Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013475.1 Kokia drynarioides strain JFW-HI SEQ_128501, 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: 68657
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Warning! 254 characters in sequence are not A, C, G, or T
Found at i:537 original size:31 final size:31
Alignment explanation
Indices: 492--561 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
482 TATAATTGGA
492 CCATTTG-TATTTGGGCCATTTGTAACTGGG
1 CCATTTGTTATTTGGGCCATTTGTAACTGGG
* *
522 CCATTTGTTATTTGGGCGATTTGTAATTGGG
1 CCATTTGTTATTTGGGCCATTTGTAACTGGG
* *
553 ACTTTTGTT
1 CCATTTGTT
562 TTGGATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 7 0.20
31 28 0.80
ACGTcount: A:0.16, C:0.13, G:0.26, T:0.46
Consensus pattern (31 bp):
CCATTTGTTATTTGGGCCATTTGTAACTGGG
Found at i:543 original size:16 final size:15
Alignment explanation
Indices: 487--565 Score: 79
Period size: 15 Copynumber: 5.3 Consensus size: 15
477 CACTTTATAA
*
487 TTGGACCATTTGTAT
1 TTGGGCCATTTGTAT
*
502 TTGGGCCATTTGTAA
1 TTGGGCCATTTGTAT
*
517 CTGGGCCATTTGTTAT
1 TTGGGCCATTTG-TAT
* *
533 TTGGGCGATTTGTAA
1 TTGGGCCATTTGTAT
* *
548 TTGGGACTTTTGT-T
1 TTGGGCCATTTGTAT
562 TTGG
1 TTGG
566 ATTTTTTTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
14 4 0.08
15 36 0.69
16 12 0.23
ACGTcount: A:0.15, C:0.11, G:0.28, T:0.46
Consensus pattern (15 bp):
TTGGGCCATTTGTAT
Found at i:613 original size:17 final size:16
Alignment explanation
Indices: 591--656 Score: 78
Period size: 17 Copynumber: 3.9 Consensus size: 16
581 TGGACTTTTC
*
591 TAAATTTAATTTTATAA
1 TAAATTTAATTTCA-AA
608 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTCAAA
625 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTCAAA
* *
642 TAAACTTAAATTCAA
1 TAAATTTAATTTCAA
657 TTTCTAACTA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.16
17 32 0.71
18 6 0.13
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTAATTTCAAA
Found at i:1479 original size:96 final size:96
Alignment explanation
Indices: 1302--1486 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
1292 GAAAAGGATG
* **
1302 TTCGATTATCCCGATTTGATGAAAGGTTACACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGG
1 TTCGATTATCCCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGG
* *
1367 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AAATAAAGAAACATTGCCTCGATTAAGGGTA
** *
1398 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTC
1 TTCGATTATCCCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TC
*
1462 -GAAATAAA-AGAATATTGCCTCGATT
64 GGAAATAAAGA-AACATTGCCTCGATT
1487 TTATAGTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
95 2 0.03
96 73 0.95
97 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (96 bp):
TTCGATTATCCCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGG
AAATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:1867 original size:29 final size:29
Alignment explanation
Indices: 1833--1969 Score: 111
Period size: 30 Copynumber: 4.7 Consensus size: 29
1823 GGGTCGAGGG
1833 TAAAAATGGAATTTTTGGAAGTTTCGGGA
1 TAAAAATGGAATTTTTGGAAGTTTCGGGA
* *
1862 TCAAAAAAT-GTATTTTTGGAAG-TTCGGGGG
1 T--AAAAATGGAATTTTTGGAAGTTTC-GGGA
* * * *
1892 TTAAAATGGAATTTTTAGAAGTTTTAGGGT
1 TAAAAATGGAATTTTTGGAAG-TTTCGGGA
*
1922 TAAAAATAGG-ATTTTTGGAAG-TTCAGGGG
1 TAAAAAT-GGAATTTTTGGAAGTTTC-GGGA
**
1951 TAAAAATAAAATTTTTGGA
1 TAAAAATGGAATTTTTGGA
1970 CAATTTAGGG
Statistics
Matches: 86, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
28 7 0.08
29 34 0.40
30 35 0.41
31 10 0.12
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTCGGGA
Found at i:1898 original size:59 final size:59
Alignment explanation
Indices: 1830--1969 Score: 176
Period size: 59 Copynumber: 2.4 Consensus size: 59
1820 AGAGGGTCGA
* * *
1830 GGGTAAAAATGGAATTTTTGGAAG-TTTCGGGATCAAAAAAT-GTATTTTTGGAAGTTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTTAGGG-T-AAAAAATAGGATTTTTGGAAGTTCAG
* * *
1889 GGGTTAAAATGGAATTTTTAGAAGTTTTAGGGTTAAAAATAGGATTTTTGGAAGTTCAG
1 GGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTAAAAAATAGGATTTTTGGAAGTTCAG
**
1948 GGGTAAAAATAAAATTTTTGGA
1 GGGTAAAAATGGAATTTTTGGA
1970 CAATTTAGGG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 6 0.09
