Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold332
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: 507797
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.32
Warning! 15717 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:385405 original size:14 final size:14
Alignment explanation
Indices: 385386--385423 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
385376 TCTAGAAAGT
*
385386 AAATCATTTTCTAG
1 AAATCATTTTCCAG
385400 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
385414 AAAACATTTT
1 AAATCATTTT
385424 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:389982 original size:30 final size:30
Alignment explanation
Indices: 389946--390007 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
389936 TCTCTAATAA
389946 AATATGTGAAAAGTGAATAACTAGAATTAT
1 AATATGTGAAAAGTGAATAACTAGAATTAT
*
389976 AATATGTGAAAAGTGAATAGCTAGAATTAT
1 AATATGTGAAAAGTGAATAACTAGAATTAT
390006 AA
1 AA
390008 CGTGTTTCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.29
Consensus pattern (30 bp):
AATATGTGAAAAGTGAATAACTAGAATTAT
Found at i:412720 original size:3 final size:3
Alignment explanation
Indices: 412712--412743 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
412702 CAAATTGCAA
412712 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
412744 AAGTATTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:427250 original size:264 final size:261
Alignment explanation
Indices: 426734--427517 Score: 842
Period size: 264 Copynumber: 3.0 Consensus size: 261
426724 TTATCAATCG
* * * * * *
426734 AAATTTGAGGGAAGAAGAACTTAATCACACATGTGAAA-TTAAGTATTGATAAGTTCTTCAGGCT
1 AAATTTGAAGG-AGAAGAACATAATTACA-ATGTGAAATTTCA-TATTGATAACTTCTTGAGGCT
* *
426798 AAATGTTGTGCAAGCATGATTTATAGTCTAAGACATACGTGCCTCCACATTGAT-ATTTACAAAT
63 AAATGTTGTGCAAGCATGATTTATAGTCCAAGACATACGTGCCTTCACATTGATCA-TTACAAAT
* *
426862 CTTGTTCTAATCTTTTTTTAGCAGTTGTTGTTGCTCCAGAAGGGTAATGATTTCTCATACTTTAT
127 CTTGTTCTAATCTTTTTTTACCAGTTGTTGTTGCTCTAGAAGGGTAATGA-TTCTCATACTTTAT
*
426927 GCGGTGTATTTATGTATTTGCCCTTAACATAATAC-GAAGGGAATCTCCATTTACTTTTCACACA
191 GCGGTGTATTTACGTATTTGCCCTTAACATAATACTG-AGGGAATCTCC-TTTACTTTTCACACA
**
426991 TTTTACCA
254 TTCAACCA
* * *
426999 AAATTTG-AGG-GAAGAACGTAATTACAATTGTGAAATTTCATATTGGTAACTTCTTGAGGCCAA
1 AAATTTGAAGGAGAAGAACATAATTACAA-TGTGAAATTTCATATTGATAACTTCTTGAGGCTAA
* * * * * *
427062 ATGTTGTTCAAACATGATTTATAGTCCAAGACATACGTTCCTTTATATTGATCATTACAAATCTC
65 ATGTTGTGCAAGCATGATTTATAGTCCAAGACATACGTGCCTTCACATTGATCATTACAAATCTT
* * *
427127 ATTCTAATCTTTTTTTTTTCCAGTTGTTGTTGCTCTAGAAGGGTAATGATTCGTCATAATTTATG
130 GTTCTAATC--TTTTTTTACCAGTTGTTGTTGCTCTAGAAGGGTAATGATTC-TCATACTTTATG
** * * *
427192 CAATGTATTTACGTATTTGCCCTTAACATAATACTGA-GGAAACGTCACTTTGCTTTTCACACGT
192 CGGTGTATTTACGTATTTGCCCTTAACATAATACTGAGGGAATC-TC-CTTTACTTTTCACACAT
**
427256 TCAACTG
255 TCAACCA
* * ** ** * * * *
427263 AAATTTGAAGGAAGAAAAACATATTTTTACCGATGAAATTACACATTGATAACTTGTTGAGACTA
1 AAATTTGAAGG-AGAAGAACATAATTACAATG-TGAAATTTCATATTGATAACTTCTTGAGGCTA
* * * * *
427328 AATGTTGTGCAAGCATGATTTATAGCCCGAGACATAAGTGCCTTCACGTTGATCATTATAAATCT
64 AATGTTGTGCAAGCATGATTTATAGTCCAAGACATACGTGCCTTCACATTGATCATTACAAATCT
* * * * * * *
427393 TGTTCTAATCTTTTTTTGCTAGTTGTTCTTACTCTAGAAGGGTAATGATTCCTAATCCTTTATGG
