAATTGGTCA
CTTGAGTTATA
Found at i:86229 original size:22 final size:23
Alignment explanation
Indices: 86204--86269 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 23
86194 CAATTATAAT
86204 ATATTAATATATATTTAA-TACA
1 ATATTAATATATATTTAATTACA
*
86226 ATATTTTAATAATATTAATTAATTACA
1 ATA--TTAAT-ATA-TATTTAATTACA
*
86253 ATA-TAATATTTATTTAA
1 ATATTAATATATATTTAA
86270 AATATTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
22 9 0.25
23 2 0.06
24 9 0.25
25 3 0.08
26 6 0.17
27 7 0.19
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTAATATATATTTAATTACA
Found at i:86252 original size:27 final size:25
Alignment explanation
Indices: 86195--86257 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
86185 ATAATGCCGC
* *
86195 AATTATAATATATTAATATATATTT
1 AATTACAATATATTAATATATAATT
*
86220 AA-TACAATATTTTAATAATATTAATT
1 AATTACAATATATTAAT-ATA-TAATT
86246 AATTACAATATA
1 AATTACAATATA
86258 ATATTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 12 0.39
25 5 0.16
26 6 0.19
27 8 0.26
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (25 bp):
AATTACAATATATTAATATATAATT
Found at i:86675 original size:2 final size:2
Alignment explanation
Indices: 86668--86707 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
86658 TATTAAAAAT
86668 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
86708 ATTATGAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:86914 original size:12 final size:13
Alignment explanation
Indices: 86897--86925 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
86887 CAAAATGGGG
86897 TTTTCCTTGTC-T
1 TTTTCCTTGTCGT
86909 TTTTCCTTGTCGT
1 TTTTCCTTGTCGT
86922 TTTT
1 TTTT
86926 GTTCGAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.21, G:0.10, T:0.69
Consensus pattern (13 bp):
TTTTCCTTGTCGT
Found at i:87966 original size:2 final size:2
Alignment explanation
Indices: 87959--87983 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
87949 TAGAAACTTC
87959 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
87984 ACTACTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89707 original size:19 final size:19
Alignment explanation
Indices: 89683--89727 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
89673 GAAGATGATT
89683 ATAGGAAATAAAAAATGAA
1 ATAGGAAATAAAAAATGAA
89702 ATAGGAAATAAAAAATGAA
1 ATAGGAAATAAAAAATGAA
*
89721 AGAGGAA
1 ATAGGAA
89728 GATGATTGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (19 bp):
ATAGGAAATAAAAAATGAA
Found at i:101416 original size:24 final size:25
Alignment explanation
Indices: 101380--101451 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 25
101370 TTTTAATTTA
101380 ATTTAATT-TTATTTTATATTTCGTT
1 ATTT-ATTATTATTTTATATTTCGTT
* **
101405 A-TTATTATTATTACATATATTTTTTT
1 ATTTATTATTATT--TTATATTTCGTT
*
101431 ATTTATTATTATATTATATTT
1 ATTTATTATTATTTTATATTT
101452 ATTATATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
23 3 0.08
24 7 0.18
25 8 0.21
26 10 0.26
27 10 0.26
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (25 bp):
ATTTATTATTATTTTATATTTCGTT
Found at i:101456 original size:24 final size:24
Alignment explanation
Indices: 101387--101476 Score: 71
Period size: 24 Copynumber: 3.8 Consensus size: 24
101377 TTAATTTAAT
**
101387 TTTATT-TTATATT-TCGTTATTA
1 TTTATTATTATATTATATTTATTA
* *
101409 -TTATTATTACA-TATATTTTTTTA
1 TTTATTATTATATTATA-TTTATTA
101432 TTTATTATTATATTATATTTATTA
1 TTTATTATTATATTATATTTATTA
*
101456 TATATATATATATATATATAT
1 TTTAT-TAT-TATAT-TATAT
101477 ATATATATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
21 6 0.11
22 5 0.09
23 5 0.09
24 20 0.38
25 7 0.13
26 5 0.09
27 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (24 bp):
TTTATTATTATATTATATTTATTA
Found at i:101461 original size:2 final size:2
Alignment explanation
Indices: 101440--101488 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