59 57 0.83
60 6 0.09
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (59 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTAAAAAATAGGATTTTTGGAAGTTCAG
Found at i:1936 original size:30 final size:30
Alignment explanation
Indices: 1829--1966 Score: 94
Period size: 29 Copynumber: 4.7 Consensus size: 30
1819 TAGAGGGTCG
*
1829 AGGG-TAAAAAT-GGAATTTTTGGAAGTTTC
1 AGGGTTAAAAATAGGAATTTTTAGAAG-TTC
* * * *
1858 -GGGATCAAAAA-ATGTATTTTTGGAAGTTC
1 AGGG-TTAAAAATAGGAATTTTTAGAAGTTC
* *
1887 GGGGGTT-AAAAT-GGAATTTTTAGAAGTTTT
1 -AGGGTTAAAAATAGGAATTTTTAGAAG-TTC
*
1917 AGGGTTAAAAATAGG-ATTTTTGGAAGTTC
1 AGGGTTAAAAATAGGAATTTTTAGAAGTTC
* *
1946 AGGGGTAAAAATA-AAATTTTT
1 AGGGTTAAAAATAGGAATTTTT
1967 GGACAATTTA
Statistics
Matches: 86, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
28 3 0.03
29 43 0.50
30 35 0.41
31 5 0.06
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
AGGGTTAAAAATAGGAATTTTTAGAAGTTC
Found at i:2982 original size:12 final size:12
Alignment explanation
Indices: 2967--3010 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
2957 TTCCCTTTTT
2967 TATTATTATTAA
1 TATTATTATTAA
*
2979 TATTTTTATTAA
1 TATTATTATTAA
* *
2991 TATTAATAATAA
1 TATTATTATTAA
*
3003 TTTTATTA
1 TATTATTA
3011 ATACCTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:2986 original size:18 final size:18
Alignment explanation
Indices: 2963--3013 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
2953 TTAGTTCCCT
*
2963 TTTTTATTATTATTAATA
1 TTTTTATTAATATTAATA
2981 TTTTTATTAATATTAATAA
1 TTTTTATTAATATTAAT-A
3000 TAATTTTATTAATA
1 T--TTTTATTAATA
3014 CCTATTAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 16 0.55
19 2 0.07
21 11 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTATTAATATTAATA
Found at i:3000 original size:21 final size:21
Alignment explanation
Indices: 2962--3013 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2952 TTTAGTTCCC
* * *
2962 TTTT-TTATTATTATTAATAT
1 TTTTATTAATATTAATAATAA
2982 TTTTATTAATATTAATAATAA
1 TTTTATTAATATTAATAATAA
3003 TTTTATTAATA
1 TTTTATTAATA
3014 CCTATTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTATTAATATTAATAATAA
Found at i:3715 original size:18 final size:17
Alignment explanation
Indices: 3677--3769 Score: 107
Period size: 18 Copynumber: 5.4 Consensus size: 17
3667 CTTTATTTAT
* *
3677 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
3694 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
3712 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
3729 TTTAAAATTTTAAACAAA
1 TTT-AAATTTAAAATAAA
*
3747 TTT-AATCCTAAAATAAA
1 TTTAAAT-TTAAAATAAA
3764 TTTAAA
1 TTTAAA
3770 ATGAGTTTGG
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
16 3 0.05
17 30 0.46
18 32 0.49
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:3727 original size:35 final size:34
Alignment explanation
Indices: 3677--3769 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 34
3667 CTTTATTTAT
* *
3677 TTTAAATTTATAATAATTTTAAATTTGAAAATAAA
1 TTTAAATTTAAAATAATTTTAAATTT-AAAACAAA
* *
3712 TTTAAATTTAAAATAAATTTAAAATTTTAAACAAA
1 TTTAAATTTAAAAT-AATTTTAAATTTAAAACAAA
* *
3747 TTT-AATCCTAAAATAAATTTAAA
1 TTTAAAT-TTAAAATAATTTTAAA
3770 ATGAGTTTGG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
34 10 0.20
35 28 0.57
36 11 0.22
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (34 bp):
TTTAAATTTAAAATAATTTTAAATTTAAAACAAA
Found at i:15846 original size:95 final size:95
Alignment explanation
Indices: 15663--15853 Score: 237
Period size: 95 Copynumber: 2.0 Consensus size: 95
15653 TCTTTGGAAA
* *
15663 AAGGATATTCGATTATCTTGATTTGAAGAAAAGTTGCACCTAGTAAGTGAAGGCACAGTATTTCA
1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTGAAGGCACAATATTTCA
*
15728 GAATCAAAGATAAGGAAACATTGCCTCGATT
66 GAATCAAAGAAAAGG-AACATTGCCTCGATT
* *
15759 AAGGGTATTCGATTAT-TTCGATTTG-AGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTT
1 AAGGATATTCGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAGTGAAGGCACAATA-TTT
* * *
15821 CGGAACTCGAAATAAAAGG-ATATTGCCTCGATT
64 CAGAA-TC-AAAGAAAAGGAACATTGCCTCGATT
15854 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
94 1 0.01
95 51 0.61
96 23 0.28
97 8 0.10
