Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001851.1 Hibiscus syriacus cultivar Beakdansim tig00003748_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: 171512
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1733 original size:182 final size:183
Alignment explanation
Indices: 1402--2064 Score: 1153
Period size: 182 Copynumber: 3.7 Consensus size: 183
1392 CTTTCAACAT
** *
1402 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAAATATACCGGTCTTATGCGCGAAT
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTAT-AAATATACCGGTCTTATGAGCGAAT
1467 AGGTCTACAACCTATATCGACACTTTT-ATATTGTGTCGGTAC-TT-TGTCCATATTGGAAGAAA
65 AGGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1529 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
130 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
1583 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAATATA-CGGTTTTATGAGCCAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
1646 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
1711 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATTGGAACCCATA
130 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
1765 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
1829 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
*
1894 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTATACATCGGAACCCATA
131 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
1947 ATTATAATGTAAAAGATAATTTTGT-ATATAACCGGTATAAATATACCGGT-TTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
2010 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTT-TAATATTGTGTCGGTACTTTATGTCCATA
2065 CCATTTAAAA
Statistics
Matches: 460, Mismatches: 15, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
178 37 0.08
179 11 0.02
180 34 0.07
181 56 0.12
182 280 0.61
183 42 0.09
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:4315 original size:23 final size:23
Alignment explanation
Indices: 4284--4347 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
4274 ATAGGTAAAC
*
4284 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
4307 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
4330 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
4348 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:4354 original size:23 final size:23
Alignment explanation
Indices: 4284--4356 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
4274 ATAGGTAAAC
* **
4284 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
4307 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
4330 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
4353 ATAT
1 ATAT
4357 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:4737 original size:21 final size:23
Alignment explanation
Indices: 4706--4767 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 23
4696 ATAGGTAAAC
*
4706 ATATGATGTAATAGGTAGC-CCT
1 ATATAATGTAATAGGTAGCGCCT
* **
4728 -TATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCCT
4750 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
4768 TGGTTATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 16 0.48
22 1 0.03
23 16 0.48
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCCT
Found at i:4774 original size:23 final size:23
Alignment explanation
Indices: 4728--4776 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
4718 AGGTAGCCCT
*
4728 TATAATGTAATAGGTATCGTTTA
1 TATAATGTAATAGGTATCGGTTA
4751 TATAATGTAATAGGTAGT-GGTTA
1 TATAATGTAATAGGTA-TCGGTTA
4774 TAT
1 TAT
4777 TGTAAAGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (23 bp):
TATAATGTAATAGGTATCGGTTA
Found at i:4780 original size:21 final size:21
Alignment explanation
Indices: 4712--4781 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
4702 AAACATATGA
** *
4712 TGTAATAGGTAGCCCTTATAA
1 TGTAATAGGTAGTGCTTATAT
*
4733 TGTAATAGGTA-TCGTTTATAT
1 TGTAATAGGTAGT-GCTTATAT
*
4754 AATGTAATAGGTAGTGGTTATAT
1 --TGTAATAGGTAGTGCTTATAT
4777 TGTAA
1 TGTAA
4782 AGTGTCTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
21 21 0.52
23 18 0.45
24 1 0.03
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (21 bp):
TGTAATAGGTAGTGCTTATAT
Found at i:5157 original size:23 final size:23
Alignment explanation
Indices: 5126--5189 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
5116 ATAGGTAAAC
*
5126 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
5149 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
5172 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5190 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:5196 original size:23 final size:23