101430 TATTTATTAT
*
101440 TA TA T- TA TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
101480 TA TA TA TA T
1 TA TA TA TA T
101489 TTTTTTGATG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:101602 original size:69 final size:69
Alignment explanation
Indices: 101518--101682 Score: 205
Period size: 69 Copynumber: 2.4 Consensus size: 69
101508 ATTTGATAAG
* * *
101518 TAGTGG-TTGATTATTTTAATATGTAG-GGTTTATTATTTTAACATGTAGT-G-TTGATTATTTT
1 TAGTGGTTTGATTATTTTAATAGGTAGTAGTTTATTATTTTAACAGGTAGTGGTTTGATTA-TTT
101579 TAATAGA
65 TAAT--A
* *
101586 TAGTGGTTTGATTATTTTTATAGGTAGTAGTTTATTATTTTAATAGGTAGTGGTTTGATTATTTT
1 TAGTGGTTTGATTATTTTAATAGGTAGTAGTTTATTATTTTAACAGGTAGTGGTTTGATTATTTT
101651 AATA
66 AATA
*
101655 T-GTTGTGTTGATTATTTTAATAGGTAGT
1 TAGTGGT-TTGATTATTTTAATAGGTAGT
101683 GATCTTAATA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
68 10 0.12
69 40 0.47
70 20 0.24
71 8 0.09
72 7 0.08
ACGTcount: A:0.26, C:0.01, G:0.21, T:0.53
Consensus pattern (69 bp):
TAGTGGTTTGATTATTTTAATAGGTAGTAGTTTATTATTTTAACAGGTAGTGGTTTGATTATTTT
AATA
Found at i:101613 original size:47 final size:47
Alignment explanation
Indices: 101517--101683 Score: 225
Period size: 47 Copynumber: 3.6 Consensus size: 47
101507 GATTTGATAA
* * *
101517 GTAGTGGTTGATTATTTTAATATGTAG-GGTTT-ATTATTTTAACAT
1 GTAGTAGTTGATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
* * *
101562 GTAGT-GTTGATTATTTTTAATAGATAGTGGTTTGATTATTTTTATAG
1 GTAGTAGTTGATTA-TTTTAATAGGTAGTGGTTTGATTATTTTAATAT
*
101609 GTAGTAGTTTATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
1 GTAGTAGTTGATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
*
101656 GTTGT-GTTGATTATTTTAATAGGTAGTG
1 GTAGTAGTTGATTATTTTAATAGGTAGTG
101684 ATCTTAATAT
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
44 8 0.07
45 16 0.15
46 27 0.25
47 49 0.46
48 7 0.07
ACGTcount: A:0.26, C:0.01, G:0.22, T:0.52
Consensus pattern (47 bp):
GTAGTAGTTGATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
Found at i:101701 original size:38 final size:38
Alignment explanation
Indices: 101649--101721 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
101639 TTTGATTATT
*
101649 TTAATATGTTGTGTTGATTATTTTAATAGGTAGTGATC
1 TTAATATGTAGTGTTGATTATTTTAATAGGTAGTGATC
*
101687 TTAATATGTAGTGTTGATTATTTTATTAGGTAGTG
1 TTAATATGTAGTGTTGATTATTTTAATAGGTAGTG
101722 GGGTAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.26, C:0.01, G:0.22, T:0.51
Consensus pattern (38 bp):
TTAATATGTAGTGTTGATTATTTTAATAGGTAGTGATC
Found at i:101719 original size:22 final size:22
Alignment explanation
Indices: 101517--101721 Score: 188
Period size: 22 Copynumber: 9.3 Consensus size: 22
101507 GATTTGATAA
*
101517 GTAGTGGTTGATTATTTTAATAT
1 GTAGT-GTTGATTATTTTAATAG
* * * *
101540 GTAGGGTTTATTATTTTAACAT
1 GTAGTGTTGATTATTTTAATAG
101562 GTAGTGTTGATTATTTTTAATAG
1 GTAGTGTTGATTA-TTTTAATAG
* *
101585 ATAGTGGTTTGATTATTTTTATAG
1 GTAGT-G-TTGATTATTTTAATAG
*
101609 GTAGTAGTTTATTATTTTAATAG
1 GTAGT-GTTGATTATTTTAATAG
*
101632 GTAGTGGTTTGATTATTTTAATAT
1 GTAGT-G-TTGATTATTTTAATAG
*
101656 GTTGTGTTGATTATTTTAATAG
1 GTAGTGTTGATTATTTTAATAG
* *
101678 GTA--G-TG---ATCTTAATAT
1 GTAGTGTTGATTATTTTAATAG
*
101694 GTAGTGTTGATTATTTTATTAG
1 GTAGTGTTGATTATTTTAATAG
101716 GTAGTG
1 GTAGTG
101722 GGGTAATTAT
Statistics
Matches: 148, Mismatches: 24, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
16 11 0.07
18 1 0.01
19 4 0.03
20 1 0.01
22 56 0.38
23 36 0.24
24 32 0.22
25 7 0.05
ACGTcount: A:0.26, C:0.01, G:0.21, T:0.52
Consensus pattern (22 bp):
GTAGTGTTGATTATTTTAATAG
Found at i:112428 original size:21 final size:21
Alignment explanation
Indices: 112386--112428 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
112376 TTTCTGGGCT
* *
112386 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