129 TGTTCTAATCTTTTTTTACCAGTTGTTGTTGCTCTAGAAGGGTAATGATT-CTCATACTTTATGC
* * * * *
427458 GGTGCATTTACATATTTTCCCTTTACATAATACTGAGGGAATCTCCCTTTTCTTTTCACA
193 GGTGTATTTACGTATTTGCCCTTAACATAATACTGAGGGAATCT-CCTTTACTTTTCACA
427518 TCTTCAATCG
Statistics
Matches: 431, Mismatches: 72, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
261 1 0.00
262 103 0.24
263 12 0.03
264 106 0.25
265 101 0.23
266 8 0.02
267 100 0.23
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (261 bp):
AAATTTGAAGGAGAAGAACATAATTACAATGTGAAATTTCATATTGATAACTTCTTGAGGCTAAA
TGTTGTGCAAGCATGATTTATAGTCCAAGACATACGTGCCTTCACATTGATCATTACAAATCTTG
TTCTAATCTTTTTTTACCAGTTGTTGTTGCTCTAGAAGGGTAATGATTCTCATACTTTATGCGGT
GTATTTACGTATTTGCCCTTAACATAATACTGAGGGAATCTCCTTTACTTTTCACACATTCAACC
A
Found at i:427533 original size:265 final size:262
Alignment explanation
Indices: 426778--427553 Score: 864
Period size: 265 Copynumber: 2.9 Consensus size: 262
426768 GAAATTAAGT
* * * *
426778 ATTGATAAGTTCTTCAGGCTAAATGTTGTGCAAGCATGATTTATAGTCTAAGACATACGTGCCTC
1 ATTGATAACTTCTTGAGGCTAAATGTTGTGCAAGCATGATTTATAGTCCAAGACATACGTGCCTT
*
426843 CACATTGAT-ATTTACAAATCTTGTTCTAATCTTTTTTTAGCAGTTGTTGTTGCTCCAGAAGGGT
66 CACATTGATCA-TTACAAATCTTGTTCTAATCTTTTTTT-GCAGTTGTTGTTGCTCTAGAAGGGT
* *
426907 AATGATTTCTCATACTTTATGCGGTGTATTTATGTATTTGCCCTTAACATAATAC-GAAGGGAAT
129 AATGATTCCTCATACTTTATGCGGTGTATTTACGTATTTGCCCTTAACATAATACTG-AGGGAAT
* * * * * * * **
426971 CTCCATTTACTTTTCACACATTTTACCAAAATTTG-AGG--GAAGAACGTAATTACAATTGTGAA
193 CTCCCTTTACTTTTCACACA-TTCAACGAAATTTGAAGGAAGAAAAACAT-ATTTCAACCGTGAA
* *
427033 ATTTCAT
256 ATTACAC
* * * * *
427040 ATTGGTAACTTCTTGAGGCCAAATGTTGTTCAAACATGATTTATAGTCCAAGACATACGTTCCTT
1 ATTGATAACTTCTTGAGGCTAAATGTTGTGCAAGCATGATTTATAGTCCAAGACATACGTGCCTT
* * ** *
427105 TATATTGATCATTACAAATCTCATTCTAATCTTTTTTTTTTCCAGTTGTTGTTGCTCTAGAAGGG
66 CACATTGATCATTACAAATCTTGTTCTAATC---TTTTTTTGCAGTTGTTGTTGCTCTAGAAGGG
* * ** *
427170 TAATGATTCGTCATAATTTATGCAATGTATTTACGTATTTGCCCTTAACATAATACTGA-GGAAA
128 TAATGATTCCTCATACTTTATGCGGTGTATTTACGTATTTGCCCTTAACATAATACTGAGGGAAT
* * * **
427234 CGTCACTTTGCTTTTCACACGTTCAACTGAAATTTGAAGGAAGAAAAACATATTTTTACCGATGA
193 C-TCCCTTTACTTTTCACACATTCAAC-GAAATTTGAAGGAAGAAAAACATATTTCAACCG-TGA
427299 AATTACAC
255 AATTACAC
* * * * *
427307 ATTGATAACTTGTTGAGACTAAATGTTGTGCAAGCATGATTTATAGCCCGAGACATAAGTGCCTT
1 ATTGATAACTTCTTGAGGCTAAATGTTGTGCAAGCATGATTTATAGTCCAAGACATACGTGCCTT
* * * *
427372 CACGTTGATCATTATAAATCTTGTTCTAATCTTTTTTTGCTAGTTGTTCTTACTCTAGAAGGGTA
66 CACATTGATCATTACAAATCTTGTTCTAATCTTTTTTTGC-AGTTGTTGTTGCTCTAGAAGGGTA
* * * * * * *
427437 ATGATTCCTAATCCTTTATGGGGTGCATTTACATATTTTCCCTTTACATAATACTGAGGGAATCT
130 ATGATTCCTCATACTTTATGCGGTGTATTTACGTATTTGCCCTTAACATAATACTGAGGGAATCT
* * *
427502 CCCTTTTCTTTTCACATC-TTCAATCGAAATTTTAGGGAAGAAAAACATATTT
195 CCCTTTACTTTTCACA-CATTCAA-CGAAATTTGAAGGAAGAAAAACATATTT
427554 ACACTAGTAA
Statistics
Matches: 426, Mismatches: 73, Indels: 27
0.81 0.14 0.05
Matches are distributed among these distances:
262 81 0.19
263 10 0.02
264 103 0.24
265 124 0.29
266 12 0.03
267 96 0.23
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (262 bp):
ATTGATAACTTCTTGAGGCTAAATGTTGTGCAAGCATGATTTATAGTCCAAGACATACGTGCCTT
CACATTGATCATTACAAATCTTGTTCTAATCTTTTTTTGCAGTTGTTGTTGCTCTAGAAGGGTAA
TGATTCCTCATACTTTATGCGGTGTATTTACGTATTTGCCCTTAACATAATACTGAGGGAATCTC
