Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold403
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: 416698
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:395397 original size:31 final size:35
Alignment explanation
Indices: 395359--395435 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 35
395349 AACAAATAAA
*
395359 AATTATATTAATAAAAT-CATT-AATTATTAAA-C
1 AATTATATTAATAAAATAAATTAAATTATTAAATC
* *
395391 AA-TATATT-ATAAATTAAATTAAATTATTAAATT
1 AATTATATTAATAAAATAAATTAAATTATTAAATC
395424 AATTATATTAAT
1 AATTATATTAAT
395436 TACTTATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 6 0.16
31 9 0.24
32 12 0.32
33 2 0.05
34 6 0.16
35 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (35 bp):
AATTATATTAATAAAATAAATTAAATTATTAAATC
Found at i:395433 original size:9 final size:9
Alignment explanation
Indices: 395400--395437 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
395390 CAATATATTA
395400 TAAATTAAAT
1 TAAATT-AAT
395410 TAAATT-AT
1 TAAATTAAT
395418 TAAATTAAT
1 TAAATTAAT
*
395427 TATATTAAT
1 TAAATTAAT
395436 TA
1 TA
395438 CTTATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 8 0.31
9 12 0.46
10 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TAAATTAAT
Found at i:395892 original size:31 final size:30
Alignment explanation
Indices: 395857--395929 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
395847 TTTCTTTCTC
*
395857 AAATAGTATTTCTGATCGAAAATTTTATCAA
1 AAATAGTATTTC-GATCGAAAATTTCATCAA
* * *
395888 AAATAATAATTGCGATGGAAAATTTCATCAA
1 AAATAGT-ATTTCGATCGAAAATTTCATCAA
395919 AAATAGTATTT
1 AAATAGTATTT
395930 TCAAAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
30 3 0.09
31 28 0.80
32 4 0.11
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (30 bp):
AAATAGTATTTCGATCGAAAATTTCATCAA
Found at i:396567 original size:33 final size:31
Alignment explanation
Indices: 396525--396586 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 31
396515 ATCACAAAAA
*
396525 ATATTATATAGATCAATTTCCGACCATAATTGT
1 ATATTATATAGAGC-ATTTCC-ACCATAATTGT
*
396558 ATATTATATAGAGCATTTCCACCGTAATT
1 ATATTATATAGAGCATTTCCACCATAATT
396587 AAACAGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 8 0.30
32 6 0.22
33 13 0.48
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (31 bp):
ATATTATATAGAGCATTTCCACCATAATTGT
Found at i:396601 original size:3 final size:3
Alignment explanation
Indices: 396593--396618 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
396583 AATTAAACAG
396593 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
396619 TTTTATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:396739 original size:2 final size:2
Alignment explanation
Indices: 396693--396723 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
396683 ATTAGTTAAG
396693 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 A
396724 AATGAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:397285 original size:50 final size:50
Alignment explanation
Indices: 397201--397435 Score: 373
Period size: 50 Copynumber: 4.7 Consensus size: 50
397191 TACTTAGAGG
*
397201 CAACAATTATGGCCACCTC-CTTTATTGTCAAAGGTTGGTGAAGAATCGT
1 CAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGT
* * * *
397250 CAACAATTATGGCAACCCCCCTCTATTGTCAAAGGTTGGTGAAGAATCAT
1 CAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGT
* *
397300 CAACAATTATGGTCACCTCTCTCTATTGTTAAAGGTTGGTGAAGAATCGT
1 CAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGT
* *
397350 CAACAATTATAGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATCGT
1 CAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGT
*
397400 CAATAATTATGGCCACCTCTCTCTATTGTCAAAGGT
1 CAACAATTATGGCCACCTCTCTCTATTGTCAAAGGT
397436 ACTTTCCACC
Statistics
Matches: 169, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
49 17 0.10
50 152 0.90
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (50 bp):
CAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGT
Found at i:401844 original size:50 final size:49
Alignment explanation
Indices: 401785--401970 Score: 205
Period size: 50 Copynumber: 3.7 Consensus size: 49
401775 TATACTTAGA
*
401785 GTCAACAATTATGACCACCTCCTTCTATTGTCAAAGATTAGTGAAGAACC
1 GTCAACAATTATGACCACCTCCTTCTATTGTCAAAGATT-GTGAAGAATC
* * * *
401835 GTCAACAATTATGGCTACCTCCCTT-TATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGACCACCT-CCTTCTATTGTCAAAGATT-GTGAAGAATC
* *
401885 GTCAACAATTATGGCCACCTCCTTTTATTGTCAAA-AGTTGATGAAGAATC
1 GTCAACAATTATGACCACCTCCTTCTATTGTCAAAGA-TTG-TGAAGAATC
* ** * *
401935 GTCAACAATTATTATTACCTCTTTCTATTGTAAAAG
1 GTCAACAATTATGACCACCTCCTTCTATTGTCAAAG
401971 GTACTTTCCA
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
49 5 0.04
50 106 0.92
51 4 0.03
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (49 bp):
GTCAACAATTATGACCACCTCCTTCTATTGTCAAAGATTGTGAAGAATC
Found at i:401954 original size:100 final size:100
Alignment explanation
Indices: 401785--401972 Score: 256
Period size: 100 Copynumber: 1.9 Consensus size: 100
401775 TATACTTAGA
*
401785 GTCAACAATTATGACCACCTCCTTCTATTGTCAAAGATTAGTGAAGAACCGTCAACAATTATGGC
1 GTCAACAATTATGACCACCTCCTTCTATTGTCAAAGATTAGTGAAGAACCGTCAACAATTATGAC
*
401850 TACCTCCCTT-TATTGTCAAAGGTTGGTGAAGAATT
66 TACCT-CCTTCTATTGTAAAAGGTTGGTGAAGAATT
* * * *
401885 GTCAACAATTATGGCCACCTCCTTTTATTGTCAAA-AGTT-GATGAAGAATCGTCAACAATTATT
1 GTCAACAATTATGACCACCTCCTTCTATTGTCAAAGA-TTAG-TGAAGAACCGTCAACAATTATG
* *
401948 ATTACCTCTTTCTATTGTAAAAGGT
64 ACTACCTCCTTCTATTGTAAAAGGT
401973 ACTTTCCACC
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
99 5 0.06
100 72 0.94
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (100 bp):
GTCAACAATTATGACCACCTCCTTCTATTGTCAAAGATTAGTGAAGAACCGTCAACAATTATGAC
TACCTCCTTCTATTGTAAAAGGTTGGTGAAGAATT
Found at i:402131 original size:3 final size:3
Alignment explanation
Indices: 402080--402113 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
402070 TATTAAAAAT
402080 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
402114 CTTACGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:402544 original size:3 final size:3
Alignment explanation
Indices: 402531--402560 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
402521 TGAAGAAAAC
*
402531 AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
402561 GCAAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:402712 original size:2 final size:2
Alignment explanation
Indices: 402705--402740 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
402695 CTGTAAAGAA
402705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
402741 GTTGGTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:402999 original size:2 final size:2