112407 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
112428 A
1 A
112429 ACGATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:112477 original size:19 final size:19
Alignment explanation
Indices: 112453--112489 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
112443 GAATGCTAGA
*
112453 GGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCAG
*
112472 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
112490 TAATGAAAAA
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:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (19 bp):
GGGGAACCGATACCCCCAG
Found at i:113392 original size:30 final size:30
Alignment explanation
Indices: 113336--113555 Score: 351
Period size: 30 Copynumber: 7.4 Consensus size: 30
113326 GGTTCTTCGG
*
113336 GACCTATGGATAGTTACCG-GGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
113365 GACCTCTGGATAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
113395 GACCTCTGGAT-GTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
113424 GACCACCTCGGTATAGTTACCGAGGATCTTTAT
1 GACC-TCT-GG-ATAGTTACCGAGGATCTTTAT
113457 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
113487 GACCTCTGGATAG--ACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
113515 GACCTCTGGATAGTTACCGA-GATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
113544 GACCTCTGGATA
1 GACCTCTGGATA
113556 TGTCCTTCGG
Statistics
Matches: 179, Mismatches: 5, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
28 28 0.16
29 60 0.34
30 61 0.34
31 4 0.02
32 4 0.02
33 22 0.12
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:117706 original size:30 final size:30
Alignment explanation
Indices: 117672--117923 Score: 486
Period size: 30 Copynumber: 8.4 Consensus size: 30
117662 GGTTCTTCGG
*
117672 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
117702 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
117732 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
117762 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
117792 GACCTCAGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
117822 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
117852 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
117882 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
117912 GACCTCTGGATA
1 GACCTCTGGATA
117924 TGTCCTTCGA
Statistics
Matches: 219, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 219 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:120734 original size:65 final size:64
Alignment explanation
Indices: 120581--120825 Score: 400
Period size: 64 Copynumber: 3.8 Consensus size: 64
120571 CGTTCCACTC
* * *
120581 AAGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTATCAACAAAATTTCCCAGTTT
1 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTT
* *
120645 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCGACAAAAATTTCCCAGTAT
1 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGTTT
* *
120710 CAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTT
1 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTT
* *
120774 AAGACAGCACAAGTTCGACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAA
1 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA
120826 CAACTTCCCA
Statistics
Matches: 167, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
64 107 0.64
65 60 0.36
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (64 bp):
AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTT
Found at i:120812 original size:129 final size:130
Alignment explanation
Indices: 120582--120868 Score: 447
Period size: 129 Copynumber: 2.2 Consensus size: 130
120572 GTTCCACTCA
120582 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTATCAACAAAATTTCCCAGTTTAA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTATCAACAAAATTTCCCAGTTTAA