CCTTTACTTTTCACACATTCAACGAAATTTGAAGGAAGAAAAACATATTTCAACCGTGAAATTAC
AC
Found at i:428081 original size:260 final size:263
Alignment explanation
Indices: 427600--428137 Score: 674
Period size: 260 Copynumber: 2.0 Consensus size: 263
427590 CCCTAAACCT
* * *
427600 TTAACCATAATACTGAGGGAACCTCCCTTTGCTTTTCACATGTTCAACCAAAAATTGAGGGAAGA
1 TTAA-CATAATACTAAGAGAACCTCCCTTTGCTTTTCACATATTCAACCAAAAATTGAGGGAAGA
* * * *
427665 AGAACATAATTATACAAGTAAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGGAAGCA
65 AGAACATAATTATAC-ACTAAAATTAAGTAGTGATAACTTCTTGAGACCAAATGTTGTGCAAGCA
* * * * *
427730 TGATTTATATTCCGAGACATACGTGCCATCATGTTAATCATTACAAATCTTATTCTAATATTTTT
129 CGATTTATATTCCAAAACATACGTGCCATCACGTTAACCATTACAAATCTTATTCTAATATTTTT
* * * * * *
427795 TTTCTAGTTTTTCTTGCTCTAGAAGGGTAAT-TATCGTCATACTTTATGC-AGTGTTTTTACGTA
194 TTGCCAGTTTTTCTTACTCCAGAAGGGTAATATATC-TCATACTTTATGCGA-TATATTTACGTA
427858 TTTGCCC
257 TTTGCCC
* * * *
427865 TTAACATAATACTAAGAGAACCTCCCTTTGCTTTTCACATATTTAATCAAAATTTGAGGGAATAA
1 TTAACATAATACTAAGAGAACCTCCCTTTGCTTTTCACATATTCAACCAAAAATTGAGGGAAGAA
* * * * *
427930 GAACATATTTGTAC-CTATAA-TACGTAGTGATAACTTGCTT-AGACCAGATGTT-TGCAAGCAC
66 GAACATAATTATACACTAAAATTAAGTAGTGATAACTT-CTTGAGACCAAATGTTGTGCAAGCAC
* * * * *
427991 GATTTATATTCTAAAACATACGTGTCTTCACGTTGACCATTACAAATCTTATTCTAATCTTTTTT
130 GATTTATATTCCAAAACATACGTGCCATCACGTTAACCATTACAAATCTTATTCTAATATTTTTT
* *
428056 TGCCAGTTTTTTTTACTCCAGAAGGGTAATGATTTCTCATACTTTATGCGATATATTTACGTATT
195 TGCCAGTTTTTCTTACTCCAGAAGGGTAAT-ATATCTCATACTTTATGCGATATATTTACGTATT
428121 TGCCC
259 TGCCC
428126 TTAACATAATAC
1 TTAACATAATAC
428138 AGAGGGAAGA
Statistics
Matches: 235, Mismatches: 34, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
260 88 0.37
261 66 0.28
262 11 0.05
264 66 0.28
265 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (263 bp):
TTAACATAATACTAAGAGAACCTCCCTTTGCTTTTCACATATTCAACCAAAAATTGAGGGAAGAA
GAACATAATTATACACTAAAATTAAGTAGTGATAACTTCTTGAGACCAAATGTTGTGCAAGCACG
ATTTATATTCCAAAACATACGTGCCATCACGTTAACCATTACAAATCTTATTCTAATATTTTTTT
GCCAGTTTTTCTTACTCCAGAAGGGTAATATATCTCATACTTTATGCGATATATTTACGTATTTG
CCC
Found at i:433499 original size:12 final size:12
Alignment explanation
Indices: 433482--433520 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
433472 ACTAGTATAA
433482 ACATATATCTAT
1 ACATATATCTAT
*
433494 ACATATATTTAT
1 ACATATATCTAT
433506 ACTATATATACTAT
1 AC-ATATAT-CTAT
433520 A
1 A
433521 TATACTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 13 0.57
13 6 0.26
14 4 0.17
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (12 bp):
ACATATATCTAT
Found at i:433517 original size:9 final size:9
Alignment explanation
Indices: 433466--433529 Score: 62
Period size: 9 Copynumber: 7.2 Consensus size: 9
433456 TACCAATTCG
433466 TATAGTACTA
1 TATA-TACTA
*
433476 GTATAAAC-A
1 -TATATACTA
433485 TATAT-CTA
1 TATATACTA
*
433493 TACATA-TA
1 TATATACTA
*
433501 TTTATACTA
1 TATATACTA
433510 TATATACTA
1 TATATACTA
433519 TATATACTA
1 TATATACTA
433528 TA
1 TA
433530 ACACTACTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 1 0.02
8 15 0.34
9 22 0.50
10 2 0.05
11 4 0.09
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (9 bp):
TATATACTA
Found at i:433835 original size:103 final size:103
Alignment explanation
