Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014882.1 Kokia drynarioides strain JFW-HI SEQ_129925, 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: 114618
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 187 characters in sequence are not A, C, G, or T
Found at i:3928 original size:2 final size:2
Alignment explanation
Indices: 3921--3950 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3911 TCACACCCAC
*
3921 AG AG AG AG AG AG AG AG TG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3951 GGGGGAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Found at i:6976 original size:277 final size:277
Alignment explanation
Indices: 6423--6947 Score: 633
Period size: 277 Copynumber: 1.9 Consensus size: 277
6413 AAATAAAAGG
* * * *
6423 ATTAAATAATTATTTGGGGCCTGAATTTAGTAACTATTTACATATTGGGACTTGAACTGTTTTAG
1 ATTAAATAATTATTTGGGACCTGAACTTAGTAACTATTCACATATTGGGACTTCAACTGTTTTAG
* * *
6488 TCCAAGTTAAAACATGAATTTGATAATTATTCTCATGTAGGGGTTTGAATTTTTTTTTAAGTTAA
66 TCCAAGTTAAAACATGAACTTGATAATTATTCTCATGTAGAGGTTTGAATTTTTTTTAAAGTTAA
*
6553 CCCCTAAACTTGAGAACTGTTCCTGTATTGATATTTGAACTTGATAAATTTTAGGGTTTTTAAAA
131 CCCCTAAACTTGAGAACTGTTCCTATATTGA-ATTTGAACTTGATAAATTTTAGGGTTTTTAAAA
* * *
6618 AAAAATACTAAAGACTAACTTGAAAAAGTAAAAGTTAAATTCCTAATATAAAAATAATTGCCAAG
195 AAAAATACTAAAGACTAACTTGAAAAAGTAAAAGTCAAAGTCCTAATATAAAAACAATTGCCAAG
6683 TTACCGAAATAAAAAAAT
260 TTACCGAAATAAAAAAAT
* * * * *
6701 ATTAAATAATTATTTGGGACTTGAACTTGGTAACTATTCACA-CTTGGGATTTCAACTTTTTTAG
1 ATTAAATAATTATTTGGGACCTGAACTTAGTAACTATTCACATATTGGGACTTCAACTGTTTTAG
* * * *
6765 TCTAAGTTAAAGCATGAACTTGATGATTATTCTCATATTA-AGGTTTG-ATTTTTTTTAAAGTTA
66 TCCAAGTTAAAACATGAACTTGATAATTATTCTCAT-GTAGAGGTTTGAATTTTTTTTAAAGTTA
** * * * * *
6828 GTCCCTAAACTTGA-ACATTGTT-TTCATATTG-A-TTGAAGTTGGTAAATTTTAGGG-TTTT-C
130 ACCCCTAAACTTGAGA-ACTGTTCCT-ATATTGAATTTGAACTTGATAAATTTTAGGGTTTTTAA
* * * *
6887 AATAAAATATTAAGGA-TAAACTTGAAAAA-TAAAAGTCAAAGT-CTCAATATAGAAACAATTG
193 AAAAAAATACTAAAGACT-AACTTGAAAAAGTAAAAGTCAAAGTCCT-AATATAAAAACAATTG
6948 TCGAGTTAAA
Statistics
Matches: 211, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
269 2 0.01
270 26 0.12
271 24 0.11
272 4 0.02
273 20 0.09
274 1 0.00
275 2 0.01
276 37 0.18
277 56 0.27
278 39 0.18
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.38
Consensus pattern (277 bp):
ATTAAATAATTATTTGGGACCTGAACTTAGTAACTATTCACATATTGGGACTTCAACTGTTTTAG
TCCAAGTTAAAACATGAACTTGATAATTATTCTCATGTAGAGGTTTGAATTTTTTTTAAAGTTAA
CCCCTAAACTTGAGAACTGTTCCTATATTGAATTTGAACTTGATAAATTTTAGGGTTTTTAAAAA
AAAATACTAAAGACTAACTTGAAAAAGTAAAAGTCAAAGTCCTAATATAAAAACAATTGCCAAGT
TACCGAAATAAAAAAAT
Found at i:40363 original size:24 final size:24
Alignment explanation
Indices: 40334--40389 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
40324 TAGACTAACA
40334 AGAGTTT-GACTCAAACAAATAAAC
1 AGAGTTTAG-CTCAAACAAATAAAC
* *
40358 AGAGTTTAGTTGAAACAAATAAAC
1 AGAGTTTAGCTCAAACAAATAAAC
*
40382 AAAGTTTA
1 AGAGTTTA
40390 ACTAAAAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAGCTCAAACAAATAAAC
Found at i:41031 original size:121 final size:121
Alignment explanation
Indices: 40817--41059 Score: 468
Period size: 121 Copynumber: 2.0 Consensus size: 121
40807 GTCTTTTTAC
*
40817 CTTTTAACAAAACGAGAGATTCATGAGACACCTTAATGCCGCTCGACTCAATTTTGATTCTGCAA
1 CTTTTAACAAAACGAGAGATCCATGAGACACCTTAATGCCGCTCGACTCAATTTTGATTCTGCAA
*
40882 CCTTTTGAATCTAAAATATTTACGGAGATGAGATTCTTTCGTAAATCAGGTACATA
66 CCTTTTGAATCTAAAATACTTACGGAGATGAGATTCTTTCGTAAATCAGGTACATA
40938 CTTTTAACAAAACGAGAGATCCATGAGACACCTTAATGCCGCTCGACTCAATTTTGATTCTGCAA
1 CTTTTAACAAAACGAGAGATCCATGAGACACCTTAATGCCGCTCGACTCAATTTTGATTCTGCAA
41003 CCTTTTGAATCTAAAATACTTACGGAGATGAGATTCTTTCGTAAATCAGGTACATA