Alignment explanation
Indices: 402994--403034 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
402984 TGGTGAAGGA
402994 AT AT 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 AT AT A
403035 GTGAAGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:403331 original size:20 final size:20
Alignment explanation
Indices: 403295--403335 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
403285 GATTACCATG
403295 ATTTCTAAATATAAATTATAT
1 ATTTCTAAATATAAATT-TAT
*
403316 ATTTCT-AATATTAATTTAT
1 ATTTCTAAATATAAATTTAT
403335 A
1 A
403336 GTAAAACGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTCTAAATATAAATTTAT
Found at i:405465 original size:33 final size:34
Alignment explanation
Indices: 405429--405495 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
405419 CTTTTGTCAA
405429 AAAAAAG-TTTATTTTTGAT-AAAAT-TTTTGTTG
1 AAAAAAGATTTATTTTTG-TCAAAATATTTTGTTG
405461 AAAAAAGATTTATTTTTGTCCAAAATATTTTGTTG
1 AAAAAAGATTTATTTTTGT-CAAAATATTTTGTTG
405496 GAGTACTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 8 0.26
33 10 0.32
34 5 0.16
35 8 0.26
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48
Consensus pattern (34 bp):
AAAAAAGATTTATTTTTGTCAAAATATTTTGTTG
Found at i:405466 original size:15 final size:17
Alignment explanation
Indices: 405429--405474 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
405419 CTTTTGTCAA
*
405429 AAAAAAGTTTATTTTTG
1 AAAAAAGTTTATTGTTG
*
405446 ATAAAA-TTT-TTGTTG
1 AAAAAAGTTTATTGTTG
405461 AAAAAAGATTTATT
1 AAAAAAG-TTTATT
405475 TTTGTCCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
15 10 0.43
16 3 0.13
17 8 0.35
18 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
AAAAAAGTTTATTGTTG
Found at i:405857 original size:21 final size:21
Alignment explanation
Indices: 405814--405858 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
405804 TTATTGAGTT
*
405814 AAAATTAAATTAAATTAAATA
1 AAAATTAAAATAAATTAAATA
*
405835 AAAATATAAAATAAA-TAAGTA
1 AAAAT-TAAAATAAATTAAATA
405856 AAA
1 AAA
405859 TAATATTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATTAAAATAAATTAAATA
Found at i:406157 original size:11 final size:11
Alignment explanation
Indices: 406141--406165 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
406131 GCGCCATAAG
406141 TAGCAAGGTAT
1 TAGCAAGGTAT
406152 TAGCAAGGTAT
1 TAGCAAGGTAT
406163 TAG
1 TAG
406166 TATTCTGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCAAGGTAT
Found at i:406726 original size:32 final size:32
Alignment explanation
Indices: 406690--406793 Score: 118
Period size: 32 Copynumber: 3.2 Consensus size: 32
406680 ATCGAACTTG
* *
406690 AAATGACTCGAACCCGAAATGACTTGAATCCA
1 AAATGACCCGAACCCGAAATGACTCGAATCCA
* * *
406722 AAATGCCCCGAACTCAAAATGACTCGAATCCA
1 AAATGACCCGAACCCGAAATGACTCGAATCCA
* * * * *
406754 AAATGACCCGAATCTGAAATGACCCGAACCCG
1 AAATGACCCGAACCCGAAATGACTCGAATCCA
406786 AAATGACC
1 AAATGACC
406794 TGAATAATTA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.15
Consensus pattern (32 bp):
AAATGACCCGAACCCGAAATGACTCGAATCCA
Found at i:406742 original size:48 final size:48
Alignment explanation
Indices: 406690--406792 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
406680 ATCGAACTTG
* ** * *
406690 AAATGACTCGAACCCGAAATGACTTGAATCCAAAATGCCCCGAACTCA
1 AAATGACTCGAACCCAAAATGACCCGAATCCAAAATGACCCGAACCCA