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (95 bp):
AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTGAAGGCACAATATTTCA
GAATCAAAGAAAAGGAACATTGCCTCGATT
Found at i:16346 original size:60 final size:59
Alignment explanation
Indices: 16183--16681 Score: 603
Period size: 59 Copynumber: 8.4 Consensus size: 59
16173 ACATCCGGGA
* ** * * *
16183 GTAAAATAGTAATCCTTGGATGTTTC-GGGTTAAAAATGGGATTTTTGGAAGTTTTG-GG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGG
* * * ** *
16241 GTAAAAT-GTTATTTTTGGATAGTTTCGGGATTAAAAATGGGATTTTTGGAAACTCGTGG
1 GTAAAATGGTAATTTTTGGA-AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGG
* *
16300 GTAAAATGGTAATTTTTAGAAGTTTCGGGGGTCAAAAATTGGATTTTTGGAAGTTCGAGG
1 GTAAAATGGTAATTTTTGGAAGTTTC-GGGGTCAAAAATGGGATTTTTGGAAGTTCGAGG
* * * *
16360 GTAAAATGGTAATTTTTAGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTTTGAGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGG
* *
16419 GTAAAATGGTAAGTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGG
* * * * *
16478 ATAAAATGGTAATTTTTGGAAGGTTCAGGGTAAAAAAATGGGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGT-CAAAAATGGGATTTTTGGAAGTTCGAGG
* * * * * *
16538 GTAAAATGATAATTATTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGG
*
16597 GTAAAATGGTAATTTTTGGATAGTTTCGGGGAT-AAAAATGGGATTTTTGGAAGTTTGAGG
1 GTAAAATGGTAATTTTTGGA-AGTTTCGGGG-TCAAAAATGGGATTTTTGGAAGTTCGAGG
*
16657 GTAAAATGATAA-TTTTGGATAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
16682 AGGGATCTTC
Statistics
Matches: 389, Mismatches: 44, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
57 9 0.02
58 14 0.04
59 205 0.53
60 160 0.41
61 1 0.00
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGG
Found at i:16384 original size:119 final size:119
Alignment explanation
Indices: 16209--16672 Score: 598
Period size: 119 Copynumber: 3.9 Consensus size: 119
16199 TGGATGTTTC
* * *
16209 GGGTTAAAAATGGGATTTTTGGAAGTTTTG-GGGTAAAAT-GTTATTTTTGGATAGTTTC-GGGA
1 GGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGGTAAAATGGTAATTTTTGGATAGTTTCAGGG-
** * * * *
16271 TTAAAAATGGGATTTTTGGAAACTCGTGGGTAAAATGGTAATTTTTAGAAGTTTCGG
64 TTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTGGAAGGTTC-G
* *
16328 GGGTCAAAAATTGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGA-AGTTTC-GAGGT
1 GGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGATAGTTTCAG-GGT
* * * * *
16391 CAAAAATGAGATTTTTGGAAGTTTGAGGGTAAAATGGTAAGTTTTGGAAGGTTCG
65 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTGGAAGGTTCG
* *
16446 GGGTCAAAAATGGGATTTTTGGAAGTTCGAGGATAAAATGGTAATTTTTGGA-AGGTTCAGGGTA
1 GGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGATAGTTTCAGGGT-
* * *
16510 AAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGATAATTATTGGAAGGTTCG
65 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTGGAAGGTTCG
* * * * *
16565 AGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGATAGTTTCGGGGAT
1 GGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGATAGTTTCAGGGTT
*
16630 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGATAATTTT
66 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTTT
16673 GGATAGTTTA
Statistics
Matches: 303, Mismatches: 36, Indels: 12
0.86 0.10 0.03
Matches are distributed among these distances:
118 61 0.20
119 222 0.73
120 20 0.07
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (119 bp):
GGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGATAGTTTCAGGGTT
AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTGGAAGGTTCG
Found at i:16675 original size:178 final size:179
Alignment explanation
Indices: 16206--16672 Score: 658
Period size: 178 Copynumber: 2.6 Consensus size: 179
16196 CCTTGGATGT
* * *
16206 TTCG-GGTTAAAAATGGGATTTTTGGAAGTTTTGGGGTAAAAT-GTTATTTTTGGATAGTTTC-G
1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGATAGTTTCGG
** * * * * *
16268 GGATTAAAAATGGGATTTTTGGAAACTCGTGGGTAAAATGGTAATTTTTAGAAGTTTCGGGGGTC
66 GGA-TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGGTA
* * * *
16333 AAAAATTGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGT
130 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTATTAGAAGG
* * * *
16383 TTCGAGGTCAAAAATGAGATTTTTGGAAGTTTGAGGGTAAAATGGTAAGTTTTGGA-AGGTTCGG