66 CCTTTTGAATCTAAAATACTTACGGAGATGAGATTCTTTCGTAAATCAGGTACATA
41059 C
1 C
41060 CTGACATATG
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 120 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (121 bp):
CTTTTAACAAAACGAGAGATCCATGAGACACCTTAATGCCGCTCGACTCAATTTTGATTCTGCAA
CCTTTTGAATCTAAAATACTTACGGAGATGAGATTCTTTCGTAAATCAGGTACATA
Found at i:42444 original size:24 final size:24
Alignment explanation
Indices: 42415--42473 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
42405 TAGACTAACA
*
42415 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
42439 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
42463 AGAGTTTAACT
1 AGAGTTTAACT
42474 AAAAGATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:43069 original size:31 final size:32
Alignment explanation
Indices: 43009--43070 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
42999 ATGTGTATGA
* * * *
43009 TTGAACCCACAATCAAAGTTTCCTGTATATAT
1 TTGAACCCACAAACAAAATTTCATATATATAT
43041 TTGAA-CCACAAACAAAATTTCATATATATA
1 TTGAACCCACAAACAAAATTTCATATATATA
43071 ATTACACCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (32 bp):
TTGAACCCACAAACAAAATTTCATATATATAT
Found at i:50701 original size:22 final size:22
Alignment explanation
Indices: 50659--50699 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
50649 TTTTCAAGTT
* *
50659 TTTTATTTTTAATTAATAAATC
1 TTTTATTTATAATAAATAAATC
50681 TTTTATTTAT-ATAAATAAA
1 TTTTATTTATAATAAATAAA
50700 ATAATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTATTTATAATAAATAAATC
Found at i:50785 original size:28 final size:26
Alignment explanation
Indices: 50723--50813 Score: 85
Period size: 28 Copynumber: 3.3 Consensus size: 26
50713 AATCATATAA
* *
50723 TAAAATATTTTTATTTATTTATCATTATG
1 TAAAATATTATTATTAATTT-T-A-TATG
*
50752 TTAAATA-TATATATATAATTTCTATATG
1 TAAAATATTAT-TAT-TAATTT-TATATG
*
50780 TAAAATATTATTATTACTTTTATATG
1 TAAAATATTATTATTAATTTTATATG
50806 TAAAATAT
1 TAAAATAT
50814 CTCAAATATT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
26 14 0.26
27 5 0.09
28 15 0.28
29 13 0.25
30 6 0.11
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (26 bp):
TAAAATATTATTATTAATTTTATATG
Found at i:50803 original size:26 final size:29
Alignment explanation
Indices: 50748--50813 Score: 86
Period size: 26 Copynumber: 2.4 Consensus size: 29
50738 TATTTATCAT
*
50748 TATGTTAAATA-TATATATATAATTTCTA
1 TATGTAAAATATTATATATATAATTTCTA
*
50776 TATGTAAAATATTAT-TAT-TACTTT-TA
1 TATGTAAAATATTATATATATAATTTCTA
50802 TATGTAAAATAT
1 TATGTAAAATAT
50814 CTCAAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 14 0.40
27 5 0.14
28 13 0.37
29 3 0.09
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (29 bp):
TATGTAAAATATTATATATATAATTTCTA
Found at i:55779 original size:28 final size:29
Alignment explanation
Indices: 55725--55779 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
55715 AATATAATTT
* **
55725 AAAATATTTATTTAATTTTAGCGGATAAC
1 AAAATATTAATTTAATTTTAAAGGATAAC
*
55754 AAAATA-TAATTTAATTTTAAATGATA
1 AAAATATTAATTTAATTTTAAAGGATA
55780 TATTTAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 16 0.73
29 6 0.27
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (29 bp):
AAAATATTAATTTAATTTTAAAGGATAAC
Found at i:56594 original size:15 final size:14
Alignment explanation
Indices: 56574--56608 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
56564 TTATTCTTTA
*
56574 TATTTTAATTTGATT
1 TATTTTAATTT-ATG
56589 TATTTTAATTTATG
1 TATTTTAATTTATG
56603 TATTTT
1 TATTTT
56609 CTAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (14 bp):
TATTTTAATTTATG
Found at i:58784 original size:59 final size:59
Alignment explanation
Indices: 58692--58809 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