* ** *
406738 AAATGACTCGAATCCAAAATGACCCGAATCTGAAATGACCCGAACCCG
1 AAATGACTCGAACCCAAAATGACCCGAATCCAAAATGACCCGAACCCA
406786 AAATGAC
1 AAATGAC
406793 CTGAATAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.41, C:0.28, G:0.16, T:0.16
Consensus pattern (48 bp):
AAATGACTCGAACCCAAAATGACCCGAATCCAAAATGACCCGAACCCA
Found at i:406793 original size:16 final size:16
Alignment explanation
Indices: 406689--406793 Score: 93
Period size: 16 Copynumber: 6.6 Consensus size: 16
406679 GATCGAACTT
*
406689 GAAATGACTCGAACCC
1 GAAATGACCCGAACCC
** *
406705 GAAATGACTTGAATCC
1 GAAATGACCCGAACCC
* * *
406721 AAAATGCCCCGAACTC
1 GAAATGACCCGAACCC
* * *
406737 AAAATGACTCGAATCC
1 GAAATGACCCGAACCC
* * *
406753 AAAATGACCCGAATCT
1 GAAATGACCCGAACCC
406769 GAAATGACCCGAACCC
1 GAAATGACCCGAACCC
406785 GAAATGACC
1 GAAATGACC
406794 TGAATAATTA
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 72 1.00
ACGTcount: A:0.40, C:0.29, G:0.16, T:0.15
Consensus pattern (16 bp):
GAAATGACCCGAACCC
Found at i:408279 original size:22 final size:19
Alignment explanation
Indices: 408250--408289 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 19
408240 ATTTTACATA
408250 ATTAAATTAAAATAAAAAATT
1 ATTAAATT--AATAAAAAATT
408271 ATTATAATTAATAAAAAAT
1 ATTA-AATTAATAAAAAAT
408290 ATAATTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAATTAATAAAAAATT
Found at i:408489 original size:22 final size:21
Alignment explanation
Indices: 408422--408490 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 21
408412 ACAAATAAAA
408422 ATTATATT-AACAAAATCATTA-
1 ATTA-ATTAAACAAAAT-ATTAT
* *
408443 ATT-ACTAAACAAGATATTAT
1 ATTAATTAAACAAAATATTAT
408463 A--AATTAAATCAAAATATTAT
1 ATTAATTAAA-CAAAATATTAT
408483 ATTAATTA
1 ATTAATTA
408491 TATTAATTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
19 11 0.29
20 19 0.50
21 3 0.08
22 5 0.13
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (21 bp):
ATTAATTAAACAAAATATTAT
Found at i:408957 original size:31 final size:31
Alignment explanation
Indices: 408922--408996 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
408912 TTTCTTTCTC
* **
408922 AAATAGTATTTTTGATCGAAAATTTTATCAA
1 AAATAGTATTTTCGATCGAAAATTCCATCAA
* * * *
408953 AAATAATAATTGCGATGGAAAATTCCATCAA
1 AAATAGTATTTTCGATCGAAAATTCCATCAA
*
408984 AAACAGTATTTTC
1 AAATAGTATTTTC
408997 AAGAAATTTC
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (31 bp):
AAATAGTATTTTCGATCGAAAATTCCATCAA
Found at i:409619 original size:3 final size:3
Alignment explanation
Indices: 409611--409643 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
409601 AATTAAACAG
409611 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
409644 ATATTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:409772 original size:2 final size:2
Alignment explanation
Indices: 409720--409756 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
409710 ATTAGTTAAG
409720 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
409757 AATGAAACTA
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:411946 original size:40 final size:38
Alignment explanation
Indices: 411901--412094 Score: 108
Period size: 41 Copynumber: 5.1 Consensus size: 38
411891 ATTAAAAAAT
411901 AATATTTAATTAACTTTTAAAAAATACATTAATAAATTAA
1 AATATTTAATTAACTTTTAAAAAA-A-ATTAATAAATTAA