1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGATAGTTTCGG
*
16447 GG-TCAAAAATGGGATTTTTGGAAGTTCGAGGATAAAATGGTAATTTTTGGAAGGTTC-AGGGTA
66 GGAT-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGGT-
* *
16510 AAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGATAATTATTGGAAGG
129 AAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTATTAGAAGG
16561 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGATAGTTTCGG
1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGATAGTTTCGG
* *
16626 GGATAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGATAATTTT
66 GGATAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTT
16673 GGATAGTTTA
Statistics
Matches: 255, Mismatches: 28, Indels: 12
0.86 0.09 0.04
Matches are distributed among these distances:
177 9 0.04
178 183 0.72
179 62 0.24
180 1 0.00
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (179 bp):
TTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGATAGTTTCGG
GGATAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGGTAA
AAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTATTAGAAGG
Found at i:17749 original size:15 final size:15
Alignment explanation
Indices: 17709--17750 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
17699 ATTATTAAAT
*
17709 ATTATTATTGATGTC
1 ATTATTATTGTTGTC
17724 ATTATTATTGTTGTC
1 ATTATTATTGTTGTC
*
17739 ATTAATATTGTT
1 ATTATTATTGTT
17751 AATGATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (15 bp):
ATTATTATTGTTGTC
Found at i:18413 original size:5 final size:5
Alignment explanation
Indices: 18403--18470 Score: 55
Period size: 5 Copynumber: 12.6 Consensus size: 5
18393 TTTAATTTTG
* * *
18403 AAATT AAATT AAATTT AAATTT AAGATT AATTT AAAATT AGATT AAATC
1 AAATT AAATT AAA-TT AAA-TT AA-ATT AAATT -AAATT AAATT AAATT
*
18452 AAATTT AAAAT AAATT AAA
1 AAA-TT AAATT AAATT AAA
18471 AAGGTCCCAG
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
5 28 0.55
6 22 0.43
7 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:18422 original size:11 final size:11
Alignment explanation
Indices: 18403--18467 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
18393 TTTAATTTTG
18403 AAATTAAA-TT
1 AAATTAAATTT
18413 AAATTTAAATTT
1 AAA-TTAAATTT
18425 AAGATT-AATTT
1 AA-ATTAAATTT
*
18436 AAAATTAGA-TT
1 -AAATTAAATTT
*
18447 AAATCAAATTT
1 AAATTAAATTT
*
18458 AAAATAAATT
1 AAATTAAATT
18468 AAAAAGGTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
10 9 0.20
11 25 0.57
12 9 0.20
13 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:30346 original size:2 final size:2
Alignment explanation
Indices: 30339--30364 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30329 TCACTCAAAA
30339 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
30365 TTTGTGTTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:31636 original size:37 final size:37
Alignment explanation
Indices: 31533--31641 Score: 123
Period size: 37 Copynumber: 2.9 Consensus size: 37
31523 ATTCTTGAAT
* * *
31533 CACCGGCACAAAGCCTGCTAGGCACAAAGCC-CAAATA
1 CACCGGCAC-AAGCCTACTAGGCACATAGCCTGAAATA
* *
31570 CACCGGCATGAAGCCTACTAGACACATAGCCTGAAA-A
1 CACCGGCA-CAAGCCTACTAGGCACATAGCCTGAAATA
*
31607 CACCGGCACACAGCCTACTAGGCATATAGCCTGAA
1 CACCGGCACA-AGCCTACTAGGCACATAGCCTGAA
31642 TTTGTGTAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
36 1 0.02
37 57 0.93
38 3 0.05
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.12
Consensus pattern (37 bp):
CACCGGCACAAGCCTACTAGGCACATAGCCTGAAATA
Found at i:32971 original size:30 final size:31
Alignment explanation
Indices: 32937--33007 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
32927 TAATTCCAAA
*
32937 ATAAAATAAAATTTA-TG-CTGTATAAC-TTTT
1 ATAAAA-AAAATTTAGTGTCT-AATAACTTTTT
32967 ATAAAAAAAATTTAGTGTCTAATAACTTTTT
1 ATAAAAAAAATTTAGTGTCTAATAACTTTTT
32998 ATAAAAAAAA
1 ATAAAAAAAA
33008 ATATATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 8 0.22
30 13 0.35
31 16 0.43
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.38
Consensus pattern (31 bp):
ATAAAAAAAATTTAGTGTCTAATAACTTTTT
Found at i:33899 original size:18 final size:18
Alignment explanation
Indices: 33876--33910 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33866 AAATTGGATC