Alignment explanation
Indices: 5126--5198 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
5116 ATAGGTAAAC
* **
5126 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
5149 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
5172 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
5195 ATAT
1 ATAT
5199 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:5226 original size:20 final size:20
Alignment explanation
Indices: 5201--5239 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5191 GGTTATATTG
* *
5201 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
5221 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
5240 CACTGTGGAA
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:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:5456 original size:423 final size:426
Alignment explanation
Indices: 4186--5602 Score: 2586
Period size: 423 Copynumber: 3.3 Consensus size: 426
4176 AATTCGCAGT
4186 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGA--CTTTTTATAA
4251 AAAGTATGGACACTTTCAATAAAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
64 AAAGTATGGACACTTTCAATAAAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
4316 AATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATA
129 AATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATA
4381 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
194 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
4446 AG--ATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGGT-TATTATTATT
259 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATTATTATT
4507 AAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAAT
324 AAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAAT
4572 GAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
389 GAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
4610 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAGTATCGA--CTTTTTATA
4674 AAAAGTATGGACACTTTC-A-AAAATAGGTAAACATATGATGTAATAGGTAGCCC-T-TATAATG
63 AAAAGTATGGACACTTTCAATAAAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
4735 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCC-TTTTAT
128 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
4799 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTA--TTTTGAGTGAGTTTT
193 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
4862 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
258 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGG--TATATTATT
4927 ATTAAATTAAAAATTCTAAA-AA-ATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
321 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
4990 AATGAAATTATTAAATCAATATTGTAGGTGG-AAACATGAA
386 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
5030 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGA-TTTTTATAAA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAGTATCGACTTTTTATAAA
5094 AAGTATGGACACTTTCAATAAAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTA
65 AAGTATGGACACTTTCAATAAAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTA
5159 ATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT-A
130 ATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAA
5223 AAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
195 AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
5287 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATTATTATTA
260 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATTATTATTA
5352 AATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAA-TTTTTGTGCAAATG
325 AATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATG
5416 AAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
390 AAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
5453 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTAT-A
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGA--CTTTTTATAA
*
5517 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
64 AAAGTATGGACACTTTCAATAAAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
*
5582 AATAGGTATCGTTTATGTAAT
129 AATAGGTATCGTTTATATAAT
5603 AGGTATCTAT
Statistics
Matches: 970, Mismatches: 2, Indels: 42
0.96 0.00 0.04
Matches are distributed among these distances:
417 18 0.02
418 26 0.03
419 89 0.09
420 130 0.13
421 181 0.19
422 171 0.18
423 213 0.22
424 135 0.14
425 7 0.01
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (426 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGACTTTTTATAAAA
AGTATGGACACTTTCAATAAAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAA
TAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAA
AGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAG
ATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATTATTATTAA
ATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGA
AATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:5829 original size:18 final size:18
Alignment explanation
Indices: 5808--5844 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5798 GTAATTGGAG
5808 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
5826 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
5844 T
1 T
5845 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:5852 original size:24 final size:24
Alignment explanation
Indices: 5800--5846 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5790 TTTCATATGT
* *
5800 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
5824 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
5847 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:13770 original size:30 final size:30
Alignment explanation
Indices: 13729--13799 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
13719 GGTGACCTAT
*
13729 ATAGTTCTCCAGGAGCATACGACAACCTCC
1 ATAGGTCTCCAGGAGCATACGACAACCTCC
13759 ATAGGTCTCCAGGAGCATACGACAACCTCC
1 ATAGGTCTCCAGGAGCATACGACAACCTCC
13789 ATAGGTCTCCA
1 ATAGGTCTCCA
13800 AGAATACACG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (30 bp):
ATAGGTCTCCAGGAGCATACGACAACCTCC
Found at i:21108 original size:2 final size:2
Alignment explanation
Indices: 21101--21126 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21091 CATTGAGATA
21101 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
21127 CGAGTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21359 original size:16 final size:15
Alignment explanation
Indices: 21338--21377 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
21328 GACTCAATTA
21338 TAAAAATAAAATAAAT
1 TAAAAATAAAAT-AAT
*
21354 TAAAAATATAATAAT
1 TAAAAATAAAATAAT
*
21369 AAAAAATAA
1 TAAAAATAA
21378 TTTTTTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAAAATAAAATAAT
Found at i:21373 original size:15 final size:16
Alignment explanation
Indices: 21339--21377 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
21329 ACTCAATTAT
*
21339 AAAAATAAAATAAATT
1 AAAAATAAAATAAATA
*
21355 AAAAATATAAT-AATA
1 AAAAATAAAATAAATA
21370 AAAAATAA
1 AAAAATAA
21378 TTTTTTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATAAAATAAATA
Found at i:23354 original size:17 final size:18
Alignment explanation
Indices: 23324--23361 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
23314 TAATTGATGA
*
23324 TATTACAATTACTGCAAG
1 TATTACAATCACTGCAAG
*
23342 TATT-CAATCACTGCTAG
1 TATTACAATCACTGCAAG
23359 TAT
1 TAT
23362 CGTCACTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (18 bp):
TATTACAATCACTGCAAG
Found at i:23738 original size:30 final size:30
Alignment explanation
Indices: 23704--23790 Score: 95
Period size: 31 Copynumber: 2.9 Consensus size: 30
23694 TTAAAAGTAT
23704 GCCCCTAATAATAAATATTGAAAAAATTAA
1 GCCCCTAATAATAAATATTGAAAAAATTAA
* * *
23734 GCCCCCTTATAATAAGTATTG-AAAAATTAG
1 G-CCCCTAATAATAAATATTGAAAAAATTAA
* * *
23764 GCCCTTAATAACAAATGTTAGAAAAAA
1 GCCCCTAATAATAAATATT-GAAAAAA
23791 ATATTGACAA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
29 13 0.28
30 11 0.24
31 22 0.48
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.26
Consensus pattern (30 bp):
GCCCCTAATAATAAATATTGAAAAAATTAA
Found at i:23773 original size:110 final size:108
Alignment explanation
Indices: 23582--23779 Score: 247
Period size: 110 Copynumber: 1.8 Consensus size: 108
23572 AGAAAAAGTA
* * * *
23582 AATTTTAAGAGTATGCTCGTAATAATAAATATAAAAAAATTAGACCTCTAATAAAATGTATTGAA
1 AATTTTAAAAGTATGCCCCTAATAATAAATATAAAAAAATTAGACCCCTAATAAAATGTATTGAA
* *
23647 AAAATAGACTTATAATAGCAAATAGATATTAGAAAAGAAATTG
66 AAAATAGACCTATAATAACAAATAGATATTAGAAAAGAAATTG
* * *
23690 AATTTTAAAAGTATGCCCCTAATAATAAATATTGAAAAAATTAAGCCCCCTTATAATAA-GTATT
1 AATTTTAAAAGTATGCCCCTAATAATAAATA-TAAAAAAATT-AGACCCCTAATAA-AATGTATT
* *
23754 GAAAAATTAGGCCCT-TAATAACAAAT
63 GAAAAAATA-GACCTATAATAACAAAT
23780 GTTAGAAAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
108 28 0.37
109 9 0.12
110 33 0.44
111 5 0.07
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (108 bp):
AATTTTAAAAGTATGCCCCTAATAATAAATATAAAAAAATTAGACCCCTAATAAAATGTATTGAA
AAAATAGACCTATAATAACAAATAGATATTAGAAAAGAAATTG
Found at i:24154 original size:12 final size:12
Alignment explanation
Indices: 24115--24156 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
24105 TTAAAAAATC
*
24115 AATTTTAAATAA
1 AATTTAAAATAA
* *
