Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold15
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: 4011073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11440 characters in sequence are not A, C, G, or T
File 25 of 25
Found at i:3955979 original size:22 final size:22
Alignment explanation
Indices: 3955913--3955986 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
3955903 CTTAAAAAAA
*
3955913 TTCTCCCCCTTAAACGATTATC
1 TTCTCCCCCTTAAACAATTATC
* * * *
3955935 -TC-CTCCTTTATAA-AA-AATA
1 TTCTCCCCCTTA-AACAATTATC
3955954 TTCTCCCCCTTAAACAATTATC
1 TTCTCCCCCTTAAACAATTATC
3955976 TTCTCCCCCTT
1 TTCTCCCCCTT
3955987 TTGTAAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
19 2 0.05
20 11 0.29
21 12 0.32
22 13 0.34
ACGTcount: A:0.26, C:0.35, G:0.01, T:0.38
Consensus pattern (22 bp):
TTCTCCCCCTTAAACAATTATC
Found at i:3963439 original size:13 final size:13
Alignment explanation
Indices: 3963421--3963451 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3963411 ACATTTCTTC
3963421 ATGTATCGATACA
1 ATGTATCGATACA
3963434 ATGTATCGATACA
1 ATGTATCGATACA
*
3963447 TTGTA
1 ATGTA
3963452 CCATATATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3963541 original size:19 final size:19
Alignment explanation
Indices: 3963496--3963568 Score: 110
Period size: 19 Copynumber: 3.7 Consensus size: 19
3963486 CTGCCAGTTT
**
3963496 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
3963517 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
3963536 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
3963555 CATGTATCGATACA
1 CATGTATCGATACA
3963569 TTGTATCGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 35 0.70
21 15 0.30
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:3963575 original size:13 final size:13
Alignment explanation
Indices: 3963557--3963581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3963547 ACAATGAACA
3963557 TGTATCGATACAT
1 TGTATCGATACAT
3963570 TGTATCGATACA
1 TGTATCGATACA
3963582 AAGCAGCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3963597 original size:33 final size:32
Alignment explanation
Indices: 3963538--3963602 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
3963528 ACAATGAACA
*
3963538 TGTATCGATACAATGAACATGTATCGATACAT
1 TGTATCGATACAAAGAACATGTATCGATACAT
*
3963570 TGTATCGATACAAAGCAGCATGTATCGATACAT
1 TGTATCGATACAAAG-AACATGTATCGATACAT
3963603 CTGGGTGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAT
Found at i:3965884 original size:20 final size:20
Alignment explanation
Indices: 3965808--3965883 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
3965798 AAGTACCCAG
* *
3965808 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTCATAA
*
3965828 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCATAA
* *
3965848 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCATAA
3965868 ATGTATCGATACATTC
1 ATGTATCGATACATTC
3965884 TATCCTTTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTCATAA
Found at i:3967987 original size:48 final size:48
Alignment explanation
Indices: 3967904--3968054 Score: 171
Period size: 48 Copynumber: 3.2 Consensus size: 48
3967894 CTCGTTTAAC
* * *
3967904 TCAAATTCAAATTTACTCTTGTTT-ATTTGTCTTGGCGTTAGGACCTGG
1 TCAAACTCAAATTTACTCTCGTTTGATTT-TATTGGCGTTAGGACCTGG
* *
3967952 TTAAACTCAAATTTACTCTCGTTTGATTTTATTGGCGTTAGGACCTAG
1 TCAAACTCAAATTTACTCTCGTTTGATTTTATTGGCGTTAGGACCTGG
** ** * * *
3968000 TCAAACTCTTA-CCACTCTCTTTTGATTGTATTGGCGTTAGGACTTGG
