Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014401.1 Kokia drynarioides strain JFW-HI SEQ_129439, 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: 25457
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:391 original size:11 final size:11
Alignment explanation
Indices: 364--394 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
354 TCAGTCTCTA
364 ATAATTTTTCT
1 ATAATTTTTCT
375 AT-ATTTTTCT
1 ATAATTTTTCT
385 ATAATTTTTC
1 ATAATTTTTC
395 AAAGTCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (11 bp):
ATAATTTTTCT
Found at i:3489 original size:29 final size:29
Alignment explanation
Indices: 3436--3850 Score: 364
Period size: 30 Copynumber: 14.1 Consensus size: 29
3426 CCCTGGAGGT
* *
3436 CCCTAAACTATCCAAAAATTTCATTTTTAC
1 CCCTGAACT-TCCAAAAATTCCATTTTTAC
*
3466 CCCTGAACTTCCAAAAATCCCATTTTTGAC
1 CCCTGAACTTCCAAAAATTCCATTTTT-AC
*
3496 CTC-GAAACTTCCAAAAATTCCATTTTTAC
1 CCCTG-AACTTCCAAAAATTCCATTTTTAC
* * *
3525 CCTTGAACTTCCAAAAATACCATTTTTGGC
1 CCCTGAACTTCCAAAAATTCCATTTTT-AC
3555 CCC-GACACTTCCAAAAATTCCATTTTTAC
1 CCCTGA-ACTTCCAAAAATTCCATTTTTAC
* *
3584 CCCCGAACTTCCAAAAA-TCCATTTTTAA
1 CCCTGAACTTCCAAAAATTCCATTTTTAC
3612 CCCTGAAACTTCCAAAAATTCCATTTTTAC
1 CCCTG-AACTTCCAAAAATTCCATTTTTAC
** *
3642 CTTTAAACTTCCAAAAATTCCA-TTTTA-
1 CCCTGAACTTCCAAAAATTCCATTTTTAC
* * *
3669 CCCTCAAACTTCTAAAAATCCCATTTTTGAC
1 CCCT-GAACTTCCAAAAATTCCATTTTT-AC
* ** * *
3700 CTCAAAACTTCCTAAAATTCCA-TTTTCC
1 CCCTGAACTTCCAAAAATTCCATTTTTAC
* *
3728 CCTCTCGAACTTCTAAAAATCCCATTTTTGAC
1 CC-CT-GAACTTCCAAAAATTCCATTTTT-AC
**
3760 CCCAAAACTTCCAAAAATT-CATTTTTTAC
1 CCCTGAACTTCCAAAAATTCCA-TTTTTAC
* *
3789 ACAC-GAGCTTCCAAAAATTCCATTTTTGA-
1 -CCCTGAACTTCCAAAAATTCCATTTTT-AC
* *
3818 CCCTAAAACTTCCAAAAATTATCA-TTTTAC
1 CCCT-GAACTTCCAAAAATT-CCATTTTTAC
3848 CCC
1 CCC
3851 CGAATGTTCG
Statistics
Matches: 315, Mismatches: 46, Indels: 48
0.77 0.11 0.12
Matches are distributed among these distances:
27 2 0.01
28 39 0.12
29 119 0.38
30 143 0.45
31 9 0.03
32 3 0.01
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
CCCTGAACTTCCAAAAATTCCATTTTTAC
Found at i:3538 original size:59 final size:58
Alignment explanation
Indices: 3440--3836 Score: 378
Period size: 59 Copynumber: 6.7 Consensus size: 58
3430 GGAGGTCCCT
* *
3440 AAACTATCCAAAAATTTCATTTTTACCCCT-GAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTA-CCCTAAAACTTCCAAAAAT-CCATTTTTGACCTCG
** * *
3500 AAACTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATACCATTTTTGGCCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAAT-CCATTTTTGACCTCG
* *** *
3559 ACACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCATTTTTAACC-CTG
1 AAACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATCCATTTTTGACCTC-G
* *
3617 AAACTTCCAAAAATTCCATTTTTACCTTTAAACTTCCAAAAATTCCA-TTTT-ACCCTC-
1 AAACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAA-TCCATTTTTGA-CCTCG
* * * ***
3674 AAACTTCTAAAAATCCCATTTTTGA-CCTCAAAACTTCCTAAAATTCCATTTTCCCCTCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCT-AAAACTTCC-AAAAATCCATTTTTGAC-CTCG
* * * * * *
3735 -AACTTCTAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCATTTTTTACACACG
1 AAACTTCCAAAAATTCCATTTTT-ACCCTAAAACTTCCAAAAATCCATTTTTGAC-CTCG
*
3794 -AGCTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAAT
1 AAACTTCCAAAAATTCCATTTTT-ACCCTAAAACTTCCAAAAAT
3837 TATCATTTTA
Statistics
Matches: 291, Mismatches: 33, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
57 25 0.09
58 71 0.24
59 152 0.52
60 41 0.14
61 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATCCATTTTTGACCTCG
Found at i:14692 original size:27 final size:27
Alignment explanation
Indices: 14657--14716 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
14647 AATTTTCAAC
14657 TAATGATTGTTTCCTTTGATCCTCCTT-T
1 TAAT-ATTGTTTCCTTTGATCCT-CTTCT
14685 TAATATTGTTTCCTTTGATCCTCTTCT