24127 AATATCAAATAA
1 AATTTAAAATAA
24139 AATTTAAAATAA
1 AATTTAAAATAA
24151 AATTTA
1 AATTTA
24157 GTAATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
AATTTAAAATAA
Found at i:34344 original size:2 final size:2
Alignment explanation
Indices: 34333--34362 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34323 ATTCAACTTC
34333 AT AT -T 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 AT AT AT A
34363 CACGAGAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37745 original size:96 final size:96
Alignment explanation
Indices: 37572--37745 Score: 303
Period size: 96 Copynumber: 1.8 Consensus size: 96
37562 TAATCAGCAT
*
37572 GATCAATTTTAATGTCAATCAATAATCTTTTTCAATAGAAGTTTTTTTTTATTGATTATCATTAT
1 GATCAATTTTAATGTCAATCAATAATCTTTTTCAAGAGAAGTTTTTTTTTATTGATTATCATTAT
***
37637 ATATGTTTAAGGATCAAGTTATCTGTTCAAG
66 ATATGAGCAAGGATCAAGTTATCTGTTCAAG
*
37668 GATCAATTTTAATGTCAATCAATAATCTTTTTCAAGAGAAGTTTTTTTTTATTGATTATCATTGT
1 GATCAATTTTAATGTCAATCAATAATCTTTTTCAAGAGAAGTTTTTTTTTATTGATTATCATTAT
37733 ATATGAGCAAGGA
66 ATATGAGCAAGGA
37746 GGTAGAATAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 73 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (96 bp):
GATCAATTTTAATGTCAATCAATAATCTTTTTCAAGAGAAGTTTTTTTTTATTGATTATCATTAT
ATATGAGCAAGGATCAAGTTATCTGTTCAAG
Found at i:38262 original size:3 final size:3
Alignment explanation
Indices: 38256--38307 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
38246 GTTAAAAAAA
*
38256 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38303 TAT TA
1 TAT TA
38308 ATTAGTTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 1 0.02
3 45 0.98
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:39913 original size:2 final size:2
Alignment explanation
Indices: 39906--39944 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
39896 ACACTTATTG
39906 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
39945 TATTCAATGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51718 original size:7 final size:7
Alignment explanation
Indices: 51696--51758 Score: 60
Period size: 7 Copynumber: 9.1 Consensus size: 7
51686 AAAAGGGAAC
*
51696 AAATAAA
1 AAATGAA
51703 AAGATGAA
1 AA-ATGAA
51711 AAATGAAA
1 AAATG-AA
51719 AAATG-A
1 AAATGAA
*
51725 AAAGGAA
1 AAATGAA
51732 AAA--AA
1 AAATGAA
51737 AAATGAA
1 AAATGAA
51744 AAATGAA
1 AAATGAA
*
51751 AAAAGAA
1 AAATGAA
51758 A
1 A
51759 TGAAAAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
5 5 0.10
6 5 0.10
7 25 0.52
8 13 0.27
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (7 bp):
AAATGAA
Found at i:51746 original size:19 final size:19
Alignment explanation
Indices: 51716--51765 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
51706 ATGAAAAATG
51716 AAAAAATG-AAAAGGAAAA
1 AAAAAATGAAAAAGGAAAA
*
51734 AAAAAATGAAAAATGAAAA
1 AAAAAATGAAAAAGGAAAA
*
51753 AAGAAATGAAAAA
1 AAAAAATGAAAAA
51766 ATAAAAAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 8 0.28
19 21 0.72
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAAAATGAAAAAGGAAAA
Found at i:51753 original size:26 final size:27
Alignment explanation
Indices: 51709--51783 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 27
51699 TAAAAAGATG
51709 AAAAATGAAAAAATG-AAAAGGAAA-AA
1 AAAAATG-AAAAATGAAAAAGGAAATAA
* *
51735 AAAAATGAAAAATGAAAAAAGAAATGA
1 AAAAATGAAAAATGAAAAAGGAAATAA
*
51762 AAAAAT-AAAAAGAGAAAAAGGA
1 AAAAATGAAAAA-TGAAAAAGGA
51784 GGGTTTGAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 7 0.17
26 20 0.48
27 15 0.36
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (27 bp):
AAAAATGAAAAATGAAAAAGGAAATAA
Found at i:51767 original size:8 final size:8
Alignment explanation
Indices: 51696--51758 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 8
51686 AAAAGGGAAC
51696 AAAT-AAA
1 AAATGAAA
51703 AAGATG-AA
1 AA-ATGAAA
51711 AAATGAAA
1 AAATGAAA
51719 AAATGAAA
1 AAATGAAA
**
51727 AGGAAAAAAA
1 A--AATGAAA
51737 AAATG-AA
1 AAATGAAA
51744 AAATGAAA
1 AAATGAAA
51752 AAA-GAAA
1 AAATGAAA
51759 TGAAAAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
7 16 0.35
8 24 0.52
10 6 0.13
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (8 bp):
AAATGAAA
Found at i:51771 original size:19 final size:19
Alignment explanation
Indices: 51719--51778 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
51709 AAAAATGAAA
* *
51719 AAATG-AAAAGGAAAAAAA
1 AAATGAAAAATGAAAAAAG
51737 AAATGAAAAATGAAAAAAG
1 AAATGAAAAATGAAAAAAG
51756 AAATGAAAAAAT-AAAAAGAG
1 AAATG-AAAAATGAAAAA-AG
51776 AAA
1 AAA
51779 AAGGAGGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.14
19 21 0.57