58682 CTGCACTTTG
*
58692 TTATTTTGTGTTTTGGCCTTGAATATGAAGGTCATCTTTTTCTTTTGCTTCTATTTTTA
1 TTATTTTGTGTTTTGGCCTTGAATATGAAGGTCATCTTTTTATTTTGCTTCTATTTTTA
58751 TTATTTTGTGTTTTGGCCTTGAATATGAAGGTCATCTTTTTATTTTGCTTCTATTTTTA
1 TTATTTTGTGTTTTGGCCTTGAATATGAAGGTCATCTTTTTATTTTGCTTCTATTTTTA
58810 ATGGAATGGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.16, C:0.11, G:0.15, T:0.58
Consensus pattern (59 bp):
TTATTTTGTGTTTTGGCCTTGAATATGAAGGTCATCTTTTTATTTTGCTTCTATTTTTA
Found at i:59682 original size:6 final size:7
Alignment explanation
Indices: 59657--59681 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
59647 TTCTTTATCT
59657 TTTTTCC
1 TTTTTCC
59664 TTTTTCC
1 TTTTTCC
59671 TTTTTCC
1 TTTTTCC
59678 TTTT
1 TTTT
59682 CAAATACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCC
Found at i:61521 original size:2 final size:2
Alignment explanation
Indices: 61514--61539 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61504 GTGCGTGACT
61514 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
61540 AGTCACGCAC
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):
TA
Found at i:62427 original size:97 final size:97
Alignment explanation
Indices: 62249--62435 Score: 218
Period size: 97 Copynumber: 1.9 Consensus size: 97
62239 GAAAATGATG
* * *
62249 TTCGATTATCTCGATTTAAAGAAAAAGTCACACCTAGTAAGTTTAGGTACAAATTTTCAGAATCA
1 TTCGATTATCTCGATTTAAAGAAAAAGTCACACCTAGTAAGTTAAGGCACAAATTTTCAAAATCA
* *
62314 AAGATAAGAAACATTGCCTCGATTTAAGGATA
66 AAGAAAAGAAACATTGCCTCAATTTAAGGATA
* ***
62346 TTCGATTAT-TCCGATTTGAAGAAAAA-TCGTGCCTAGTAAGTTAAGGCACAAATTTTCAAAATT
1 TTCGATTATCT-CGATTTAAAGAAAAAGTCACACCTAGTAAGTTAAGGCACAAATTTTCAAAA--
* * *
62409 TGAAATAAAAG-AATATTGCCTCAATTT
63 TCAAAGAAAAGAAACATTGCCTCAATTT
62436 TAAAGTTTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
96 30 0.40
97 37 0.49
98 8 0.11
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (97 bp):
TTCGATTATCTCGATTTAAAGAAAAAGTCACACCTAGTAAGTTAAGGCACAAATTTTCAAAATCA
AAGAAAAGAAACATTGCCTCAATTTAAGGATA
Found at i:62845 original size:59 final size:56
Alignment explanation
Indices: 62766--62928 Score: 195
Period size: 56 Copynumber: 2.8 Consensus size: 56
62756 AAATCGAGAT
* * *
62766 AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATA-GTAATTTTGGGAAAAATCAAGGTC
1 AAAAATGGAATTTTAGGAAGTTTGAGGGTAAAA-ACGTAATTTT-GG-AAAA-CAAAGTC
* *
62825 AAAAATGGAATTTTAAGAAGTTCGAGGGTAAAAACGTAATTTTGGAAAACAAAGTC
1 AAAAATGGAATTTTAGGAAGTTTGAGGGTAAAAACGTAATTTTGGAAAACAAAGTC
* *
62881 AAAAATGGATTTTTAGGAA-TTTCGAGGGTAAAAACATAATTTTTGGAA
1 AAAAATGGAATTTTAGGAAGTTT-GAGGGTAAAAACGTAA-TTTTGGAA
62929 GTTTAGGGGT
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
55 2 0.02
56 38 0.41
57 12 0.13
58 3 0.03
59 37 0.40
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.29
Consensus pattern (56 bp):
AAAAATGGAATTTTAGGAAGTTTGAGGGTAAAAACGTAATTTTGGAAAACAAAGTC
Found at i:62965 original size:29 final size:27
Alignment explanation
Indices: 62935--63072 Score: 87
Period size: 29 Copynumber: 4.7 Consensus size: 27
62925 GGAAGTTTAG
62935 GGGTAAAATGTAATTCTTGGAAAAATCA
1 GGGTAAAATGTAATT-TTGGAAAAATCA
* ** *
62963 GGGTCAAAATGGAATTTTGGAAAGTTTAA
1 GGGT-AAAATGTAATTTTGGAAA-AATCA
* *
62992 GGGTAAACATGTAATTTTTAGAAAAATTA
1 GGGTAAA-ATGTAA-TTTTGGAAAAATCA
* * ** *
63021 AGGTCAAAAATGGAATTTTGGAAAGTTTGA
1 GGGT--AAAATGTAATTTTGGAAA-AATCA
63051 GGGTAAAAATGTAAATTTTGGA
1 GGGT-AAAATGT-AATTTTGGA
63073 TAGTTCGGGT
Statistics
Matches: 85, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
28 14 0.16
29 41 0.48
30 27 0.32
31 3 0.04
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (27 bp):
GGGTAAAATGTAATTTTGGAAAAATCA
Found at i:63026 original size:58 final size:58
Alignment explanation