**
411941 AATA-TTAATTATTTTTTAAAATAAAA--AATAAATTAA
1 AATATTTAATTAACTTTTAAAA-AAAATTAATAAATTAA
* *
411977 AAAACGTTTATTATTATTA-TTTT-AATAAAATTAA-AAATT--
1 AATA--TTTA--ATTA--ACTTTTAAAAAAAATTAATAAATTAA
412016 -ATATTTAATTAAC-TTTAAAAAATTTACATTAATAAATTAA
1 AATATTTAATTAACTTTTAAAAAA---A-ATTAATAAATTAA
**
412056 AATA-TTAATTATTTTTTAAAATAAAA--AATTAAATTAA
1 AATATTTAATTAACTTTTAAAA-AAAATTAA-TAAATTAA
412093 AA
1 AA
412095 AGCATTTATT
Statistics
Matches: 122, Mismatches: 9, Indels: 49
0.68 0.05 0.27
Matches are distributed among these distances:
32 4 0.03
33 4 0.03
34 4 0.03
36 20 0.16
37 15 0.12
38 9 0.07
39 20 0.16
40 17 0.14
41 21 0.17
42 8 0.07
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (38 bp):
AATATTTAATTAACTTTTAAAAAAAATTAATAAATTAA
Found at i:412016 original size:24 final size:24
Alignment explanation
Indices: 411989--412086 Score: 71
Period size: 23 Copynumber: 4.2 Consensus size: 24
411979 AACGTTTATT
411989 ATTATTATTTTAATAAAATTAAAA
1 ATTATTATTTTAATAAAATTAAAA
**
412013 ATTA-TA-TTTAATTAACTTTAAAA
1 ATTATTATTTTAA-TAAAATTAAAA
* **
412036 AAT-TTACATTAAT-AAATTAAAA
1 ATTATTATTTTAATAAAATTAAAA
* *
412058 TATTAATTATTTT-TTAAAATAAAAA
1 -ATT-ATTATTTTAATAAAATTAAAA
412083 ATTA
1 ATTA
412087 AATTAAAAAG
Statistics
Matches: 56, Mismatches: 11, Indels: 15
0.68 0.13 0.18
Matches are distributed among these distances:
22 12 0.21
23 19 0.34
24 12 0.21
25 13 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTATTATTTTAATAAAATTAAAA
Found at i:412068 original size:115 final size:115
Alignment explanation
Indices: 411890--412126 Score: 397
Period size: 115 Copynumber: 2.1 Consensus size: 115
411880 TATTATTTTT
411890 AATTAAAAAATAATATTTAATTAACTTTTAAAAAATACATTAATAAATTAAAATATTAATTATTT
1 AATT-AAAAATAATATTTAATTAACTTTTAAAAAATACATTAATAAATTAAAATATTAATTATTT
*
411955 TTTAAAATAAAAAA-TAAATTAAAAAACGTTTATTATTATTATTTTAATAA
65 TTTAAAATAAAAAATTAAATTAAAAAACATTTATTATTATTATTTTAATAA
*
412005 AATTAAAAATTATATTTAATTAAC-TTTAAAAAATTTACATTAATAAATTAAAATATTAATTATT
1 AATTAAAAATAATATTTAATTAACTTTTAAAAAA--TACATTAATAAATTAAAATATTAATTATT
* *
412069 TTTTAAAATAAAAAATTAAATTAAAAAGCATTTATTATTATTTTTTTAATAA
64 TTTTAAAATAAAAAATTAAATTAAAAAACATTTATTATTATTATTTTAATAA
412121 AATTAA
1 AATTAA
412127 TTAAATTTAA
Statistics
Matches: 115, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
113 9 0.08
114 19 0.17
115 48 0.42
116 39 0.34
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.43
Consensus pattern (115 bp):
AATTAAAAATAATATTTAATTAACTTTTAAAAAATACATTAATAAATTAAAATATTAATTATTTT
TTAAAATAAAAAATTAAATTAAAAAACATTTATTATTATTATTTTAATAA
Found at i:412144 original size:42 final size:42
Alignment explanation
Indices: 412058--412144 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 42
412048 TAAATTAAAA
412058 TATTAATTATTTTTTAAAATAAAAAATTAAATTAAAAAGCATT
1 TATTAATTATTTTTTAAAATAAAAAATTAAATTAAAAA-CATT
*
412101 TATT-ATTATTTTTT-TAATAAAATTAATTAAATTTAAAAA-ATT
1 TATTAATTATTTTTTAAAATAAAA--AATTAAA-TTAAAAACATT
412143 TA
1 TA
412145 ATAAATAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
41 7 0.17
42 15 0.38
43 11 0.28
44 7 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (42 bp):
TATTAATTATTTTTTAAAATAAAAAATTAAATTAAAAACATT
Found at i:412145 original size:19 final size:18
Alignment explanation
Indices: 412113--412150 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