Indices: 433656--433860 Score: 286
Period size: 103 Copynumber: 2.0 Consensus size: 103
433646 TATATCTGAT
* * * * ** *
433656 TTTTCTATTCTGAGTATAGTGCTGACTTTTCCGTTGTTTGTATTCTAGTAGTTTGAACTCCCTGT
1 TTTTCTATTCTGAGTACAGTGCTGACTTTTCCATTGCTTGTATTCTACTAGACTAAACTCCCTGT
433721 TGTGTCTTTATTGCCATATATGC-TATTGCCATAAGAAA
66 TGTGTCTTTATTGCCATATAT-CTTATTGCCATAAGAAA
* * * *
433759 TTTTCTATTCTGAGTACAGTGTTGATTTTTCCATTGCTTGTATTCTACTAGACTAAACTTCGTGT
1 TTTTCTATTCTGAGTACAGTGCTGACTTTTCCATTGCTTGTATTCTACTAGACTAAACTCCCTGT
*
433824 TGTGTCTTTATTGCCATATATCTTATTTCCATAAGAA
66 TGTGTCTTTATTGCCATATATCTTATTGCCATAAGAA
433861 TTCCCTGGTA
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
102 1 0.01
103 88 0.99
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46
Consensus pattern (103 bp):
TTTTCTATTCTGAGTACAGTGCTGACTTTTCCATTGCTTGTATTCTACTAGACTAAACTCCCTGT
TGTGTCTTTATTGCCATATATCTTATTGCCATAAGAAA
Found at i:434021 original size:50 final size:50
Alignment explanation
Indices: 433965--434067 Score: 188
Period size: 50 Copynumber: 2.1 Consensus size: 50
433955 TTAGGCCTTA
*
433965 TTTATCATTATGTCCATGGCTTGATAGTTTTTACTTATTTCTTGTATTTG
1 TTTATCATTATGTCCATGGCTTGATAGTTTTTACTTATTTCTTGTATCTG
*
434015 TTTATCATTATGTCCATGGCTTGATAGTTTTTACTTCTTTCTTGTATCTG
1 TTTATCATTATGTCCATGGCTTGATAGTTTTTACTTATTTCTTGTATCTG
434065 TTT
1 TTT
434068 GTTCTCTCTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.56
Consensus pattern (50 bp):
TTTATCATTATGTCCATGGCTTGATAGTTTTTACTTATTTCTTGTATCTG
Found at i:443421 original size:5 final size:5
Alignment explanation
Indices: 443411--443443 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
443401 AAAACTCATA
443411 AAAAT AAAAT AAAAT AAAAT AAAAT AAATAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AA
443444 CTAGTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:444243 original size:18 final size:18
Alignment explanation
Indices: 444212--444263 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
444202 TGTATTATAA
* *
444212 TATTAATTAATAAAATAT
1 TATTACTTATTAAAATAT
444230 TATTACTTATTAAAATAT
1 TATTACTTATTAAAATAT
444248 TATTACTTAATTAAAA
1 TATTACTT-ATTAAAA
444264 AATCATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 24 0.77
19 7 0.23
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTACTTATTAAAATAT
Found at i:452077 original size:38 final size:38
Alignment explanation
Indices: 452033--452118 Score: 154
Period size: 38 Copynumber: 2.2 Consensus size: 38
452023 ACACCAAATT
452033 ACACAATATGAGTACATTATAATTACAAATGCCGATTC
1 ACACAATATGAGTACATTATAATTACAAATGCCGATTC
*
452071 ACACAATATGAGTACATTATAATTACTAATGCCGATTC
1 ACACAATATGAGTACATTATAATTACAAATGCCGATTC
452109 ACACATATAT
1 ACACA-ATAT
452119 TTCATTTAGC
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 42 0.91
39 4 0.09
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (38 bp):
ACACAATATGAGTACATTATAATTACAAATGCCGATTC
Found at i:453403 original size:43 final size:43
Alignment explanation
Indices: 453351--453435 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
453341 ACATGTAATC
453351 ACAAATCGATGCC-ACTGTCCCAGACAAGGTCTTACACGAAAAT
1 ACAAATCGATGCCAAC-GTCCCAGACAAGGTCTTACACGAAAAT
* *** *
453394 ACAAGTCGATGCCAACGTCCCAGATGTGGTCTTACATGAAAA
1 ACAAATCGATGCCAACGTCCCAGACAAGGTCTTACACGAAAA