33876 ATTTTTGTAA-TTAATTTA
1 ATTTTT-TAAGTTAATTTA
33894 ATTTTTTAAGTTAATTT
1 ATTTTTTAAGTTAATTT
33911 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
ATTTTTTAAGTTAATTTA
Found at i:36243 original size:30 final size:30
Alignment explanation
Indices: 36070--36275 Score: 222
Period size: 30 Copynumber: 6.9 Consensus size: 30
36060 ACTCGAGATG
* *
36070 AAAATGAAATTTTAGAGAAGTTTTA-GGGTC
1 AAAATGTAATTTTAGAAAAG-TTTAGGGGTC
* * *
36100 AAAATGTGATTTTGGAAAAGTTTAAGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTC
* * *
36130 AAAATATGATTTTAGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTC
* * *
36160 AAAATGTAATTTTGGAAAAGTTTGGGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTC
36190 AAAATGTAATTTTAGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTC
* * *
36220 AAATTGTAATTTTTGAAAAGTTTATGGGT-
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTC
*
36249 TAAATGGTAATTTCT--AAAAGTTTAGGG
1 AAAAT-GTAATTT-TAGAAAAGTTTAGGG
36276 ACCTATTGGG
Statistics
Matches: 152, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
29 18 0.12
30 133 0.88
31 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAGTTTAGGGGTC
Found at i:36249 original size:60 final size:60
Alignment explanation
Indices: 36070--36275 Score: 249
Period size: 60 Copynumber: 3.5 Consensus size: 60
36060 ACTCGAGATG
* * * *
36070 AAAATGAAATTTTAGAGAAGTTTTA-GGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTC
1 AAAATGTAATTTTAGAAAAG-TTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTT
* * * **
36130 AAAATATGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGGGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTT
* * *
36190 AAAATGTAATTTTAGAAAAGTTTAGGGGTCAAATTGTAATTTTTGAAAAGTTTATGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTT
36250 -AAATGGTAATTTCT--AAAAGTTTAGGG
1 AAAAT-GTAATTT-TAGAAAAGTTTAGGG
36276 ACCTATTGGG
Statistics
Matches: 127, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
59 20 0.16
60 106 0.83
61 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (60 bp):
AAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTT
Found at i:36716 original size:21 final size:22
Alignment explanation
Indices: 36690--36731 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
36680 AAAAATTTTT
36690 AAAAATCCTC-CTTTTTTAAAA
1 AAAAATCCTCTCTTTTTTAAAA
36711 AAAAATCCTCTCTTTTTTAAA
1 AAAAATCCTCTCTTTTTTAAA
36732 GATTAGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATCCTCTCTTTTTTAAAA
Found at i:37836 original size:16 final size:16
Alignment explanation
Indices: 37815--37861 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
37805 GTTTCTACAT
37815 TATAATAATAATTATA
1 TATAATAATAATTATA
* *
37831 TATAATAGTAA-TACA
1 TATAATAATAATTATA
37846 T-TATATAATAATTATA
1 TATA-ATAATAATTATA
37862 GATTTTAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 10 0.40
16 13 0.52
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
TATAATAATAATTATA
Found at i:38355 original size:18 final size:18
Alignment explanation
Indices: 38332--38366 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38322 AGTTTTTTTT
*
38332 ATTAAATTGAAAACTAAA
1 ATTAAATTAAAAACTAAA
38350 ATTAAATTAAAAACTAA
1 ATTAAATTAAAAACTAA
38367 TTTAAGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (18 bp):
ATTAAATTAAAAACTAAA
Found at i:39746 original size:11 final size:11
Alignment explanation
Indices: 39727--39811 Score: 55
Period size: 11 Copynumber: 7.4 Consensus size: 11
39717 AAATAGTTGT
39727 AAAATTAATAAC
1 AAAA-TAATAAC
*
39739 AAAATAATAATT
1 AAAATAATAA-C
*
39751 ATATAATACCTAA-
1 A-A-AATA-ATAAC
* *
39764 AAAATAACAAT
1 AAAATAATAAC
39775 AAAATAATAAC
1 AAAATAATAAC
*
39786 AATATAATAAC
1 AAAATAATAAC
* *
39797 GAAATGATAAC
1 AAAATAATAAC
39808 AAAA
1 AAAA
39812 CAACGAAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
10 2 0.04
11 40 0.70
12 6 0.11
13 2 0.04
14 4 0.07
15 3 0.05
ACGTcount: A:0.66, C:0.08, G:0.02, T:0.24
Consensus pattern (11 bp):
AAAATAATAAC
Found at i:39783 original size:14 final size:14
Alignment explanation
Indices: 39761--39795 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39751 ATATAATACC
39761 TAAAA-AATAACAA
1 TAAAATAATAACAA