Indices: 62921--63069 Score: 203
Period size: 59 Copynumber: 2.6 Consensus size: 58
62911 AAAACATAAT
* * * *
62921 TTTTGG-AAGTTTAGGGGTAAAATGTAATTCTTGGAAAAATCAGGGTC-AAAATGGAA
1 TTTTGGAAAGTTTAAGGGTAAAATGTAATTTTTAGAAAAATCAAGGTCAAAAATGGAA
*
62977 TTTTGGAAAGTTTAAGGGTAAACATGTAATTTTTAGAAAAATTAAGGTCAAAAATGGAA
1 TTTTGGAAAGTTTAAGGGTAAA-ATGTAATTTTTAGAAAAATCAAGGTCAAAAATGGAA
* *
63036 TTTTGGAAAGTTTGAGGGTAAAAATGTAAATTTT
1 TTTTGGAAAGTTTAAGGGT-AAAATGTAATTTTT
63070 GGATAGTTCG
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
56 6 0.07
57 14 0.17
58 22 0.27
59 37 0.45
60 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (58 bp):
TTTTGGAAAGTTTAAGGGTAAAATGTAATTTTTAGAAAAATCAAGGTCAAAAATGGAA
Found at i:63038 original size:30 final size:30
Alignment explanation
Indices: 62939--63044 Score: 94
Period size: 29 Copynumber: 3.6 Consensus size: 30
62929 GTTTAGGGGT
* * * *
62939 AAAATGTAATTCTTGGAAAAATCAGGGTC-
1 AAAATGGAATTTTTGGAAAAATTAAGGTCA
**
62968 AAAATGGAA-TTTTGGAAAGTTTAAGGGT-A
1 AAAATGGAATTTTTGGAAAAATTAA-GGTCA
* * *
62997 AACATGTAATTTTTAGAAAAATTAAGGTCA
1 AAAATGGAATTTTTGGAAAAATTAAGGTCA
63027 AAAATGGAA-TTTTGGAAA
1 AAAATGGAATTTTTGGAAA
63045 GTTTGAGGGT
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
28 10 0.17
29 29 0.49
30 20 0.34
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAAATTAAGGTCA
Found at i:63087 original size:29 final size:31
Alignment explanation
Indices: 62962--63131 Score: 119
Period size: 29 Copynumber: 5.8 Consensus size: 31
62952 TGGAAAAATC
* *
62962 AGGGTC-AAAATG-GAATTTTGGAAAGTTTA
1 AGGGTCAAAAATGTAAATTTTGGAAAGTTTG
* * * **
62991 AGGGT-AAACATGTAATTTTTAGAAAAATT-
1 AGGGTCAAAAATGTAAATTTTGGAAAGTTTG
* *
63020 AAGGTCAAAAATG-GAATTTTGGAAAGTTTG
1 AGGGTCAAAAATGTAAATTTTGGAAAGTTTG
*
63050 AGGGT-AAAAATGTAAATTTTGGATAG-TT-
1 AGGGTCAAAAATGTAAATTTTGGAAAGTTTG
* *
63078 CGGGTCAAAAATATAAA-TTTGGAGAAGTTT-
1 AGGGTCAAAAATGTAAATTTTGGA-AAGTTTG
* *
63108 AGTGGTC-AAAATATAATTTTTGGA
1 AG-GGTCAAAAATGTAAATTTTGGA
63132 TAATTTAGGG
Statistics
Matches: 110, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
28 10 0.09
29 46 0.42
30 44 0.40
31 10 0.09
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.33
Consensus pattern (31 bp):
AGGGTCAAAAATGTAAATTTTGGAAAGTTTG
Found at i:63097 original size:59 final size:57
Alignment explanation
Indices: 62921--63136 Score: 188
Period size: 59 Copynumber: 3.7 Consensus size: 57
62911 AAAACATAAT
* * * * *
62921 TTTTGG-AAGTTTAGGGGT-AAAATGTAATTCTTGGAAAAATCAGGGTC-AAAATGGAA
1 TTTTGGAAAGTTTA-GGGTAAAAATGTAATTTTTGG-ATAATTAAGGTCAAAAATGAAA
* * * *
62977 TTTTGGAAAGTTTAAGGGTAAACATGTAATTTTTAGAAAAATTAAGGTCAAAAATGGAA
1 TTTTGGAAAGTTT-AGGGTAAAAATGTAATTTTT-GGATAATTAAGGTCAAAAATGAAA
* * **
63036 TTTTGGAAAGTTTGAGGGTAAAAATGTAAATTTTGGATAGTTCGGGTCAAAAAT-ATAA
1 TTTTGGAAAGTTT-AGGGTAAAAATGTAATTTTTGGATAATTAAGGTCAAAAATGA-AA
* * *
63094 ATTTGGAGAAGTTTAGTGGTCAAAATATAATTTTTGGATAATT
1 TTTTGGA-AAGTTTAG-GGTAAAAATGTAATTTTTGGATAATT
63137 TAGGGACCTT
Statistics
Matches: 133, Mismatches: 19, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
56 6 0.05
57 10 0.08
58 48 0.36
59 69 0.52
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (57 bp):
TTTTGGAAAGTTTAGGGTAAAAATGTAATTTTTGGATAATTAAGGTCAAAAATGAAA
Found at i:63130 original size:31 final size:30
Alignment explanation
Indices: 63080--63139 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
63070 GGATAGTTCG
63080 GGTCAAAAATATAAATTTGGAGAAGTTTAGT
1 GGTCAAAAATATAAATTTGGAGAA-TTTAGT
* *
63111 GGTC-AAAATATAATTTTTGGATAATTTAG
1 GGTCAAAAATATAA-ATTTGGAGAATTTAG
63140 GGACCTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (30 bp):
GGTCAAAAATATAAATTTGGAGAATTTAGT
Found at i:64068 original size:13 final size:14