1 TCAAACTCAAATTTACTCTCGTTTGATTTTATTGGCGTTAGGACCTGG
3968047 TCAAACTC
1 TCAAACTC
3968055 TTTCCACTCT
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
47 38 0.43
48 46 0.52
49 4 0.05
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (48 bp):
TCAAACTCAAATTTACTCTCGTTTGATTTTATTGGCGTTAGGACCTGG
Found at i:3968035 original size:47 final size:47
Alignment explanation
Indices: 3967930--3968290 Score: 265
Period size: 47 Copynumber: 7.7 Consensus size: 47
3967920 TCTTGTTTAT
* * *
3967930 TTGTCTTGGCGTTAGGACCTGGTTAAACTCAAATTT--ACTCTCGTTTGA
1 TTGTATTGGCGTTAGGACCTGGTCAAACTC---TTTCCACTCTCTTTTGA
* * *
3967978 TTTTATTGGCGTTAGGACCTAGTCAAACTCTTACCACTCTCTTTTGA
1 TTGTATTGGCGTTAGGACCTGGTCAAACTCTTTCCACTCTCTTTTGA
*
3968025 TTGTATTGGCGTTAGGACTTGGTCAAACTCTTTCCACTCT-TGTTTGA
1 TTGTATTGGCGTTAGGACCTGGTCAAACTCTTTCCACTCTCT-TTTGA
* ** * * * *
3968072 CTACATTGGCATTAAGACCTGGTTAAACTCTTTCCATTCT-TGTTTGA
1 TTGTATTGGCGTTAGGACCTGGTCAAACTCTTTCCACTCTCT-TTTGA
* * * *
3968119 CTGCATTGGCGTTAGGACCTGGTC-AAC-CCTTCTCA-TCCTCATTTGA
1 TTGTATTGGCGTTAGGACCTGGTCAAACTCTTTC-CACT-CTCTTTTGA
* * *
3968165 TTATATTGGCGTTAGGACCTTGTCAAACTCTTTCCAC-CTTCATTTGA
1 TTGTATTGGCGTTAGGACCTGGTCAAACTCTTTCCACTC-TCTTTTGA
* ** * * * * * * *
3968212 CTACATTTGCATTGGGGCCTGGTCAAACTTTTTTCACCCT-TATTTGA
1 TTGTATTGGCGTTAGGACCTGGTCAAACTCTTTCCACTCTCT-TTTGA
* * *
3968259 CTGTATTAGCGTTA-GTCCTGGTCAAACTCTTT
1 TTGTATTGGCGTTAGGACCTGGTCAAACTCTTT
3968291 TCATCCTCAT
Statistics
Matches: 255, Mismatches: 46, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
45 7 0.03
46 50 0.20
47 167 0.65
48 31 0.12
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.40
Consensus pattern (47 bp):
TTGTATTGGCGTTAGGACCTGGTCAAACTCTTTCCACTCTCTTTTGA
Found at i:3968193 original size:140 final size:141
Alignment explanation
Indices: 3967982--3968301 Score: 391
Period size: 140 Copynumber: 2.3 Consensus size: 141
3967972 GTTTGATTTT
* * *
3967982 ATTGGCGTTAGGACCTAGTCAAACTCTTAC-CA-CTCTCTTTTGATTGTATTGGCGTTAGGACTT
1 ATTGGCGTTAGGACCTGGTCAAACTCTT-CTCATC-CTCATTTGATTATATTGGCGTTAGGACTT
* * *
3968045 GGTCAAACTCTTTCCACTCTT-GTTTGACTACATTGGCATTAAGACCTGGTTAAACTCTTTCCAT
64 GGTCAAACTCTTTCCAC-CTTCATTTGACTACATTGGCATTAAGACCTGGTCAAACTCTTTCCAC
* *
3968109 TCTTGTTTGACTGC
128 CCTTATTTGACTGC
*
3968123 ATTGGCGTTAGGACCTGGTC-AACCCTTCTCATCCTCATTTGATTATATTGGCGTTAGGACCTT-
1 ATTGGCGTTAGGACCTGGTCAAACTCTTCTCATCCTCATTTGATTATATTGGCGTTAGGA-CTTG
* ** * * *
3968186 GTCAAACTCTTTCCACCTTCATTTGACTACATTTGCATTGGGGCCTGGTCAAACTTTTTTCACCC
65 GTCAAACTCTTTCCACCTTCATTTGACTACATTGGCATTAAGACCTGGTCAAACTCTTTCCACCC
*
3968251 TTATTTGACTGT
130 TTATTTGACTGC
* * *
3968263 ATTAGCGTTA-GTCCTGGTCAAACTCTTTTCATCCTCATT
1 ATTGGCGTTAGGACCTGGTCAAACTCTTCTCATCCTCATT
3968302 CAACATGATG
Statistics
Matches: 154, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
139 12 0.08
140 119 0.77
141 23 0.15
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (141 bp):
ATTGGCGTTAGGACCTGGTCAAACTCTTCTCATCCTCATTTGATTATATTGGCGTTAGGACTTGG
TCAAACTCTTTCCACCTTCATTTGACTACATTGGCATTAAGACCTGGTCAAACTCTTTCCACCCT
TATTTGACTGC
Found at i:3968514 original size:85 final size:84
Alignment explanation
Indices: 3968399--3968718 Score: 308
Period size: 85 Copynumber: 3.8 Consensus size: 84
3968389 ATCCTCGGTT
*** * *
3968399 AACCCATTACCCTTATGGTGATAAAGT-AGCTCAGTCTCCAGTCAATCTTCATCTCCTTGTTTAC
1 AACCCATTACCCTTATGGTGA-CCTGTCAGCTCAGTCTCCGGTCAACCTTCATCTCCTTGTTTAC
* *