20 11 0.30
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (19 bp):
AAATGAAAAATGAAAAAAG
Found at i:51772 original size:33 final size:34
Alignment explanation
Indices: 51696--51772 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
51686 AAAAGGGAAC
*
51696 AAATAAAAAGATGAAAAATGAAAAAATGAAAAGGAA
1 AAAT-AAAA-ATGAAAAATGAAAAAATGAAAAGAAA
*
51732 AAA-AAAAATGAAAAATGAAAAAA-GAAATGAAA
1 AAATAAAAATGAAAAATGAAAAAATGAAAAGAAA
51764 AAATAAAAA
1 AAATAAAAA
51773 GAGAAAAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 10 0.26
33 21 0.55
34 4 0.11
36 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (34 bp):
AAATAAAAATGAAAAATGAAAAAATGAAAAGAAA
Found at i:52885 original size:136 final size:136
Alignment explanation
Indices: 52639--52984 Score: 542
Period size: 136 Copynumber: 2.6 Consensus size: 136
52629 GGTGAACCAG
*
52639 CATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* * *
52704 AGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGACACCTTGCTTGAAG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
52769 GATC-A
131 GATCGA
*
52774 GTATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 -CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* *
52839 GAGAAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGACACCTCGCTTGAG
65 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAA
52904 GGATCGA
130 GGATCGA
* * *
52911 CATTTCCAATGAAGAGTTCATAATGAGAAGAACTCAT-C-ATA-AAGGA-AA-AAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
*
52971 AGAAGAACTTGTTC
66 AGAAGAGCTTGTTC
52985 CTTTCAAATT
Statistics
Matches: 197, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
131 25 0.13
132 2 0.01
133 4 0.02
134 2 0.01
135 1 0.01
136 162 0.82
137 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (136 bp):
CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
GATCGA
Found at i:52952 original size:19 final size:17
Alignment explanation
Indices: 52927--52980 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
52917 CAATGAAGAG
52927 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
* * *
52944 TCATCATAAAG-GAAAAAG
1 T--TCATAATGAGAAGAAC
52962 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
52979 TT
1 TT
52981 GTTCCTTTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 7 0.25
17 8 0.29
18 6 0.21
19 7 0.25
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (17 bp):
TTCATAATGAGAAGAAC
Found at i:53261 original size:3 final size:3
Alignment explanation
Indices: 53255--53297 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
53245 GTTAAAAAAA
*
53255 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
53298 ATTAGTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 36 0.97
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:55852 original size:17 final size:17
Alignment explanation
Indices: 55832--55866 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
55822 ATTGGGGTCT
55832 AATTAAAACTTTTAAAA
1 AATTAAAACTTTTAAAA
* *
55849 AATTAGAATTTTTAAAA
1 AATTAAAACTTTTAAAA
55866 A
1 A
55867 TTATGGGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTAAAACTTTTAAAA
Found at i:56753 original size:27 final size:27
Alignment explanation
Indices: 56715--56774 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
56705 ATATATTCTC
**
56715 ATTTTCTATTGTTAATCTCGGTCATCT
1 ATTTTCTATTGTTAATCTCAATCATCT
* *
56742 ATTTTCTATTGTTAGTCTCAATTATCT
1 ATTTTCTATTGTTAATCTCAATCATCT
56769 ATTTTC
1 ATTTTC
56775 ACTCATTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.08, T:0.55
Consensus pattern (27 bp):
ATTTTCTATTGTTAATCTCAATCATCT
Found at i:57034 original size:18 final size:18
Alignment explanation
Indices: 57013--57047 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57003 GCATTGTTCC
57013 TTTCATTATAAAAAAATG
1 TTTCATTATAAAAAAATG
* *
57031 TTTCATTTTAAGAAAAT
1 TTTCATTATAAAAAAAT
57048 TAAATAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTCATTATAAAAAAATG
Found at i:62937 original size:24 final size:24
Alignment explanation
Indices: 62905--62952 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
62895 TAAAAATTCG
62905 CCCAAAATATAAAATCTTGTATCA
1 CCCAAAATATAAAATCTTGTATCA
*
62929 CCCATAATATAAAATCTTGTATCA
1 CCCAAAATATAAAATCTTGTATCA
62953 GTGTTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (24 bp):
CCCAAAATATAAAATCTTGTATCA
Found at i:67560 original size:2 final size:2
Alignment explanation
Indices: 67555--67583 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
67545 TTAATCATTA
67555 AT AT 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 AT AT A