Alignment explanation
Indices: 64041--64075 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
64031 TTTTAAAAGG
64041 TATTTAAACCCCAT
1 TATTTAAACCCCAT
64055 TATTTAAA-CCCAT
1 TATTTAAACCCCAT
64068 TATTTAAA
1 TATTTAAA
64076 TTTATTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (14 bp):
TATTTAAACCCCAT
Found at i:64314 original size:3 final size:3
Alignment explanation
Indices: 64301--64366 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
64291 CTTTCAACTC
* * *
64301 TTA TT- TTA TTA TTA TTA ATA TTA CTAA TTA TTA TTA TTA TTA -AA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* *
64345 ATA GTTA TTA TTA ATA TTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA
64367 ATTCTTTTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
2 3 0.06
3 43 0.86
4 4 0.08
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:65032 original size:17 final size:17
Alignment explanation
Indices: 65012--65047 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
65002 AATTATTTTT
65012 AATTTAA-ACTAAATTTA
1 AATTTAATA-TAAATTTA
65029 AATTTAATATAAATTTA
1 AATTTAATATAAATTTA
65046 AA
1 AA
65048 ACTAATCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAATATAAATTTA
Found at i:65978 original size:11 final size:12
Alignment explanation
Indices: 65963--65995 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
65953 TATAAAAAAT
65963 ATAAATTTAAT-
1 ATAAATTTAATA
*
65974 TTAAATTTAATA
1 ATAAATTTAATA
65986 ATAAATTTAA
1 ATAAATTTAA
65996 AAACAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAAATTTAATA
Found at i:66407 original size:23 final size:22
Alignment explanation
Indices: 66377--66429 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
66367 TTAAAACAAA
*
66377 AACATAATGACAGGAGAGTTACC
1 AACATAATGACAAGAGAGTTA-C
*
66400 AACATAATGGCAAGAGAGTTAC
1 AACATAATGACAAGAGAGTTAC
*
66422 AAAATAAT
1 AACATAAT
66430 AATAATTGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (22 bp):
AACATAATGACAAGAGAGTTAC
Found at i:69741 original size:41 final size:41
Alignment explanation
Indices: 69675--69768 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 41
69665 GAATTTTCAT
* * *
69675 TTAATAAGAATTCTAATCACTCAATTCTAACAATCTTCACC
1 TTAACAAGAATTCTAATCACCCAATTCTAACAATCTCCACC
* *
69716 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACT
1 TTAACAAGAATTCTAATCACCCAATTCTAACAATCTCCACC
*
69757 TTGACAAGAATT
1 TTAACAAGAATT
69769 ATCTACAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.32
Consensus pattern (41 bp):
TTAACAAGAATTCTAATCACCCAATTCTAACAATCTCCACC
Found at i:74280 original size:14 final size:12
Alignment explanation
Indices: 74248--74272 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
74238 ATAAACATTG
74248 ATTTAATATATA
1 ATTTAATATATA
74260 ATTTAATATATA
1 ATTTAATATATA
74272 A
1 A
74273 ATTTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATATA
Found at i:74290 original size:29 final size:29
Alignment explanation
Indices: 74256--74311 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
74246 TGATTTAATA
74256 TATAATTTAATATAT-AAATTTTAATTTTG
1 TATAATTT-ATATATGAAATTTTAATTTTG
*
74285 TATAATTTTTATATGAAATTTTAATTT
1 TATAATTTATATATGAAATTTTAATTT
74312 AATTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (29 bp):
TATAATTTATATATGAAATTTTAATTTTG
Found at i:74319 original size:29 final size:28
Alignment explanation
Indices: 74248--74326 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
74238 ATAAACATTG
*
74248 ATTTAATATATAATTTAATATATAAATTTTA
1 ATTTAAT-T-TAATTT-TTATATAAATTTTA
** *
74279 ATTTTGTATAATTTTTATATGAAATTTTA
1 ATTTAATTTAATTTTTATAT-AAATTTTA
74308 ATTTAATTTAATTTTTATA
1 ATTTAATTTAATTTTTATA
74327 AATTAATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 5 0.12