3968463 CCGTCAGTTTAGTCTCCTGTA
65 CCATC-GCTTAGTCTCCTGTA
* * *
3968484 AACCCATTACCCTTATGGTGACCTGTTAGCTCAGTCTCTGATCAACCTTCATCTCCTTGTTTACC
1 AACCCATTACCCTTATGGTGACCTGTCAGCTCAGTCTCCGGTCAACCTTCATCTCCTTGTTTACC
* * * *
3968549 TATCGGCTTAATCCCCAGTA
66 CATC-GCTTAGTCTCCTGTA
* * *
3968569 AACCCCTTACACC-TATGGTGACCTGTCAGCTTAGTCTCTGGTCAACCTTCATC-CCTTGTTTAC
1 AACCCATTAC-CCTTATGGTGACCTGTCAGCTCAGTCTCCGGTCAACCTTCATCTCCTTGTTTAC
** *
3968632 TTATCGCCTCAGT-TCCTAGTAA
65 CCATCG-CTTAGTCTCCT-GT-A
* * * * * *
3968654 AACCC-TTACCCTTTTAGTGACCTGTCAGCTTAGTCTCTGGTCAACCTCCATCTCATTGTTTACC
1 AACCCATTACCCTTATGGTGACCTGTCAGCTCAGTCTCCGGTCAACCTTCATCTCCTTGTTTACC
3968718 C
66 C
3968719 GTCGACCCAG
Statistics
Matches: 199, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
83 5 0.03
84 63 0.32
85 129 0.65
86 2 0.01
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (84 bp):
AACCCATTACCCTTATGGTGACCTGTCAGCTCAGTCTCCGGTCAACCTTCATCTCCTTGTTTACC
CATCGCTTAGTCTCCTGTA
Found at i:3968679 original size:84 final size:85
Alignment explanation
Indices: 3968483--3968717 Score: 312
Period size: 84 Copynumber: 2.8 Consensus size: 85
3968473 AGTCTCCTGT
* * *
3968483 AAACCCATTACCCTTATGGTGACCTGTTAGCTCAGTCTCTGATCAACCTTCATCTCCTTGTTTAC
1 AAACCC-TTACCCTTATGGTGACCTGTCAGCTTAGTCTCTGGTCAACCTTCATCTCCTTGTTTAC
* *
3968548 CTATCGGCTTAATCCCCAGTA
65 CTATCGCCTCAATCCCCAGTA
*
3968569 AACCCCTTACACC-TATGGTGACCTGTCAGCTTAGTCTCTGGTCAACCTTCATC-CCTTGTTTAC
1 AAACCCTTAC-CCTTATGGTGACCTGTCAGCTTAGTCTCTGGTCAACCTTCATCTCCTTGTTTAC
* * * *
3968632 TTATCGCCTCAGTTCCTAGTA
65 CTATCGCCTCAATCCCCAGTA
* * * *
3968653 AAACCCTTACCCTTTTAGTGACCTGTCAGCTTAGTCTCTGGTCAACCTCCATCTCATTGTTTACC
1 AAACCCTTACCCTTATGGTGACCTGTCAGCTTAGTCTCTGGTCAACCTTCATCTCCTTGTTTACC
3968718 CGTCGACCCA
Statistics
Matches: 130, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
83 2 0.02
84 71 0.55
85 50 0.38
86 7 0.05
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.34
Consensus pattern (85 bp):
AAACCCTTACCCTTATGGTGACCTGTCAGCTTAGTCTCTGGTCAACCTTCATCTCCTTGTTTACC
TATCGCCTCAATCCCCAGTA
Found at i:3971656 original size:15 final size:17
Alignment explanation
Indices: 3971636--3971668 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3971626 AATTGAATCA
3971636 AATTTGA-AA-ATAAAT
1 AATTTGATAATATAAAT
3971651 AATTTGATAATATAAAT
1 AATTTGATAATATAAAT
3971668 A
1 A
3971669 TTAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
AATTTGATAATATAAAT
Found at i:3974559 original size:2 final size:2
Alignment explanation
Indices: 3974552--3974580 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3974542 ATAGACCAAA
3974552 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3974581 ATGTCAATAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3976343 original size:19 final size:19
Alignment explanation
Indices: 3976307--3976345 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3976297 GTGGTTTATA
*
3976307 TTTATAATATAATGTATCT
1 TTTATAATATAATATATCT
3976326 TTTAT-ATATATATATATCT
1 TTTATAATATA-ATATATCT
3976345 T
1 T
3976346 GTTCCTCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTATAATATAATATATCT
Found at i:3980225 original size:20 final size:20
Alignment explanation
Indices: 3980193--3980236 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3980183 GTAGTTTATG
*
3980193 ATTTTTTTTAATAT-TTAAT
1 ATTTTTTTAAATATATTAAT
*
3980212 ATTTTTTTAAAATATATTATT
1 ATTTTTTT-AAATATATTAAT
3980233 ATTT
1 ATTT
3980237 CGTATGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTTTTAAATATATTAAT
Found at i:3988480 original size:13 final size:13
Alignment explanation
Indices: 3988462--3988487 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3988452 CAATTTTTGG
3988462 TGTATCGATACAT
1 TGTATCGATACAT
3988475 TGTATCGATACAT
1 TGTATCGATACAT
3988488 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3988499 original size:32 final size:33
Alignment explanation
Indices: 3988442--3988505 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3988432 TACAAGCCAA
**
3988442 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
3988475 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
3988506 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:3988512 original size:19 final size:18
Alignment explanation
Indices: 3988442--3988512 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
3988432 TACAAGCCAA
3988442 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
3988462 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
3988475 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
3988494 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
3988513 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:3991081 original size:13 final size:13
Alignment explanation
Indices: 3991062--3991101 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
3991052 TATAATCCCC
3991062 ATGTATCGATACA
1 ATGTATCGATACA
*
3991075 GTGTATCGATACA
1 ATGTATCGATACA
3991088 ATGTATCGATACA
1 ATGTATCGATACA
3991101 A
1 A
3991102 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3991279 original size:13 final size:14
Alignment explanation
Indices: 3991261--3991300 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
3991251 AATAAAAACA
3991261 CAAAATCATTCA-T
1 CAAAATCATTCATT
3991274 CAAAATCATTCATTT
1 CAAAATCATTCA-TT
*
3991289 CAACATCATTCA
1 CAAAATCATTCA
3991301 ACATAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
15 12 0.50
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (14 bp):
CAAAATCATTCATT
Found at i:3997817 original size:79 final size:79
Alignment explanation
Indices: 3997674--3997849 Score: 246
Period size: 79 Copynumber: 2.2 Consensus size: 79
3997664 TAACATTTTG
* *
3997674 AAATAAAAACGAGGTTGGAGTATCCCCTTGAAAATAACAAGGTTGGAGTATCCCCGAGAAGAAAA
1 AAATAAAAACGAGGTTGGAGTATCCCCTAGAAAATAACAAGATTGGAGTATCCCCGAGAAGAAAA
3997739 ATTTAATATTTTAA
66 ATTTAATATTTTAA
* * * * *
3997753 AAATGAAAATGAGGTTGGAGTATTCCCTCAG-AAATAACGAGATTGGAGTATCCCCGAGATGAAA
1 AAATAAAAACGAGGTTGGAGTATCCCCT-AGAAAATAACAAGATTGGAGTATCCCCGAGAAGAAA
*
3997817 AATTTAATATTTTGA
65 AATTTAATATTTTAA
* *
3997832 AAATAACAACGGGGTTGG
1 AAATAAAAACGAGGTTGG
3997850 CGTAATCTCG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 83 0.99
80 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (79 bp):
AAATAAAAACGAGGTTGGAGTATCCCCTAGAAAATAACAAGATTGGAGTATCCCCGAGAAGAAAA
ATTTAATATTTTAA
Found at i:3999712 original size:12 final size:13
Alignment explanation
Indices: 3999682--3999722 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
3999672 CATGTGGCAA
*
3999682 ATTTATTTTATTTT
1 ATTT-TTTTAATTT
3999696 ATATTTTTTAATTT
1 AT-TTTTTTAATTT
3999710 ATTTTTTTAATTT
1 ATTTTTTTAATTT
3999723 TAAAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 11 0.44
14 12 0.48
15 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTTTTAATTT
Found at i:3999722 original size:28 final size:28
Alignment explanation
Indices: 3999682--3999754 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