67584 ATGATATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79513 original size:21 final size:21
Alignment explanation
Indices: 79481--79535 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
79471 ATTTATAATA
79481 ATAAATTTAATT-TTAAATATTT
1 ATAAA-TTAATTCTT-AATATTT
*
79503 ATAAATTAATTCTTATTATTT
1 ATAAATTAATTCTTAATATTT
79524 ATTAATATTAAT
1 A-TAA-ATTAAT
79536 ATGGTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 13 0.45
22 10 0.34
23 6 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATAAATTAATTCTTAATATTT
Found at i:80838 original size:23 final size:24
Alignment explanation
Indices: 80798--80848 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
80788 AAAAAAAATT
*
80798 GGGTTCGGGTTCGGGTCGGGTTTA
1 GGGTTCGGGTTCGGGTCGAGTTTA
80822 GGGTTCGGG-TCGGGTCGAGTTTA
1 GGGTTCGGGTTCGGGTCGAGTTTA
80845 GGGT
1 GGGT
80849 GAAAAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.06, C:0.12, G:0.51, T:0.31
Consensus pattern (24 bp):
GGGTTCGGGTTCGGGTCGAGTTTA
Found at i:97409 original size:49 final size:50
Alignment explanation
Indices: 97341--97444 Score: 165
Period size: 49 Copynumber: 2.1 Consensus size: 50
97331 ACACCAAAAC
* * *
97341 CAAAAAAAAGCAATTACCACAAGATGAAATAAGAACATCTTCTAGCTTTG
1 CAAACAAAAGCAATTACCACAAGATGAAATAAGAACATATTCAAGCTTTG
*
97391 TAAACAAAA-CAATTACCACAAGATGAAATAAGAACATATTCAAGCTTTG
1 CAAACAAAAGCAATTACCACAAGATGAAATAAGAACATATTCAAGCTTTG
97440 CAAAC
1 CAAAC
97445 CAGTACCTGC
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 42 0.86
50 7 0.14
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (50 bp):
CAAACAAAAGCAATTACCACAAGATGAAATAAGAACATATTCAAGCTTTG
Found at i:98455 original size:2 final size:2
Alignment explanation
Indices: 98448--98472 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
98438 AGATACGATG
98448 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
98473 CTTTGCTGTT
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:98898 original size:28 final size:29
Alignment explanation
Indices: 98874--98939 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
98864 AAATTAATAC
98874 ATTTAATGATT-ATTTTATAATTTAATAAA
1 ATTTAAT-ATTAATTTTATAATTTAATAAA
*
98903 ATTTGATATTAATTTTATAACTTT--TGAAA
1 ATTTAATATTAATTTTATAA-TTTAAT-AAA
98932 ATTTAATA
1 ATTTAATA
98940 ATCAAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 4 0.12
29 25 0.78
30 3 0.09
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (29 bp):
ATTTAATATTAATTTTATAATTTAATAAA
Found at i:114686 original size:26 final size:25
Alignment explanation
Indices: 114657--114711 Score: 92
Period size: 26 Copynumber: 2.2 Consensus size: 25
114647 AAGACTCTAC
114657 TTCATACATCTTTCCTATATTATTGT
1 TTCATACATCTTTCCTATATTATT-T
*
114683 TTCATACATTTTTCCTATATTATTT
1 TTCATACATCTTTCCTATATTATTT
114708 TTCA
1 TTCA
114712 AAGCACTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.24, C:0.18, G:0.02, T:0.56
Consensus pattern (25 bp):
TTCATACATCTTTCCTATATTATTT
Found at i:120149 original size:25 final size:22
Alignment explanation
Indices: 120121--120171 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
120111 TCAAGTCTCA
120121 TTAAAAGCAATATAACTTATTTTAT
1 TTAAAA-CAA-ATAA-TTATTTTAT
**
120146 TTAAAATTAATAATTATTTTAT
1 TTAAAACAAATAATTATTTTAT
120168 TTAA
1 TTAA
120172 GTTCATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.54
23 4 0.17
24 1 0.04
25 6 0.25
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAAAACAAATAATTATTTTAT
Found at i:120217 original size:15 final size:16
Alignment explanation
Indices: 120192--120224 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
120182 AAATAATTAT
120192 ATTATTTTTATTAATA
1 ATTATTTTTATTAATA
*
120208 ATTA-TTTTATTTATA
1 ATTATTTTTATTAATA
120223 AT
1 AT
120225 ATTATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTATTTTTATTAATA
Found at i:120942 original size:14 final size:14
Alignment explanation
Indices: 120923--120954 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
120913 AGCTATAGTA
120923 TATTATCATAAATT
1 TATTATCATAAATT
*
120937 TATTATCATAACTT
1 TATTATCATAAATT
120951 TATT
1 TATT
120955 TCAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATCATAAATT
Found at i:121985 original size:21 final size:22
Alignment explanation
Indices: 121948--121988 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
121938 ACGTCTATAC
*
121948 AATTTTAAAAACTTAAAATTAT
1 AATTTTAAAAACATAAAATTAT
121970 AATTTTAAAAA-ATAAAATT
1 AATTTTAAAAACATAAAATT
121989 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTTTAAAAACATAAAATTAT
Found at i:121990 original size:14 final size:15
Alignment explanation