39774 TAAAATAATAACAA
1 TAAAATAATAACAA
*
39788 TATAATAA
1 TAAAATAA
39796 CGAAATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAAATAATAACAA
Found at i:39807 original size:36 final size:36
Alignment explanation
Indices: 39739--39809 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
39729 AATTAATAAC
** * *
39739 AAAATAATAATTATATAATACCTAAAAAATAACAAT
1 AAAATAATAACAATATAATAACGAAAAAATAACAAT
**
39775 AAAATAATAACAATATAATAACGAAATGATAACAA
1 AAAATAATAACAATATAATAACGAAAAAATAACAA
39810 AACAACGAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.65, C:0.08, G:0.03, T:0.24
Consensus pattern (36 bp):
AAAATAATAACAATATAATAACGAAAAAATAACAAT
Found at i:45700 original size:58 final size:57
Alignment explanation
Indices: 45571--45707 Score: 177
Period size: 58 Copynumber: 2.4 Consensus size: 57
45561 TATTAAAAAT
* * *
45571 ATAATTATATTAAAAATGTTATTAAATTATATATTATTTTATTAAATTATATTTAATA
1 ATAATTGTATT-AAAATATAATTAAATTATATATTATTTTATTAAATTATATTTAATA
* * *
45629 ATAATTGTGTTAAAATATAATTAAATTATTTATTATTTTTATTAAATTATATTTAATT
1 ATAATTGTATTAAAATATAATTAAATTATATATTA-TTTTATTAAATTATATTTAATA
*
45687 ATAATCT-TATTAAAATTTAAT
1 ATAAT-TGTATTAAAATATAAT
45708 AATAATAATC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
57 21 0.30
58 47 0.68
59 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (57 bp):
ATAATTGTATTAAAATATAATTAAATTATATATTATTTTATTAAATTATATTTAATA
Found at i:51371 original size:30 final size:31
Alignment explanation
Indices: 51337--51399 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
51327 TAGTATTGGT
*
51337 AAAATTATAATTTGAT-TCTT-AAAAATGATA
1 AAAATT-TAATTTAATCTCTTAAAAAATGATA
* *
51367 AAAATTTGATTTAATCTTTTAAAAAATGATA
1 AAAATTTAATTTAATCTCTTAAAAAATGATA
51398 AA
1 AA
51400 GATATAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 7 0.25
30 9 0.32
31 12 0.43
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (31 bp):
AAAATTTAATTTAATCTCTTAAAAAATGATA
Found at i:53625 original size:24 final size:24
Alignment explanation
Indices: 53593--53648 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
53583 TTCGTCTTAA
53593 TGGGCTATTTAATTTAAAACTTGT
1 TGGGCTATTTAATTTAAAACTTGT
53617 TGGGCTATTTAATTTAAAACTTGT
1 TGGGCTATTTAATTTAAAACTTGT
*
53641 TGTGCTAT
1 TGGGCTAT
53649 GTTTTGTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (24 bp):
TGGGCTATTTAATTTAAAACTTGT
Found at i:54104 original size:14 final size:15
Alignment explanation
Indices: 54071--54104 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54061 ATTTACATGT
*
54071 CCAATTACCCTAAGC
1 CCAATTAACCTAAGC
54086 CCAATTAACCTAA-C
1 CCAATTAACCTAAGC
54100 CCAAT
1 CCAAT
54105 ACATTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.38, C:0.38, G:0.03, T:0.21
Consensus pattern (15 bp):
CCAATTAACCTAAGC
Found at i:55699 original size:15 final size:15
Alignment explanation
Indices: 55667--55719 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 15
55657 GTTTTTAAAT
*
55667 TTTAAGGATC--GTA
1 TTTAAGGATCATGCA
55680 TTTAAGGATCATGCA
1 TTTAAGGATCATGCA
55695 TTTAAGGATCATGCA
1 TTTAAGGATCATGCA
55710 TTTAAGGATC
1 TTTAAGGATC
55720 GTATTTTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
13 10 0.27
15 27 0.73
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (15 bp):
TTTAAGGATCATGCA
Found at i:58795 original size:49 final size:49
Alignment explanation
Indices: 58723--59002 Score: 245
Period size: 49 Copynumber: 5.7 Consensus size: 49
58713 TGGTACCTTA
* * * * * * *
58723 GAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGTGTACCCGGTATCAT
1 GAAGATTTGAAGGGAAAGATTGAGGCCGCAACGGTGAACCCGATACCAT
* * * * * *
58772 GAATATTTGAAGGGAAAGATTGAGGCCTCGACAGTGAATCCGATACCTT
1 GAAGATTTGAAGGGAAAGATTGAGGCCGCAACGGTGAACCCGATACCAT
* * * * *
58821 AGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGCGAACCCGATACCAT
1 -GAAGATTTGAAGGGAAAGATTGAGGCCGCAACGGTGAACCCGATACCAT
* * * * * ** *
58871 GAAGATTTGAAAGGATAGATTGAGGCCGCATCGATAAATTCGATACCTT
1 GAAGATTTGAAGGGAAAGATTGAGGCCGCAACGGTGAACCCGATACCAT
* * * ** *
58920 AGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCAT
1 -GAAGATTTGAAGGGAAAGATTGAGGCCGCAACGGTGAACCCGATACCAT
*
58970 GAAGATTTGAAGGGAAGGATTGAGGCCGCAACG
1 GAAGATTTGAAGGGAAAGATTGAGGCCGCAACG
59003 ACGAATCCAG