* * * *
120647 GACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCGACAAA-AATTTCCCAGTATC
66 GACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATATC
* *
120711 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTTAA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTATCAACAAAATTTCCCAGTTTAA
* *
120776 GACAGCACAAGTTCGACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATGTC
66 GACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATATC
* * *
120841 AG--AGC-CAATTTCAACTTCACAGCGAAGG
1 AGACAACACAAGTTCAACTTCACAACGAAGG
120869 ATATTGGACT
Statistics
Matches: 146, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
127 21 0.14
128 2 0.01
129 110 0.75
130 13 0.09
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (130 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTATCAACAAAATTTCCCAGTTTAA
GACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATATC
Found at i:122572 original size:16 final size:17
Alignment explanation
Indices: 122551--122583 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
122541 CTTCAGTTCA
122551 TATTTTAATTTA-ATTT
1 TATTTTAATTTATATTT
*
122567 TATTTTATTTTATATTT
1 TATTTTAATTTATATTT
122584 CGTTTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTTTAATTTATATTT
Found at i:122595 original size:3 final size:3
Alignment explanation
Indices: 122587--122662 Score: 77
Period size: 3 Copynumber: 25.3 Consensus size: 3
122577 TATATTTCGT
* * *
122587 TTA TTA TTA TTA TTA -CA TATA TTT TTT TTA TTTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA -TTA TTA TTA TTA TTA
122632 -TA TTTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
122663 ATATATATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
2 5 0.08
3 51 0.81
4 7 0.11
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:122642 original size:12 final size:12
Alignment explanation
Indices: 122566--122682 Score: 52
Period size: 12 Copynumber: 9.5 Consensus size: 12
122556 TAATTTAATT
122566 TTAT-TTTATT-
1 TTATATTTATTA
*
122576 TTATATTTCGTTTA
1 TTATATTT--ATTA
122590 TTAT-TATTATTA
1 TTATAT-TTATTA
*
122602 CATATATTT-TT-
1 -TTATATTTATTA
122613 TT-TATTTATTA
1 TTATATTTATTA
122624 TTATATTATATTTA
1 TTATATT-TA-TTA
122638 TTAT-TATTATTA
1 TTATAT-TTATTA
122650 TTAT-TATTATTA
1 TTATAT-TTATTA
*
122662 TATATATATATATA
1 T-TATATTTAT-TA
122676 TATATAT
1 T-TATAT
122683 ATTTGATGGT
Statistics
Matches: 86, Mismatches: 5, Indels: 28
0.72 0.04 0.24
Matches are distributed among these distances:
9 5 0.06
10 7 0.08
11 5 0.06
12 25 0.29
13 19 0.22
14 25 0.29
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (12 bp):
TTATATTTATTA
Found at i:122667 original size:2 final size:2
Alignment explanation
Indices: 122660--122684 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
122650 TTATTATTAT
122660 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
122685 TTGATGGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:122792 original size:69 final size:69
Alignment explanation
Indices: 122710--122874 Score: 205
Period size: 69 Copynumber: 2.4 Consensus size: 69
122700 ATTTGATAAG
* * *
122710 TAGTGG-TTGATTATTTTAATATGTAG-GGTTTATTATTTTAACATGTAGT-G-TTGATTATTTT
1 TAGTGGTTTGATTATTTTAATAGGTAGTAGTTTATTATTTTAACAGGTAGTGGTTTGATTA-TTT
122771 TAATAGA
65 TAAT--A
* *
122778 TAGTGGTTTGATTATTTTTATAGGTAGTAGTTTATTATTTTAATAGGTAGTGGTTTGATTATTTT
1 TAGTGGTTTGATTATTTTAATAGGTAGTAGTTTATTATTTTAACAGGTAGTGGTTTGATTATTTT
122843 AATA
66 AATA
*
122847 T-GTTGTGTTGATTATTTTAATAGGTAGT
1 TAGTGGT-TTGATTATTTTAATAGGTAGT
122875 GATCTTAATA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
68 10 0.12
69 40 0.47
70 20 0.24
71 8 0.09
72 7 0.08
ACGTcount: A:0.26, C:0.01, G:0.21, T:0.53
Consensus pattern (69 bp):
TAGTGGTTTGATTATTTTAATAGGTAGTAGTTTATTATTTTAACAGGTAGTGGTTTGATTATTTT
AATA
Found at i:122805 original size:47 final size:47