29 30 0.75
31 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
ATTTAATTTAATTTTTATATAAATTTTA
Found at i:85909 original size:28 final size:28
Alignment explanation
Indices: 85877--85941 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
85867 TTAAAAAATT
85877 ATTAATCGACCCTGATCAAAATTGGTTG
1 ATTAATCGACCCTGATCAAAATTGGTTG
85905 ATTAATCGACCCTGATCAAAATTGGTTG
1 ATTAATCGACCCTGATCAAAATTGGTTG
85933 ATTAATCGA
1 ATTAATCGA
85942 ATTAATTCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (28 bp):
ATTAATCGACCCTGATCAAAATTGGTTG
Found at i:86504 original size:40 final size:40
Alignment explanation
Indices: 86453--86530 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
86443 TTTCCGTTAG
86453 AATTTAATTTAATTATTAAAATATCATTTTTAATATTTTAA
1 AATTTAATTTAATTATTAAAATATCA-TTTTAATATTTTAA
* *
86494 AATTT-ATTTAATTGTTAAAATATCATTTTAATTTTTT
1 AATTTAATTTAATTATTAAAATATCATTTTAATATTTT
86531 GAGGGATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 11 0.31
40 19 0.54
41 5 0.14
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (40 bp):
AATTTAATTTAATTATTAAAATATCATTTTAATATTTTAA
Found at i:86525 original size:20 final size:20
Alignment explanation
Indices: 86460--86526 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 20
86450 TAGAATTTAA
86460 TTTAATTATTAAAATATCATT
1 TTTAATTATTAAAATATCA-T
* *
86481 TTTAATATTTTAAAAT-TTA-
1 TTTAAT-TATTAAAATATCAT
*
86500 TTTAATTGTTAAAATATCAT
1 TTTAATTATTAAAATATCAT
86520 TTTAATT
1 TTTAATT
86527 TTTTGAGGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 8 0.21
19 8 0.21
20 7 0.18
21 8 0.21
22 8 0.21
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (20 bp):
TTTAATTATTAAAATATCAT
Found at i:95629 original size:15 final size:16
Alignment explanation
Indices: 95609--95639 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
95599 AATATTTAAC
95609 TCTTTTTT-TTTTTTT
1 TCTTTTTTCTTTTTTT
95624 TCTTTTTTCTTTTTTT
1 TCTTTTTTCTTTTTTT
95640 ATAATTTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TCTTTTTTCTTTTTTT
Found at i:97783 original size:2 final size:2
Alignment explanation
Indices: 97776--97806 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
97766 AAAGCAAAAG
97776 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
97807 GGTTGGAATT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:102332 original size:18 final size:17
Alignment explanation
Indices: 102309--102343 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
102299 TTTTTTAAAT
102309 TAAATTTTAAATTAATAA
1 TAAATTTTAAA-TAATAA
102327 TAAATTTTAAATAATAA
1 TAAATTTTAAATAATAA
102344 ACAATATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTTAAATAATAA
Found at i:103242 original size:28 final size:28
Alignment explanation
Indices: 103211--103279 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
103201 TTTTACAATT
103211 TTTTATATTTTTAAAGAA-TTATAATACA
1 TTTTATATTTTTAAAGAAGTTATAATA-A
* * * *
103239 TTTTTTA-TTTTAAATAAGTTTTATTAA
1 TTTTATATTTTTAAAGAAGTTATAATAA
103266 TTTTATAATTTTTA
1 TTTTAT-ATTTTTA
103280 TAATTCATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
27 15 0.45
28 13 0.39
29 5 0.15
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTATATTTTTAAAGAAGTTATAATAA
Found at i:103324 original size:20 final size:20
Alignment explanation
Indices: 103301--103365 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 20
103291 AATTTATTAG
103301 ATTTTTTAAAATTTTATAAT
1 ATTTTTTAAAATTTTATAAT
* *
103321 A-TTTATAAAGTTTTTATAAT
1 ATTTTTTAAA-ATTTTATAAT
* *
103341 -TTTTTTTATATTTT-TAAT
1 ATTTTTTAAAATTTTATAAT
103359 ATTTTTT
1 ATTTTTT
103366 CTTATTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 4 0.11
19 17 0.47
20 15 0.42
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTTTTTAAAATTTTATAAT
Found at i:103344 original size:9 final size:9
Alignment explanation
Indices: 103162--103386 Score: 82
Period size: 10 Copynumber: 23.8 Consensus size: 9
103152 TTTTTTTTTT
*
103162 TTTTTGTAA
1 TTTTTATAA
103171 TTTTTATAA
1 TTTTTATAA
**
103180 CTTAATATAA
1 -TTTTTATAA
*
103190 TTTTTAATAT
1 TTTTT-ATAA
*
103200 TTTTTACAA
1 TTTTTATAA
103209 TTTTT-TATA
1 TTTTTATA-A
*
103218 TTTTTAAAGAA
1 TTTTT--ATAA
* *
103229 TTATAATACA
1 TTTTTATA-A
103239 TTTTT-T-A
1 TTTTTATAA
*
103246 TTTTAAATAA
1 TTTT-TATAA
*
103256 GTTTTATTAA
1 TTTTTA-TAA
103266 -TTTTATAA
1 TTTTTATAA
103274 TTTTTATAA
1 TTTTTATAA
* *
103283 TTCATTACAA
1 TT-TTTATAA
* *
103293 TTTATTAGAT
1 TTT-TTATAA
103303 TTTTTA-AA
1 TTTTTATAA
*
103311 ATTTTATAA
1 TTTTTATAA
*
103320 TATTTATAAA
1 TTTTTAT-AA
103330 GTTTTTATAA
1 -TTTTTATAA
*
103340 TTTTTTTTATA
1 -TTTTTATA-A
*
103351 TTTTTAATAT
1 TTTTT-ATAA
* *
103361 TTTTTCTTA
1 TTTTTATAA
*
103370 TTTTTAGTCA
1 TTTTTA-TAA
103380 TTTTTAT
1 TTTTTAT
103387 GAAGAAATAT
Statistics
Matches: 159, Mismatches: 37, Indels: 40
0.67 0.16 0.17
Matches are distributed among these distances:
7 5 0.03
8 10 0.06
9 61 0.38
10 69 0.43
11 13 0.08
12 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:103363 original size:19 final size:18
Alignment explanation
Indices: 103332--103375 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
103322 TTTATAAAGT
103332 TTTTATAATTTTTTT-TATA
1 TTTT-TAATTTTTTTCT-TA
103351 TTTTTAATATTTTTTCTTA
1 TTTTTAAT-TTTTTTCTTA
103370 TTTTTA
1 TTTTTA
103376 GTCATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.17
19 18 0.78
20 1 0.04
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTAATTTTTTTCTTA
Found at i:103364 original size:21 final size:19
Alignment explanation
Indices: 103331--103374 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
103321 ATTTATAAAG
*
103331 TTTTTATAATTTTTTTTAT
1 TTTTTATAATTTTTCTTAT
*
103350 ATTTTTAATATTTTTTCTTAT
1 -TTTTT-ATAATTTTTCTTAT
103371 TTTT
1 TTTT
103375 AGTCATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTATAATTTTTCTTAT
Found at i:103545 original size:7 final size:7
Alignment explanation
Indices: 103535--103580 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
103525 GATATATGTC
103535 ATATCAT
1 ATATCAT
103542 ATATCAT
1 ATATCAT
103549 ATATCAT
1 ATATCAT
103556 ATATCAT
1 ATATCAT
103563 ATATCAT
1 ATATCAT
103570 ATATCAT
1 ATATCAT
103577 ATAT
1 ATAT
103581 AAAAGAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATCAT
Found at i:104358 original size:14 final size:14
Alignment explanation
Indices: 104339--104379 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
104329 TTGTTTCGTT
104339 AAAAATGACTTTTG
1 AAAAATGACTTTTG
*
104353 AAAAATGATTTTTG
1 AAAAATGACTTTTG
*
104367 GAAAATGACTTTT
1 AAAAATGACTTTT
104380 TTGTTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (14 bp):
AAAAATGACTTTTG
Found at i:105246 original size:2 final size:2
Alignment explanation
Indices: 105241--105271 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
105231 ATATATGTAA
105241 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
105272 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:110426 original size:90 final size:90
Alignment explanation
Indices: 110304--110486 Score: 366
Period size: 90 Copynumber: 2.0 Consensus size: 90
110294 AAGTTTGTTT
110304 CCATTTTAAAAGAATCATGCAAATGTAAGTAAGTTTTTCAATCTCTCTCGCCGGATCTCTAAACC
1 CCATTTTAAAAGAATCATGCAAATGTAAGTAAGTTTTTCAATCTCTCTCGCCGGATCTCTAAACC
110369 CTTTCCATGAAATCACAATTTCCTC
66 CTTTCCATGAAATCACAATTTCCTC
110394 CCATTTTAAAAGAATCATGCAAATGTAAGTAAGTTTTTCAATCTCTCTCGCCGGATCTCTAAACC
1 CCATTTTAAAAGAATCATGCAAATGTAAGTAAGTTTTTCAATCTCTCTCGCCGGATCTCTAAACC
110459 CTTTCCATGAAATCACAATTTCCTC