3999672 CATGTGGCAA
3999682 ATTTATTTT-ATTTTATATTTTTTAATTT
1 ATTT-TTTTAATTTTATATTTTTTAATTT
* * **
3999710 ATTTTTTTAATTTTAAAATTTTTGGTTT
1 ATTTTTTTAATTTTATATTTTTTAATTT
3999738 A--TTTTTAATTTTATATT
1 ATTTTTTTAATTTTATATT
3999755 GTAAATAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 14 0.37
27 4 0.11
28 20 0.53
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (28 bp):
ATTTTTTTAATTTTATATTTTTTAATTT
Found at i:4000061 original size:143 final size:144
Alignment explanation
Indices: 3999868--4000201 Score: 351
Period size: 144 Copynumber: 2.3 Consensus size: 144
3999858 GGTTTTTTAG
* * * * *
3999868 TTTTTATTTTA-TTTTTAATTGATGTATTT-AAAGAGTTGATTTGCTTAGTAACTCACTAGTCAA
1 TTTTTATTTTATTTTTTAAATAATATATTTAAAAGAGTTGATTTGATTAGTAACTCACGAGTCAA
* * * * ***
3999931 TTTAGAATTCGCATTCGA-CT-TTCTTAATA-AATAAAAAAATTATTTTATTAATTATTTTTAGT
66 TTTAGAATTCACATTCGACCTATTC--AAAACAATAAAAAAATTAATTTATTAATAACACTTAGT
3999993 TTTTTTAGATTTA-AGA
129 TTTTTTAGATTTATA-A
* *
4000009 TTTTTATTTTATTTTTTAAATAATATATTTAAAATAGTTGATTT-ATATAGTAACTCACGAGTCG
1 TTTTTATTTTATTTTTTAAATAATATATTTAAAAGAGTTGATTTGAT-TAGTAACTCACGAGTCA
* * *
4000073 ATTTAGAATTTATATTTGACCTATTCAAAACAATAAAAAAATTAATTTATTAATAACACTTAGTT
65 ATTTAGAATTCACATTCGACCTATTCAAAACAATAAAAAAATTAATTTATTAATAACACTTAGTT
*
4000138 TTTTTAGATTTATAT
130 TTTTTAGATTTATAA
* *
4000153 TTTTTATTTTTATTTGATTTTTAAATTATATATTTAAAAGATTTG-TTTG
1 TTTTTA-TTTTA--T--TTTTTAAATAATATATTTAAAAGAGTTGATTTG
4000202 GTGTGTGACC
Statistics
Matches: 159, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
141 11 0.07
142 16 0.10
143 45 0.28
144 49 0.31
145 9 0.06
147 1 0.01
148 3 0.02
149 25 0.16
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (144 bp):
TTTTTATTTTATTTTTTAAATAATATATTTAAAAGAGTTGATTTGATTAGTAACTCACGAGTCAA
TTTAGAATTCACATTCGACCTATTCAAAACAATAAAAAAATTAATTTATTAATAACACTTAGTTT
TTTTAGATTTATAA
Found at i:4001122 original size:3 final size:3
Alignment explanation
Indices: 4001114--4001141 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4001104 GCATTTGAAC
4001114 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4001142 CTAGTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4001839 original size:3 final size:3
Alignment explanation
Indices: 4001833--4001867 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4001823 CATCATCATC
*
4001833 ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4001868 CTTCTTCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4001873 original size:3 final size:3
Alignment explanation
Indices: 4001867--4001899 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
4001857 ATTGTTATTA
*
4001867 TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
4001900 AACAATGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:4002395 original size:19 final size:17
Alignment explanation
Indices: 4002371--4002405 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
4002361 CATGTTGGAG
4002371 TTTTCTTTGTTTCTTTCCT
1 TTTTCTTT-TTT-TTTCCT
4002390 TTTTCTTTTTTTTTCC
1 TTTTCTTTTTTTTTCC
4002406 CCCCTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTCTTTTTTTTTCCT
Found at i:4007109 original size:2 final size:2
Alignment explanation
Indices: 4007102--4007127 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4007092 TTTAAATCTA
4007102 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
4007128 TAAACTAGCT
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
Done.