Alignment explanation
Indices: 122709--122875 Score: 225
Period size: 47 Copynumber: 3.6 Consensus size: 47
122699 GATTTGATAA
* * *
122709 GTAGTGGTTGATTATTTTAATATGTAG-GGTTT-ATTATTTTAACAT
1 GTAGTAGTTGATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
* * *
122754 GTAGT-GTTGATTATTTTTAATAGATAGTGGTTTGATTATTTTTATAG
1 GTAGTAGTTGATTA-TTTTAATAGGTAGTGGTTTGATTATTTTAATAT
*
122801 GTAGTAGTTTATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
1 GTAGTAGTTGATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
*
122848 GTTGT-GTTGATTATTTTAATAGGTAGTG
1 GTAGTAGTTGATTATTTTAATAGGTAGTG
122876 ATCTTAATAT
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
44 8 0.07
45 16 0.15
46 27 0.25
47 49 0.46
48 7 0.07
ACGTcount: A:0.26, C:0.01, G:0.22, T:0.52
Consensus pattern (47 bp):
GTAGTAGTTGATTATTTTAATAGGTAGTGGTTTGATTATTTTAATAT
Found at i:122893 original size:38 final size:38
Alignment explanation
Indices: 122841--122913 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
122831 TTTGATTATT
*
122841 TTAATATGTTGTGTTGATTATTTTAATAGGTAGTGATC
1 TTAATATGTAGTGTTGATTATTTTAATAGGTAGTGATC
*
122879 TTAATATGTAGTGTTGATTATTTTATTAGGTAGTG
1 TTAATATGTAGTGTTGATTATTTTAATAGGTAGTG
122914 GGGTAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.26, C:0.01, G:0.22, T:0.51
Consensus pattern (38 bp):
TTAATATGTAGTGTTGATTATTTTAATAGGTAGTGATC
Found at i:122911 original size:22 final size:22
Alignment explanation
Indices: 122709--122913 Score: 188
Period size: 22 Copynumber: 9.3 Consensus size: 22
122699 GATTTGATAA
*
122709 GTAGTGGTTGATTATTTTAATAT
1 GTAGT-GTTGATTATTTTAATAG
* * * *
122732 GTAGGGTTTATTATTTTAACAT
1 GTAGTGTTGATTATTTTAATAG
122754 GTAGTGTTGATTATTTTTAATAG
1 GTAGTGTTGATTA-TTTTAATAG
* *
122777 ATAGTGGTTTGATTATTTTTATAG
1 GTAGT-G-TTGATTATTTTAATAG
*
122801 GTAGTAGTTTATTATTTTAATAG
1 GTAGT-GTTGATTATTTTAATAG
*
122824 GTAGTGGTTTGATTATTTTAATAT
1 GTAGT-G-TTGATTATTTTAATAG
*
122848 GTTGTGTTGATTATTTTAATAG
1 GTAGTGTTGATTATTTTAATAG
* *
122870 GTA--G-TG---ATCTTAATAT
1 GTAGTGTTGATTATTTTAATAG
*
122886 GTAGTGTTGATTATTTTATTAG
1 GTAGTGTTGATTATTTTAATAG
122908 GTAGTG
1 GTAGTG
122914 GGGTAATTAT
Statistics
Matches: 148, Mismatches: 24, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
16 11 0.07
18 1 0.01
19 4 0.03
20 1 0.01
22 56 0.38
23 36 0.24
24 32 0.22
25 7 0.05
ACGTcount: A:0.26, C:0.01, G:0.21, T:0.52
Consensus pattern (22 bp):
GTAGTGTTGATTATTTTAATAG
Found at i:135812 original size:22 final size:22
Alignment explanation
Indices: 135787--135831 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
135777 CTTTCCTAAG
135787 AATTTGATAAAGCTCATAGAAA
1 AATTTGATAAAGCTCATAGAAA
135809 AATTTGATAAAGCTCATAGAAA
1 AATTTGATAAAGCTCATAGAAA
135831 A
1 A
135832 CAAGACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (22 bp):
AATTTGATAAAGCTCATAGAAA
Found at i:140805 original size:12 final size:12
Alignment explanation
Indices: 140788--140812 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
140778 AGAGCTACAG
140788 AGAAATGAAAAA
1 AGAAATGAAAAA
140800 AGAAATGAAAAA
1 AGAAATGAAAAA
140812 A
1 A
140813 AAAGACAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AGAAATGAAAAA
Found at i:142790 original size:47 final size:48
Alignment explanation
Indices: 142693--142791 Score: 128
Period size: 47 Copynumber: 2.1 Consensus size: 48
142683 GTTTAATATC
* * *
142693 TAATTTTTATTTCATTTTAATATTTCATTGTTAAAAACTTTAGGTATT
1 TAATTTTTATTTCATTTTAATATTTCATTATTAAAAACTTAACGTATT
* * * *
142741 TAATTTTTATTTTATTTTAGTA-TTCATTATTGAAAACTTAACGTGTT
1 TAATTTTTATTTCATTTTAATATTTCATTATTAAAAACTTAACGTATT
142788 TAAT
1 TAAT
142792 ACTTAAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 24 0.55
48 20 0.45
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.56
Consensus pattern (48 bp):
TAATTTTTATTTCATTTTAATATTTCATTATTAAAAACTTAACGTATT
Done.