453436 CACTTATCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 34 0.94
44 2 0.06
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (43 bp):
ACAAATCGATGCCAACGTCCCAGACAAGGTCTTACACGAAAAT
Found at i:461439 original size:43 final size:44
Alignment explanation
Indices: 461352--461449 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 44
461342 AACGTCCCAA
*
461352 CTTACATG-TAATCACAAATCGATGCCACTGTCCCAAACAGGGT
1 CTTACATGAAAATCACAAATCGATGCCACTGTCCCAAACAGGGT
* * * *
461395 CTTACATGAAAAT-ACAAGTCGATGCCAAC-GTCCTAGACATGGT
1 CTTACATGAAAATCACAAATCGATGCC-ACTGTCCCAAACAGGGT
*
461438 CTTTCATGAAAA
1 CTTACATGAAAA
461450 CACCTATCAG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 42 0.89
44 5 0.11
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (44 bp):
CTTACATGAAAATCACAAATCGATGCCACTGTCCCAAACAGGGT
Found at i:463476 original size:84 final size:84
Alignment explanation
Indices: 463287--463677 Score: 386
Period size: 84 Copynumber: 4.7 Consensus size: 84
463277 ACCAATATCG
* * * * *
463287 AATAAAATCTTGTTAAACAGCGGGAATAAATCCCAAAACATATTTTGTTTAATTCAATTCAAATT
1 AATAAAATCTTGTTAAACGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCAATTCAAATT
463352 A-G----AAAATAAAATAA
66 AGGAAACAAAATAAAATAA
* * * * *
463366 AATAAAATCTTATTAAATGG-AGGGAATAAATCTCGAAATAGATTTTATTTAATTCAATCCAAAT
1 AATAAAATCTTGTTAAACGGCA-GGAATAAATCCCGAAACAGATTTTATTTAATTCAATTCAAAT
*
463430 TAGGAAACAAAATAAAATCA
65 TAGGAAACAAAATAAAATAA
*
463450 AATAAAATCTTGTTAAACGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCAATTCATATT
1 AATAAAATCTTGTTAAACGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCAATTCAAATT
*
463515 AGGAAATAAAATAAAATAA
66 AGGAAACAAAATAAAATAA
* * * * * * * **
463534 AATACAATCTTGTTAAACGACGGGAAGAAATACCGAAATAGATTTTATTTAATTTAATTTCTCGT
1 AATAAAATCTTGTTAAACGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCAA--T-TCAA
* * * * *
463599 TTTTGGAAA-AATATCAAATCA
63 ATTAGGAAACAAAATAAAATAA
* ** * *
463620 AA-AAAATCATT-ATAAACGGTGGGAATAAATCCCGAAACAGATTTAATTTAATTTAATT
1 AATAAAATC-TTGTTAAACGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCAATT
463678 TCTAATTTTT
Statistics
Matches: 261, Mismatches: 40, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
79 55 0.21
80 1 0.00
82 1 0.00
83 1 0.00
84 135 0.52
85 44 0.17
86 14 0.05
87 10 0.04
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (84 bp):
AATAAAATCTTGTTAAACGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCAATTCAAATT
AGGAAACAAAATAAAATAA
Found at i:463905 original size:89 final size:87
Alignment explanation
Indices: 463767--464172 Score: 327
Period size: 89 Copynumber: 4.8 Consensus size: 87
463757 CTCGTTTTTA
* * *
463767 GAAATAAAACAAAAT-ATGGAATAAAAT-TGTTAAACGGCGGGAATCAATCCCGAAATAGATTTT
1 GAAATAAAACAAAATAATGGAATAAAATCCGTTGAACGGCGGGAATAAATCCCGAAA-AGATTTT
*
463830 ATTTACCTTTAATTTCTCATTTG
65 ATTTACCTTTAATTTCCCATTTG
** *
463853 GAAATAGAAACAAAATAATATAATAAAATCCGTTGAACGGCGGGAATAAATCCCGAAACGAATTT
1 GAAATA-AAACAAAATAATGGAATAAAATCCGTTGAACGGCGGGAATAAATCCCGAAAAG-ATTT
*
463918 TATTTACCTTTAATTTCCCGTTTG
64 TATTTACCTTTAATTTCCCATTTG
* ** * *
463942 AAAATAAAATCAAAATAATGGAATAAAATCCGTTGAACAACGAGAATAAATCTCGAAACAGATTT
1 GAAATAAAA-CAAAATAATGGAATAAAATCCGTTGAACGGCGGGAATAAATCCCGAAA-AGATTT
*
464007 TATTTACTTTTAA--T----TTTG
64 TATTTACCTTTAATTTCCCATTTG
* * * *