Statistics
Matches: 176, Mismatches: 53, Indels: 4
0.76 0.23 0.02
Matches are distributed among these distances:
49 101 0.57
50 75 0.43
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (49 bp):
GAAGATTTGAAGGGAAAGATTGAGGCCGCAACGGTGAACCCGATACCAT
Found at i:59016 original size:49 final size:49
Alignment explanation
Indices: 58769--59010 Score: 195
Period size: 50 Copynumber: 4.9 Consensus size: 49
58759 TACCCGGTAT
* * * * *
58769 CATGAATATTTGAAGGGAAAGATTGAGGCCTCGAC-AGTGAATCCGATAC
1 CATGAAGATTTGAAGGGAAGGATTGAGGCCGCAACGA-CGAATCCGATAC
* * * * * *
58818 CTTAGAAGATGTGATGGGAAAGG-TTGAGGCCGTAACGGCGAACCCGATAC
1 CAT-GAAGATTTGAAGGG-AAGGATTGAGGCCGCAACGACGAATCCGATAC
* * ** *
58868 CATGAAGATTTGAAAGGATA-GATTGAGGCCGCATCGATAAATTCGATAC
1 CATGAAGATTTGAAGGGA-AGGATTGAGGCCGCAACGACGAATCCGATAC
* * * * * * *
58917 CTTAGAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGCAAACCCGGTAC
1 CAT-GAAGATTTGAAGGG-AAGGATTGAGGCCGCAACGACGAATCCGATAC
58967 CATGAAGATTTGAAGGGAAGGATTGAGGCCGCAACGACGAATCC
1 CATGAAGATTTGAAGGGAAGGATTGAGGCCGCAACGACGAATCC
59011 AGTACCTTAA
Statistics
Matches: 146, Mismatches: 38, Indels: 18
0.72 0.19 0.09
Matches are distributed among these distances:
48 6 0.04
49 67 0.46
50 68 0.47
51 5 0.03
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.19
Consensus pattern (49 bp):
CATGAAGATTTGAAGGGAAGGATTGAGGCCGCAACGACGAATCCGATAC
Found at i:59017 original size:99 final size:98
Alignment explanation
Indices: 58716--59019 Score: 423
Period size: 99 Copynumber: 3.1 Consensus size: 98
58706 GCGAACTTGG
* * * *
58716 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGTGTACCCGGTATCATGAATATTTG
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCATGAAGATTTG
* *
58781 AAGGGAAAGATTGAGGCCTCGAC-AGTGAATCCGA
66 AAGGG-AAGATTGAGGCCGCAACGA-TGAATCCGA
*
58815 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGCGAACCCGATACCATGAAGATTTG
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCATGAAGATTTG
* * * *
58880 AAAGGATAGATTGAGGCCGCATCGATAAATTCGA
66 AAGGGA-AGATTGAGGCCGCAACGATGAATCCGA
* *
58914 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCATGAAGATTTG
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCATGAAGATTTG
*
58979 AAGGGAAGGATTGAGGCCGCAACGACGAATCC-A
66 AAGGGAA-GATTGAGGCCGCAACGATGAATCCGA
59012 GTACCTTA
1 -TACCTTA
59020 AAAACATGAC
Statistics
Matches: 182, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
98 3 0.02
99 178 0.98
100 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (98 bp):
TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCATGAAGATTTG
AAGGGAAGATTGAGGCCGCAACGATGAATCCGA
Found at i:61334 original size:30 final size:29
Alignment explanation
Indices: 61290--61524 Score: 188
Period size: 30 Copynumber: 7.9 Consensus size: 29
61280 ATAGGTCCCT
* * * *
61290 AAACTTTCCGAAAATCACATTCTGACCTCA
1 AAACTTTCC-AAAATCACATTTTAACCCCC
* *
61320 AAACATTTCCAAAATTATATTTTAACCCCC
1 AAAC-TTTCCAAAATCACATTTTAACCCCC
* *
61350 AAACTTCTCCAAAATTATATTTTAACCCCC
1 AAACTT-TCCAAAATCACATTTTAACCCCC
61380 AAACTTCTCCAAAATCACATTTTAACCCCC
1 AAACTT-TCCAAAATCACATTTTAACCCCC
* *
61410 AAACTTTCCCAAAATCACATTTTAA-TCCT
1 AAACTTT-CCAAAATCACATTTTAACCCCC
* **
61439 AAACTTCTTCAAAATCTTATTTTAA-CCCC
1 AAACTT-TCCAAAATCACATTTTAACCCCC
* * * *
61468 AAAATTTCCTAAAATTACATTACT-ACCCCT
1 AAACTTTCC-AAAATCACATT-TTAACCCCC
* * *
61498 AAACTTTTCTAAAATTATATTTTAACC
1 AAAC-TTTCCAAAATCACATTTTAACC
61525 TCGAATTCTC
Statistics
Matches: 170, Mismatches: 26, Indels: 18
0.79 0.12 0.08
Matches are distributed among these distances:
28 2 0.01
29 42 0.25
30 117 0.69
31 9 0.05
ACGTcount: A:0.38, C:0.28, G:0.01, T:0.34
Consensus pattern (29 bp):
AAACTTTCCAAAATCACATTTTAACCCCC
Found at i:61499 original size:59 final size:58
Alignment explanation
Indices: 61329--61524 Score: 218
Period size: 59 Copynumber: 3.3 Consensus size: 58
61319 AAAACATTTC
* * *
61329 CAAAATTATATTTTAACCCCCAAACTTCTCCAAAATTATATTTTAACCCCCAAACTTCTC
1 CAAAATTATATTTTAACCCCCAAACTT-TCCAAAATTACATTTT-ACCCCTAAACTTCTT
* * * **
61389 CAAAATCACATTTTAACCCCCAAACTTTCCCAAAATCACATTTTAATCCTAAACTTCTT
1 CAAAATTATATTTTAACCCCCAAACTTT-CCAAAATTACATTTTACCCCTAAACTTCTT
* *
61448 CAAAATCT-TATTTTAA-CCCCAAAATTTCCTAAAATTACATTACTACCCCTAAACTT-TT