412103 TTATTATTTT
412113 TTTAATAAAATTAATTAAA
1 TTTAATAAAATTAA-TAAA
412132 TTTAA-AAAATTTAATAAA
1 TTTAATAAAA-TTAATAAA
412150 T
1 T
412151 AATATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTAATAAAATTAATAAA
Found at i:412181 original size:115 final size:113
Alignment explanation
Indices: 411873--412161 Score: 338
Period size: 115 Copynumber: 2.5 Consensus size: 113
411863 AATAATAATG
* * * *
411873 TATTGATTATTATTTTTAATTAAA--AAA-TAATATTTAATTAACTTTTAAAAA-ATACATTAAT
1 TATT-ATTATTA-TTTTAATAAAATTAAATTAA-ATTTAATAAAATTTAAAAAATATACATTAAT
* *
411934 AAATTAAAATATTAATTATTTTTTAAAATAAAAAATAAATTAAAAAACGTT
63 AAATTAAAATATAAATTATTTTTTAAAATAAAAAATAAATTAAAAAACATT
* * * *
411985 TATTATTATTATTTTAATAAAATTAAAAATTATATTTAATTAACTTTAAAAAATTTACATTAATA
1 TATTATTATTATTTTAATAAAATT--AAATTAAATTTAATAAAATTTAAAAAATATACATTAATA
* *
412050 AATTAAAATATTAATTATTTTTTAAAATAAAAAATTAAATTAAAAAGCATT
64 AATTAAAATATAAATTATTTTTTAAAATAAAAAA-TAAATTAAAAAACATT
* * *
412101 TATTATTATTTTTTTAATAAAATT-AATTAAATTTAA-AAAATTTAATAAATAATATATTAAT
1 TATTATTATTATTTTAATAAAATTAAATTAAATTTAATAAAATTTAAAAAAT-ATACATTAAT
412162 TATTATTTTT
Statistics
Matches: 156, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
110 10 0.06
111 7 0.04
112 15 0.10
113 19 0.12
114 22 0.14
115 46 0.29
116 37 0.24
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (113 bp):
TATTATTATTATTTTAATAAAATTAAATTAAATTTAATAAAATTTAAAAAATATACATTAATAAA
TTAAAATATAAATTATTTTTTAAAATAAAAAATAAATTAAAAAACATT
Found at i:412210 original size:31 final size:32
Alignment explanation
Indices: 412116--412213 Score: 101
Period size: 34 Copynumber: 2.9 Consensus size: 32
412106 TTATTTTTTT
*
412116 AATAAAATTAATTAAA-TTTAAAAAATTTAATA
1 AATAATATTAATTAAATTTTAAAAAA-TTAATA
* *
412148 AATAATATATTAATTATTATTTTTTATAAAATTAA-A
1 AAT-A-ATATTAATTA--A-ATTTTAAAAAATTAATA
412184 AATAATATTAATTAAATTTTAAAAAATTAA
1 AATAATATTAATTAAATTTTAAAAAATTAA
412214 GCTATGATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
31 13 0.24
32 4 0.07
33 1 0.02
34 19 0.35
35 1 0.02
36 5 0.09
37 4 0.07
38 8 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AATAATATTAATTAAATTTTAAAAAATTAATA
Found at i:412907 original size:20 final size:20
Alignment explanation
Indices: 412884--412998 Score: 140
Period size: 20 Copynumber: 5.8 Consensus size: 20
412874 AAGTACCTAG
412884 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
412904 ATGTATCGATATATATATGA
1 ATGTATCGATACATTTTTCA
412924 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
412944 ATGTATCGATATATATATGA
1 ATGTATCGATACATTTTTCA
*
412964 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
412984 ATGTATCAATACATT
1 ATGTATCGATACATT
412999 CTGTCTTTTT
Statistics
Matches: 77, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:412939 original size:40 final size:40
Alignment explanation
Indices: 412884--412990 Score: 205
Period size: 40 Copynumber: 2.7 Consensus size: 40
412874 AAGTACCTAG
412884 ATGTATCGATACATTTTTCAATGTATCGATATATATATGA
1 ATGTATCGATACATTTTTCAATGTATCGATATATATATGA
412924 ATGTATCGATACATTTTTCAATGTATCGATATATATATGA
1 ATGTATCGATACATTTTTCAATGTATCGATATATATATGA
*
412964 ATGTATCGATACATTCTTCAATGTATC
1 ATGTATCGATACATTTTTCAATGTATC
412991 AATACATTCT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (40 bp):
ATGTATCGATACATTTTTCAATGTATCGATATATATATGA
Done.