1 TAATATTGTTTCCTTTGATCCTCTTCT
14712 TAATA
1 TAATA
14717 GAATTTTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 3 0.10
27 24 0.77
28 4 0.13
ACGTcount: A:0.18, C:0.20, G:0.08, T:0.53
Consensus pattern (27 bp):
TAATATTGTTTCCTTTGATCCTCTTCT
Found at i:15588 original size:205 final size:205
Alignment explanation
Indices: 15165--15935 Score: 1065
Period size: 205 Copynumber: 3.8 Consensus size: 205
15155 GATTATTCAC
* * * *
15165 AAACAAGCGACGTGGTCATCTTCCTGATGAGATACT-----GAAGACCAGGTCGAACCCACGCTC
1 AAACAAGAGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
* * * *
15225 GGTATGAGCAAAGCTTCGAATCTCAGCTTCCTGGTGAGATACTGAGAAGCAGGTCGAAGCAATAA
66 GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGC-ATTA
* *
15290 AACGGTTAGCTTCCTGATGAGAT-CTTGAGAAGTGAACCAAATTTGTTCTCCTGATAAGATACAG
130 AACGGTTAGCTTCCTGATGAGATAC-TGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAG
15354 AGAAGCGGATTG
194 AGAAGCGGATTG
* *
15366 AAACAAGAGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACACTC
1 AAACAAGAGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
*
15431 GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCAAGAAGCAGGTCGAAGCATTAA
66 GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATTAA
* * *
15496 ACGGTTAACTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAAAG
131 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGAG
15561 AAGCGGATTG
196 AAGCGGATTG
* *
15571 AAACAA-ACGACGCGGTCATCTTCCTGACGAGATACTGAGAAGAAGACCAAGTCAAACTCACGCT
1 AAACAAGA-GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCT
* *
15635 CGGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACTGAGAAGCAGGTCGAAGCAATA
65 CGGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATTA
*
15700 AACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATATAGA
130 AACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGA
15765 GAAGCGGATTG
195 GAAGCGGATTG
* * * *
15776 AAATAAGAGATGCGTTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAGAGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
* * * *** **
15841 -G-AAGCAAGCGAAATCTTCGAACCCCAGCTTCCTGACAAGACACCGAGAAGTTGGTCGAAGCAA
66 GGTATG--AGC-AAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGC-A
* *
15904 GTAATAAAACGGTTAGCTTTCTGATGAAATAC
127 -T--T-AAACGGTTAGCTTCCTGATGAGATAC
15936 AAGGAAATGA
Statistics
Matches: 509, Mismatches: 45, Indels: 22
0.88 0.08 0.04
Matches are distributed among these distances:
201 33 0.06
203 2 0.00
204 2 0.00
205 324 0.64
206 122 0.24
207 1 0.00
210 1 0.00
211 24 0.05
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (205 bp):
AAACAAGAGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATTAA
ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGAG
AAGCGGATTG
Found at i:16376 original size:17 final size:16
Alignment explanation
Indices: 16350--16408 Score: 73
Period size: 17 Copynumber: 3.6 Consensus size: 16
16340 GCCCCCTCTT
16350 TTTAATTTATTTTAAA
1 TTTAATTTATTTTAAA
16366 TTTATATTTATTTTAAA
1 TTTA-ATTTATTTTAAA
* * *
16383 TTTAAATTAATCTAAA
1 TTTAATTTATTTTAAA
16399 TTTAAATTTA
1 TTT-AATTTA
16409 ATTTCAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 16 0.43
17 21 0.57
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAATTTATTTTAAA
Found at i:16387 original size:6 final size:6
Alignment explanation
Indices: 16360--16422 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
16350 TTTAATTTAT
* * *
16360 TTTAAA TTTATA TTT-AT TTTAAA TTTAAA -TT-AA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
16405 TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTT-AAA TTTAAA
16423 AAAGTCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 2 0.04
5 11 0.24
6 28 0.62
7 4 0.09
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:17706 original size:13 final size:13
Alignment explanation
Indices: 17688--17715 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17678 CGAGAAGGGG