1 CAAAAT-TATATTTTAACCCCCAAACTTTCC-AAAATTACATT-TTACCCCTAAACTTCTT
61506 CTAAAATTATATTTTAACC
1 C-AAAATTATATTTTAACC
61525 TCGAATTCTC
Statistics
Matches: 114, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
57 2 0.02
58 24 0.21
59 49 0.43
60 39 0.34
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.35
Consensus pattern (58 bp):
CAAAATTATATTTTAACCCCCAAACTTTCCAAAATTACATTTTACCCCTAAACTTCTT
Found at i:67980 original size:96 final size:96
Alignment explanation
Indices: 67796--67983 Score: 229
Period size: 96 Copynumber: 2.0 Consensus size: 96
67786 TTTTTGTGAA
* ** *
67796 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGACGCAATATTTCA
1 AAGGATATTCGAGTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAATATTTCA
*
67861 AAATCGAAGATAAGGAAACATTGCCTCAATT
66 AAATCGAAGATAAAGAAACATTGCCTCAATT
* * * *
67892 AAGGGTATTCGAGTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGAGTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAATA-TTTC
* *
67956 GAAACTCGAA-ATAAA-AGAATATTGCCTC
65 -AAAATCGAAGATAAAGA-AACATTGCCTC
67984 GATTTTAAAG
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
95 2 0.03
96 68 0.87
97 8 0.10
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (96 bp):
AAGGATATTCGAGTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAATATTTCA
AAATCGAAGATAAAGAAACATTGCCTCAATT
Found at i:68299 original size:28 final size:28
Alignment explanation
Indices: 68249--68471 Score: 168
Period size: 29 Copynumber: 7.8 Consensus size: 28
68239 ATCGAGGTTA
* *
68249 AAAATGTAATTTTTAGACA-TTCGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTC-GGGGTC
*
68277 AAAATGGAATTTTTGG-AGTTTCGAGGTC
1 AAAATGGAATTTTTGGAAG-TTCGGGGTC
* * * **
68305 GAAAATAGAGTTTTTGG-AGTTCAAGGGAA
1 -AAAATGGAATTTTTGGAAGTTC-GGGGTC
* *
68334 AAAATGGAATTTTTGGTAGTTACGAGGTC
1 AAAATGGAATTTTTGGAAGTT-CGGGGTC
* * **
68363 GAAAATGAAATTTTTGGAAGTTCGAGGAA
1 -AAAATGGAATTTTTGGAAGTTCGGGGTC
*
68392 AAAAT-GAGATTTTTGGAAGTTTCGAGGTC
1 AAAATGGA-ATTTTTGGAAG-TTCGGGGTC
*
68421 AAAAATGGAATTTTTGGAAGTTCAGGGGTA
1 -AAAATGGAATTTTTGGAAGTTC-GGGGTC
68451 AAAATGGAATTTTTGGAAGTT
1 AAAATGGAATTTTTGGAAGTT
68472 AGGGTGTATT
Statistics
Matches: 158, Mismatches: 24, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
26 1 0.01
27 5 0.03
28 50 0.32
29 60 0.38
30 40 0.25
31 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGTC
Found at i:68310 original size:29 final size:29
Alignment explanation
Indices: 68277--68471 Score: 211
Period size: 29 Copynumber: 6.7 Consensus size: 29
68267 ATTCGGGGGT
*
68277 AAAATGGAATTTTTGG-AGTTTCGAGGTCG
1 AAAATGGAATTTTTGGAAG-TTCGAGGTCA
* * * **
68306 AAAATAGAGTTTTTGG-AGTTCAAGGGAA
1 AAAATGGAATTTTTGGAAGTTCGAGGTCA
* *
68334 AAAATGGAATTTTTGGTAGTTACGAGGTCG
1 AAAATGGAATTTTTGGAAGTT-CGAGGTCA
* *
68364 AAAATGAAATTTTTGGAAGTTCGAGG-AA
1 AAAATGGAATTTTTGGAAGTTCGAGGTCA
68392 AAAAT-GAGATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGA-ATTTTTGGAAG-TTCGAGGTCA
*
68422 AAAATGGAATTTTTGGAAGTTCAGGGGT-A
1 AAAATGGAATTTTTGGAAGTTC-GAGGTCA
68451 AAAATGGAATTTTTGGAAGTT
1 AAAATGGAATTTTTGGAAGTT
68472 AGGGTGTATT
Statistics
Matches: 140, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
27 1 0.01
28 36 0.26
29 57 0.41
30 44 0.31
31 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGTCA
Found at i:68377 original size:58 final size:59
Alignment explanation
Indices: 68277--68472 Score: 258
Period size: 58 Copynumber: 3.4 Consensus size: 59
68267 ATTCGGGGGT
* *
68277 AAAATGGAATTTTTGG-AGTTTCGAGGTCGAAAAT-AGAGTTTTTGG-AGTTCAAGGGAA
1 AAAATGGAATTTTTGGAAGTTACGAGGTCGAAAATGA-AATTTTTGGAAGTTCAAGGGAA
* *
68334 AAAATGGAATTTTTGGTAGTTACGAGGTCGAAAATGAAATTTTTGGAAGTTCGA-GGAA
1 AAAATGGAATTTTTGGAAGTTACGAGGTCGAAAATGAAATTTTTGGAAGTTCAAGGGAA
* * * * *
68392 AAAAT-GAGATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCAGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTACGAGGTCGAAAATGAAATTTTTGGAAGTTCAAGGGAA
68451 AAAATGGAATTTTTGGAAGTTA
1 AAAATGGAATTTTTGGAAGTTA
68473 GGGTGTATTT
Statistics
Matches: 122, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
57 18 0.15
58 74 0.61
59 28 0.23
60 2 0.02
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTACGAGGTCGAAAATGAAATTTTTGGAAGTTCAAGGGAA
Done.