464025 G-----AAACAAAAT---CGAATAAAATCTGTTAAACGACGGGAA-AAATCCCGAAACAGATTTT
1 GAAATAAAACAAAATAATGGAATAAAATCCGTTGAACGGCGGGAATAAATCCCGAAA-AGATTTT
* ** *
464081 A-TGAGTTTTTATATT--CATTTG
65 ATTTACCTTTAAT-TTCCCATTTG
* *
464102 GAAATAAAACAAAAATAGA-GGAAAAAGAAATCTGTTGAACGGCGGGAA-AAATCCCGAAATAGA
1 GAAATAAAAC-AAAATA-ATGG-AATA-AAATCCGTTGAACGGCGGGAATAAATCCCGAAA-AGA
464165 -TTTATTTA
61 TTTTATTTA
464173 ATTTTTAAAA
Statistics
Matches: 264, Mismatches: 33, Indels: 44
0.77 0.10 0.13
Matches are distributed among these distances:
72 7 0.03
73 19 0.07
74 22 0.08
75 1 0.00
77 11 0.04
78 3 0.01
82 4 0.02
83 9 0.03
86 7 0.03
87 17 0.06
88 49 0.19
89 114 0.43
90 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (87 bp):
GAAATAAAACAAAATAATGGAATAAAATCCGTTGAACGGCGGGAATAAATCCCGAAAAGATTTTA
TTTACCTTTAATTTCCCATTTG
Found at i:466430 original size:29 final size:25
Alignment explanation
Indices: 466344--466416 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
466334 GAAATCTTCG
* *
466344 TTATATATATACACATACATGTGTTT
1 TTATA-ATATATATATACATGTGTTT
466370 TTATAATATATATATACATGTGTTT
1 TTATAATATATATATACATGTGTTT
466395 TTATAATATATATATACATGTG
1 TTATAATATATATATACATGTG
466417 CATATTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 40 0.89
26 5 0.11
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (25 bp):
TTATAATATATATATACATGTGTTT
Found at i:469556 original size:30 final size:30
Alignment explanation
Indices: 469520--469581 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
469510 TCAAATAAAG
469520 TTAATTGATTCGGCGCTGATAAGCGTACTA
1 TTAATTGATTCGGCGCTGATAAGCGTACTA
* *
469550 TTAATTGATTCGGCGTTGATTAGCGTACTA
1 TTAATTGATTCGGCGCTGATAAGCGTACTA
469580 TT
1 TT
469582 GAAAGTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.39
Consensus pattern (30 bp):
TTAATTGATTCGGCGCTGATAAGCGTACTA
Found at i:470505 original size:28 final size:28
Alignment explanation
Indices: 470442--470512 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
470432 TTTTTGGAAT
* *
470442 TTTTTTTGAAAATTTTAGAATTTTTATAA
1 TTTTTTTG-AAATTTAAAAATTTTTATAA
* *
470471 ATATTTTGAAATTTAAAAATTATTT-TAA
1 TTTTTTTGAAATTTAAAAATT-TTTATAA
*
470499 TTTTTTTGTAATTT
1 TTTTTTTGAAATTT
470513 TTTTTGACAG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
28 25 0.74
29 9 0.26
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (28 bp):
TTTTTTTGAAATTTAAAAATTTTTATAA
Found at i:471536 original size:20 final size:20
Alignment explanation
Indices: 471511--471550 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
471501 CGTAAAATAA
*
471511 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
471531 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
471551 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:471540 original size:34 final size:35
Alignment explanation
Indices: 471496--471562 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
471486 TAGTAAAATG
*
471496 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
* *
471530 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
471563 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:473705 original size:28 final size:27
Alignment explanation
Indices: 473658--473711 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
473648 TTCTTAGTAA
* *
473658 TGAAGAAGCTGAAGATGAGAACGGAGT