Indices: 121970--122001 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
121960 TTAAAATTAT
*
121970 AATTTTAAAAAATAA
1 AATTTAAAAAAATAA
121985 AATTTAAAAAAATAA
1 AATTTAAAAAAATAA
122000 AA
1 AA
122002 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATTTAAAAAAATAA
Found at i:122543 original size:2 final size:2
Alignment explanation
Indices: 122442--122530 Score: 132
Period size: 2 Copynumber: 46.5 Consensus size: 2
122432 TAATTTTGTT
122442 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
* *
122484 TA TA TA TA TA TA TA TA T- TC T- TA T- TT TA T- 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
122522 TA TA TA TA T
1 TA TA TA TA T
122531 GTGTGTGTAT
Statistics
Matches: 82, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
1 4 0.05
2 78 0.95
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:122637 original size:77 final size:75
Alignment explanation
Indices: 122537--122906 Score: 218
Period size: 77 Copynumber: 5.0 Consensus size: 75
122527 ATATGTGTGT
* * *
122537 GTATATAGTAATACAGTTTTTGAAAATGTTTTGACAAAATATA-AT-GTATAAT-TTTTGGAAAA
1 GTATATA-TTATATAGTTTTTGAAAACGTTTT--CAAAATATATATAGTAT-ATGTTTT-GAAAA
* *
122599 CGATTTTCGAAAATAA
61 AGATTTT-GAAAACAA
* *
122615 GTATATATTATATAGTTTTTGAAAACGTTTTTAAAATATATATAGTATATGGTTTTGAAAAATAT
1 GTATATATTATATAGTTTTTGAAAACGTTTTCAAAATATATATAGTATAT-GTTTTGAAAAAGAT
*
122680 TTTGAAAACAT
65 TTTGAAAACAA
* * * * * * *
122691 TTATATATTATATAGTTTTT-AAAACATTTTGAAAGTATATATAATATATAGTTTT-TAAAACAT
1 GTATATATTATATAGTTTTTGAAAACGTTTTCAAAATATATATAGTATAT-GTTTTGAAAAAGAT
*
122754 TTTAAAAACATA
65 TTTGAAAACA-A
* * * * * **
122766 -TATTATATAAAACA-TTTTTGAAAAC-ATTT----ATATA-ATA-TATA-GTTTTTAAAATCAT
1 GTA-TATATTATATAGTTTTTGAAAACGTTTTCAAAATATATATAGTATATGTTTTGAAAAAGAT
*
122821 TTTGAAAACAT
65 TTTGAAAACAA
* * * *
122832 TTATATAATATATAGTTTTT-AAAATCATTTTCAAAACT-TATATAATATATAGTTTTTGAAAAT
1 GTATATATTATATAGTTTTTGAAAA-CGTTTTCAAAA-TATATATAGTATAT-G-TTTTGAAAA-
*
122895 A-TTTTTGAAAAC
61 AGATTTTGAAAAC
122907 TTATATATAA
Statistics
Matches: 234, Mismatches: 35, Indels: 47
0.74 0.11 0.15
Matches are distributed among these distances:
66 16 0.07
67 23 0.10
68 7 0.03
69 3 0.01
70 4 0.02
72 3 0.01
73 4 0.02
74 29 0.12
75 51 0.22
76 30 0.13
77 53 0.23
78 11 0.05
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (75 bp):
GTATATATTATATAGTTTTTGAAAACGTTTTCAAAATATATATAGTATATGTTTTGAAAAAGATT
TTGAAAACAA
Found at i:122703 original size:39 final size:38
Alignment explanation
Indices: 122616--122932 Score: 283
Period size: 39 Copynumber: 8.6 Consensus size: 38
122606 CGAAAATAAG
* ** * *
122616 TATATATTATATAGTTTTTGAAAACGTTTT-TAAA-ATA
1 TATATAATATATAGTTTTT-AAAATATTTTGAAAACATT
* * *
122653 TATATAGTATATGGTTTTGAAAAATATTTTGAAAACATT
1 TATATAATATATAGTTTT-TAAAATATTTTGAAAACATT
* * * *
122692 TATATATTATATAGTTTTTAAAACATTTTG-AAA-GTA
1 TATATAATATATAGTTTTTAAAATATTTTGAAAACATT
* *
122728 TATATAATATATAGTTTTTAAAACATTTTAAAAACA--
1 TATATAATATATAGTTTTTAAAATATTTTGAAAACATT
122764 TATAT--TATATA------AAACAT-TTTTGAAAACATT
1 TATATAATATATAGTTTTTAAA-ATATTTTGAAAACATT
122794 TATATAATATATAGTTTTTAAAATCATTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAAT-ATTTTGAAAACATT
*
122833 TATATAATATATAGTTTTTAAAATCATTTTCAAAAC--T
1 TATATAATATATAGTTTTTAAAAT-ATTTTGAAAACATT
122870 TATATAATATATAGTTTTTGAAAATATTTTTGAAAAC-TT
1 TATATAATATATAGTTTTT-AAAATA-TTTTGAAAACATT
* *
122909 ATATATAATATATAATTTTAAAAA
1 -TATATAATATATAGTTTTTAAAA
122933 AACATTTTTG
Statistics
Matches: 236, Mismatches: 22, Indels: 42
0.79 0.07 0.14
Matches are distributed among these distances:
28 13 0.06
29 1 0.00
30 5 0.02
32 6 0.03
34 6 0.03
36 34 0.14
37 53 0.22
38 30 0.13
39 71 0.30
40 17 0.07
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (38 bp):
TATATAATATATAGTTTTTAAAATATTTTGAAAACATT
Found at i:122914 original size:141 final size:146
Alignment explanation
Indices: 122653--123042 Score: 414
Period size: 141 Copynumber: 2.7 Consensus size: 146
122643 TTTTAAAATA
* * *
122653 TATATAGTATATGGTTTTGAAAAAT-ATTTTGAAAACATTTATATATTATATAGTTTTTAAAA-C
1 TATATAATATATAGTTTT-AAAAATCATTTTGAAAACATTTATATAATATATAGTTTTTAAAATC
*
122716 ATTTTGAAAGTATATATAATATATAGTTTTT-AAAACA-TTTTAAAAACATATATTATATAA-A-
65 ATTTTGAAA-T-TATATAATATATAGTTTTTGAAAATATTTTTAAAAACATATATTATATAATAT
* **
122777 A-CATTTT-TGAAAACATT
128 ATAATTTTAAAAAAACATT
*
122794 TATATAATATATAGTTTTTAAAATCATTTTGAAAACATTTATATAATATATAGTTTTTAAAATCA
1 TATATAATATATAGTTTTAAAAATCATTTTGAAAACATTTATATAATATATAGTTTTTAAAATCA
* *
122859 TTTTCAAAACTTATATAATATATAGTTTTTGAAAATATTTTTGAAAAC-T-TA-TATATAATATA
66 TTTT-GAAA-TTATATAATATATAGTTTTTGAAAATATTTTTAAAAACATATATTATATAATATA