66 CTTTCCATGAAATCACAATTTCCTC
110484 CCA
1 CCA
110487 GCCTCCATAC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 93 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (90 bp):
CCATTTTAAAAGAATCATGCAAATGTAAGTAAGTTTTTCAATCTCTCTCGCCGGATCTCTAAACC
CTTTCCATGAAATCACAATTTCCTC
Found at i:111927 original size:22 final size:23
Alignment explanation
Indices: 111887--111930 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
111877 TCCTAACTTA
* *
111887 ACACGTTTTTTTTTTTTTAAAAG
1 ACACGTTTTTATTTATTTAAAAG
111910 ACACG-TTTTATTTATTTAAAA
1 ACACGTTTTTATTTATTTAAAA
111931 ATTGATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (23 bp):
ACACGTTTTTATTTATTTAAAAG
Found at i:111931 original size:23 final size:23
Alignment explanation
Indices: 111887--111931 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
111877 TCCTAACTTA
* * *
111887 ACACGTTTTTTTTTTTTTAAAAG
1 ACACGTTTTATTTATTTAAAAAG
111910 ACACGTTTTATTTATTTAAAAA
1 ACACGTTTTATTTATTTAAAAA
111932 TTGATAATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (23 bp):
ACACGTTTTATTTATTTAAAAAG
Found at i:113984 original size:43 final size:42
Alignment explanation
Indices: 113851--114150 Score: 350
Period size: 43 Copynumber: 7.0 Consensus size: 42
113841 TTTTTCCTAT
* *
113851 AGAACATGGT-TGTTAGTGGCGCTTTCCCACAAACTCCGCTAA
1 AGAACATGGTCT-TTAGCGGCGCTTTCCCACAAACGCCGCTAA
*
113893 AGAACATGGTCTTTAGCGGTGCTTTCCCACAAACGCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTCCCACAAACGCCGCTAA
* *
113935 AGAACATGGTCTTTAGCGGCGCTTTCACCAAAAACGCCACTAA
1 AGAACATGGTCTTTAGCGGCGCTTTC-CCACAAACGCCGCTAA
* * *
113978 AAAACATGGTCTTTAGCGGCGCTTTCTCCGCAAACGCCGTTAA
1 AGAACATGGTCTTTAGCGGCGCTTTC-CCACAAACGCCGCTAA
* * ** *
114021 AGAATATGGTATTTAGCGGCGCATTTCCCGTAAACGCCACTAA
1 AGAACATGGTCTTTAGCGGCGC-TTTCCCACAAACGCCGCTAA
* * *
114064 AGAACATGGTCTTTAGCGGCGCTTCTCTCAAAAACTCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTT-TCCCACAAACGCCGCTAA
* * * **
114107 AGAACATTGTCTTTAGCGGCACTTTTTCCACAAATTCCGCTAA
1 AGAACATGGTCTTTAGCGGCGC-TTTCCCACAAACGCCGCTAA
114150 A
1 A
114151 ATTAACAGAT
Statistics
Matches: 222, Mismatches: 31, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
42 64 0.29
43 152 0.68
44 6 0.03
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (42 bp):
AGAACATGGTCTTTAGCGGCGCTTTCCCACAAACGCCGCTAA
Found at i:114537 original size:6 final size:6
Alignment explanation
Indices: 114528--114581 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
114518 AATCTTTAAC
* * * *
114528 TTTATA TTTATA TTTATA TTAATA ATTA-A TATATT TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
*
114575 TTAATA T
1 TTTATA T
114582 ATTTCGATTT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (6 bp):
TTTATA
Found at i:114573 original size:41 final size:41
Alignment explanation
Indices: 114497--114581 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
114487 TATTATTTGT
*
114497 TATTAATATTAAGTAATTAATAATCTTTAACTTTATATTTA
1 TATTAATATTAAGTAATTAATAATCTTTAACTTTATATTAA
* *
114538 TATTTATATTAA-TAATTAATATATTTTTATA-TTTATATTAA
1 TATTAATATTAAGTAATTAATA-ATCTTTA-ACTTTATATTAA
114579 TAT
1 TAT
114582 ATTTCGATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 9 0.23
41 29 0.74
42 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (41 bp):
TATTAATATTAAGTAATTAATAATCTTTAACTTTATATTAA
Found at i:114580 original size:22 final size:23
Alignment explanation
Indices: 114540--114585 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
114530 TATATTTATA
114540 TTTATATTAATAATTAATATATT
1 TTTATATTAATAATTAATATATT
*
114563 TTTATATTTAT-ATTAATATATT
1 TTTATATTAATAATTAATATATT
114585 T
1 T
114586 CGATTTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTATATTAATAATTAATATATT
Done.