1 TGAAGAAGCTGAAGAAGAGAAAGGAGT
*
473685 TGAAGAAGGTTGAAGAAGAGAAAGGAG
1 TGAAGAA-GCTGAAGAAGAGAAAGGAG
473712 AAAGGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.44, C:0.04, G:0.39, T:0.13
Consensus pattern (27 bp):
TGAAGAAGCTGAAGAAGAGAAAGGAGT
Found at i:482352 original size:18 final size:19
Alignment explanation
Indices: 482318--482354 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
482308 ATTTGAAAAT
482318 CTGAGTCAACACCTGCTTC
1 CTGAGTCAACACCTGCTTC
482337 CTGAGTCAAC-CCTGCTTC
1 CTGAGTCAACACCTGCTTC
482355 ACACTGAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.19, C:0.38, G:0.16, T:0.27
Consensus pattern (19 bp):
CTGAGTCAACACCTGCTTC
Found at i:487904 original size:102 final size:102
Alignment explanation
Indices: 487663--488028 Score: 583
Period size: 103 Copynumber: 3.6 Consensus size: 102
487653 TAACCGTTAT
* *
487663 CGGTGGATTCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTCGGGG
487728 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCT-TCACATTTAAAATA
* **
487766 CGGTGGAATCAGCACTTAGCAACCACCAAT-AGGTAGGGGAATCAGCACTTAGCAACCCCTCGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGA-ATAGGGGAATCAGCACACAGCAACCCCTCGGG
487830 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATA
65 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATA
* * * ** *
487868 CGGTGGAATCAGCACTTAGCAACCACCAAT-AGGTAGGGAAACCAGCACTTAGCAACCCCTCGAG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGA-ATAGGGGAATCAGCACACAGCAACCCCTCGGG
487932 GGAATCAGCACTTAGCAACCCCCTTCCACATTTAAAATA
65 GGAATCAGCACTTAGCAACCCCCTT-CACATTTAAAATA
487971 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCC
488029 TTTTATATGC
Statistics
Matches: 247, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
102 101 0.41
103 145 0.59
104 1 0.00
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (102 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTCGGGG
GAATCAGCACTTAGCAACCCCCTTCACATTTAAAATA
Found at i:487942 original size:27 final size:30
Alignment explanation
Indices: 487872--487953 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 30
487862 AAAATACGGT
*
487872 GGAATCAGCACTTAGCAACCACCAATAGGTAG
1 GGAATCAGCACTTAGCAACC-CC-ATACGTAG
*
487904 GGAAACCAGCACTTAGCAACCCC-T-CG-AG
1 GG-AATCAGCACTTAGCAACCCCATACGTAG
487932 GGAATCAGCACTTAGCAACCCC
1 GGAATCAGCACTTAGCAACCCC
487954 CTTCCACATT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
27 19 0.41
28 4 0.09
29 1 0.02
30 1 0.02
32 4 0.09
33 17 0.37
ACGTcount: A:0.34, C:0.32, G:0.21, T:0.13
Consensus pattern (30 bp):
GGAATCAGCACTTAGCAACCCCATACGTAG
Found at i:490636 original size:5 final size:5
Alignment explanation
Indices: 490628--490667 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
490618 TGAAATGGAA
* *
490628 ATGAG ATGAG ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT
490668 GAATTATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (5 bp):
ATGAT
Found at i:492447 original size:16 final size:16
Alignment explanation
Indices: 492426--492456 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
492416 TTGTATATAC
*
492426 ATGAATTGATGATGAG
1 ATGAATTGATAATGAG
492442 ATGAATTGATAATGA
1 ATGAATTGATAATGA
492457 TGATATATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (16 bp):
ATGAATTGATAATGAG