122921 TAATTTTAAAAAAACATT
129 TAATTTTAAAAAAACATT
* * * * ** * *
122939 TTTGAAAACTATATAATTTTGAAAA-CATTTTTTAAA-A-GTATATAATATATA-ATTTTAAAAT
1 TAT-ATAA-TATATAGTTTTAAAAATCATTTTGAAAACATTTATATAATATATAGTTTTTAAAAT
* * *
123000 AATTTTGAAATTATATATTATATAGGTTTTGGAAAATATTTTT
64 CATTTTGAAATTATATAATATATA-GTTTTTGAAAATATTTTT
123043 TATATATAAT
Statistics
Matches: 214, Mismatches: 23, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
140 5 0.02
141 72 0.34
142 48 0.22
143 25 0.12
144 27 0.13
145 11 0.05
146 12 0.06
147 14 0.07
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (146 bp):
TATATAATATATAGTTTTAAAAATCATTTTGAAAACATTTATATAATATATAGTTTTTAAAATCA
TTTTGAAATTATATAATATATAGTTTTTGAAAATATTTTTAAAAACATATATTATATAATATATA
ATTTTAAAAAAACATT
Found at i:122952 original size:40 final size:40
Alignment explanation
Indices: 122774--122953 Score: 226
Period size: 39 Copynumber: 4.6 Consensus size: 40
122764 TATATTATAT
*
122774 AAAACATTTTTGAAAACATTTATATAATATATAGTTTTTA
1 AAAACATTTTTGAAAACATATATATAATATATAGTTTTTA
* *
122814 AAATCA-TTTTGAAAACATTTATATAATATATAGTTTTTA
1 AAAACATTTTTGAAAACATATATATAATATATAGTTTTTA
* * *
122853 AAATCA-TTTTCAAAAC-T-TATATAATATATAGTTTTTG
1 AAAACATTTTTGAAAACATATATATAATATATAGTTTTTA
* * * *
122890 AAAATATTTTTGAAAACTTATATATAATATATAATTTTAAA
1 AAAACATTTTTGAAAACATATATATAATATATAGTTTT-TA
122931 AAAACATTTTTGAAAAC-TATATA
1 AAAACATTTTTGAAAACATATATA
122954 ATTTTGAAAA
Statistics
Matches: 126, Mismatches: 10, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
37 23 0.18
38 10 0.08
39 49 0.39
40 28 0.22
41 16 0.13
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (40 bp):
AAAACATTTTTGAAAACATATATATAATATATAGTTTTTA
Found at i:122963 original size:29 final size:30
Alignment explanation
Indices: 122917--122984 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
122907 TTATATATAA
122917 TATATAATTTTAAAAAAACATTTTTGAAAAC
1 TATATAATTTT-AAAAAACATTTTTGAAAAC
* * *
122948 TATATAATTTT-GAAAACATTTTTTAAAAG
1 TATATAATTTTAAAAAACATTTTTGAAAAC
122977 TATATAAT
1 TATATAAT
122985 ATATAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 23 0.68
31 11 0.32
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (30 bp):
TATATAATTTTAAAAAACATTTTTGAAAAC
Found at i:123034 original size:25 final size:24
Alignment explanation
Indices: 123002--123048 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
122992 TTTAAAATAA
*
123002 TTTTGAAATTATATATTATATAGG
1 TTTTGAAAATATATATTATATAGG
* *
123026 TTTTGGAAAATATTTTTTATATA
1 TTTT-GAAAATATATATTATATA
123049 TAATATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (24 bp):
TTTTGAAAATATATATTATATAGG
Found at i:145728 original size:3 final size:3
Alignment explanation
Indices: 145720--145750 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
145710 GGTGTAATTC
145720 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
145751 TGGAATAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:152361 original size:30 final size:30
Alignment explanation
Indices: 152301--152370 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
152291 AACTTGTGTT
* *
152301 TATAGATACTTAATAAATTGATATTTAAAA
1 TATAGATAATTAATAAATTGATATTAAAAA
* * *
152331 TATATATAATTAATAAATTGTTGTTAAAAA
1 TATAGATAATTAATAAATTGATATTAAAAA
*
152361 T-TAGTTAATT
1 TATAGATAATT
152371 GATTTTTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 7 0.21
30 26 0.79
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (30 bp):
TATAGATAATTAATAAATTGATATTAAAAA
Found at i:160632 original size:2 final size:2
Alignment explanation
Indices: 160625--160661 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
160615 TGTTTCCTCG
160625 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
160662 AAAAGGACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:168252 original size:21 final size:23
Alignment explanation
Indices: 168228--168269 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
168218 TTAAATATCT
*
168228 ATATTAAT-AAAAAA-AATAAAC
1 ATATAAATGAAAAAATAATAAAC
168249 ATATAAATGAAAAAATAATAA
1 ATATAAATGAAAAAATAATAA
168270 TTTGATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (23 bp):
ATATAAATGAAAAAATAATAAAC
Found at i:170972 original size:21 final size:21
Alignment explanation
Indices: 170921--170973 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
170911 TTTAAGAAAA
*
170921 TTAAAGTTTAAGTTTATGATT
1 TTAAAGTTTAAGTTTATGAGT
*
170942 TTAGAGTTTAAGATTTATG-GT
1 TTAAAGTTTAAG-TTTATGAGT
*
170963 TTAAATTTTAA
1 TTAAAGTTTAA
170974 ATTAAAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (21 bp):
TTAAAGTTTAAGTTTATGAGT
Done.