Found at i:501048 original size:43 final size:43
Alignment explanation
Indices: 500985--501170 Score: 185
Period size: 43 Copynumber: 4.3 Consensus size: 43
500975 TTATTTTTAA
* ** *
500985 AAACGTCGCTAAAGGTCATGTTCTTTAGTGGCAC-TTTCTCCAC
1 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCACTTTTC-CCAC
*
501028 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCACTTTTCCCAC
* *** *
501071 AAACGCCGCTAAAGACCTTAACCTTTAGCGACACTTTTCCCAC
1 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCACTTTTCCCAC
* ** *** *
501114 AAACACCGCTAAAGACTTTAACCTTTAGCGGCGCTTTTTCCCAC
1 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCAC-TTTTCCCAC
*
501158 AAACGCTGCTAAA
1 AAACGCCGCTAAA
501171 AACATAACCT
Statistics
Matches: 124, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
43 100 0.81
44 24 0.19
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGTTCTTTAGCGGCACTTTTCCCAC
Found at i:501098 original size:86 final size:86
Alignment explanation
Indices: 501019--501183 Score: 224
Period size: 86 Copynumber: 1.9 Consensus size: 86
501009 TTAGTGGCAC
* ***
501019 TTTCTCCACAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAA
1 TTTC-CCACAAACACCGCTAAAGACCATAACCTTTAGCGGCGCTTTTTCCCACAAACGCCGCTAA
* *
501083 AGACCTTAACCTTTAGCGACACT
65 A-AACATAACCTTTAGCGACACT
** *
501106 TTTCCCACAAACACCGCTAAAGACTTTAACCTTTAGCGGCGCTTTTTCCCACAAACGCTGCTAAA
1 TTTCCCACAAACACCGCTAAAGACCATAACCTTTAGCGGCGCTTTTTCCCACAAACGCCGCTAAA
501171 AACATAACCTTTA
66 AACATAACCTTTA
501184 AAAATACATA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
86 43 0.63
87 25 0.37
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (86 bp):
TTTCCCACAAACACCGCTAAAGACCATAACCTTTAGCGGCGCTTTTTCCCACAAACGCCGCTAAA
AACATAACCTTTAGCGACACT
Found at i:501169 original size:44 final size:42
Alignment explanation
Indices: 501019--501183 Score: 195
Period size: 43 Copynumber: 3.8 Consensus size: 42
501009 TTAGTGGCAC
* ***
501019 TTTCTCCACAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCT
1 TTTC-CCACAAACGCCGCTAAAGA-CTTAACCTTTAGCGGCGCT
* *
501063 TTTCCCACAAACGCCGCTAAAGACCTTAACCTTTAGCGACACT
1 TTTCCCACAAACGCCGCTAAAGA-CTTAACCTTTAGCGGCGCT
*
501106 TTTCCCACAAACACCGCTAAAGACTTTAACCTTTAGCGGCGCTT
1 TTTCCCACAAACGCCGCTAAAGAC-TTAACCTTTAGCGGCGC-T
* * *
501150 TTTCCCACAAACGCTGCTAAAAACATAACCTTTA
1 TTTCCCACAAACGCCGCTAAAGACTTAACCTTTA
501184 AAAATACATA
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
42 1 0.01
43 79 0.75
44 26 0.25
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (42 bp):
TTTCCCACAAACGCCGCTAAAGACTTAACCTTTAGCGGCGCT
Found at i:501275 original size:13 final size:13
Alignment explanation
Indices: 501259--501285 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
501249 AATTTGAACT
501259 TTAAATATACATA
1 TTAAATATACATA
501272 TTAAATATACATA
1 TTAAATATACATA
501285 T
1 T
501286 GAGCAACAGA
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATATACATA
Found at i:506252 original size:16 final size:16
Alignment explanation
Indices: 506231--506276 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
506221 TATTGCTAAT
506231 GTATTAAATAATAAAA
1 GTATTAAATAATAAAA
* *
506247 GTATTATATAATATAA
1 GTATTAAATAATAAAA
506263 -TATTAAAATAATAA
1 GTATT-AAATAATAA
506277 TATAGTAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (16 bp):
GTATTAAATAATAAAA
Done.