17688 TGAGAGGTTTTTT
1 TGAGAGGTTTTTT
17701 TGAGAGGTTTTTT
1 TGAGAGGTTTTTT
17714 TG
1 TG
17716 GTTTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.32, T:0.54
Consensus pattern (13 bp):
TGAGAGGTTTTTT
Found at i:18292 original size:29 final size:29
Alignment explanation
Indices: 18260--18497 Score: 284
Period size: 29 Copynumber: 8.1 Consensus size: 29
18250 TAAACTGTCA
18260 AAAAATTCCATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCC
* *
18289 AAAAATCCCATTTTTGACCC-CAAAACTTCC
1 AAAAATTCCATTTTT-ACCCTC-GAACTTCC
* * *
18319 AAAAATCCCATTTTTACCCTTGAACTTCA
1 AAAAATTCCATTTTTACCCTCGAACTTCC
* * *
18348 AAAAATCCCGTTTTTACCCCCGAACTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCC
*
18377 -AAAATTCCATTTTTACCCCCGAACTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCC
*
18405 AAAAATTCCATTTTTAACCTCGAAACTTCC
1 AAAAATTCCATTTTTACCCTCG-AACTTCC
* *
18435 AAAAATTCCATTTTTACCCCCGAGCTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCC
**
18464 -AAAATTCCCATTTTTGACCCTAAAACTTCC
1 AAAAATT-CCATTTTT-ACCCTCGAACTTCC
18494 AAAA
1 AAAA
18498 TTTATCATTT
Statistics
Matches: 181, Mismatches: 20, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
28 32 0.18
29 83 0.46
30 63 0.35
31 3 0.02
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCTCGAACTTCC
Found at i:18344 original size:59 final size:59
Alignment explanation
Indices: 18251--18515 Score: 329
Period size: 59 Copynumber: 4.5 Consensus size: 59
18241 GAAGGTCCCT
* *
18251 AAACTGTCAAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCA
* ** * * *
18311 AAACTTCCAAAAATCCCATTTTTACCCTTGAACTTCAAAAAATCCCGTTTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * *
18369 GAACTTCC-AAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
18427 AAACTTCCAAAAATTCCATTTTTACCCCCGAGCTTCCAAAATTCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCA
* *
18486 AAACTTCCAAAATTTATCA-TTTTACCCCCG
1 AAACTTCCAAAAATT-CCATTTTTACCCCCG
18516 GATGTTCGAA
Statistics
Matches: 177, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
57 37 0.21
58 23 0.13
59 110 0.62
60 7 0.04
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:19006 original size:96 final size:96
Alignment explanation
Indices: 18864--19055 Score: 235
Period size: 96 Copynumber: 2.0 Consensus size: 96
18854 AGCTTTAAAA
* * * * **
18864 AATCGAGGCAATATTCTTTTATTTCGAGTTTCAAAAATTTGTGCCTTAACTCACTAGTTGTAATT
1 AATCGAGGCAATATTCTCTTATTTCGAGTTTCAAAAATTTGCGCCTTAACTCACTAGGTGCAACC
18929 TTTCTTCAAATCAAAATAATCGAATACCCTT
66 TTTCTTCAAATCAAAATAATCGAATACCCTT
* * * *
18960 AATCGAGGCAATGTT-TCCTTATCTTCGATTTTGAAAAA-TTGCGCCTTAACTTACTAGGTGCAA
1 AATCGAGGCAATATTCT-CTTAT-TTCGAGTTTCAAAAATTTGCGCCTTAACTCACTAGGTGCAA
* * *
19023 CCTTTCTTCAAATCGAGATAATCGAATATCCTT
64 CCTTTCTTCAAATCAAAATAATCGAATACCCTT
19056 TCTGCAAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
95 1 0.01
96 67 0.83
97 13 0.16
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTCTCTTATTTCGAGTTTCAAAAATTTGCGCCTTAACTCACTAGGTGCAACC
TTTCTTCAAATCAAAATAATCGAATACCCTT
Found at i:23543 original size:29 final size:28
Alignment explanation
Indices: 23511--23573 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
23501 AAAATGAGAC
23511 TTTTCGGATACCCGGGGGTAAAATAGTAA
1 TTTT-GGATACCCGGGGGTAAAATAGTAA
* * * * *
23540 TTTTGGATTCTCGGGGGTGAAATGGTAG
1 TTTTGGATACCCGGGGGTAAAATAGTAA
23568 TTTTGG
1 TTTTGG
23574 GAAATTTTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.22, C:0.10, G:0.33, T:0.35
Consensus pattern (28 bp):
TTTTGGATACCCGGGGGTAAAATAGTAA
Found at i:23652 original size:58 final size:58
Alignment explanation
Indices: 23588--23737 Score: 160
Period size: 58 Copynumber: 2.6 Consensus size: 58
23578 TTTTGGGGTT
* * *
23588 AAAAATGGAATTTTTAGACATTCAGGGGTAAAAGGGTAATTTTGA-GAGTTTCGAGGTC
1 AAAAATGG-ATTTTTAGACATTCGGGGGTAAAAGGGTAATTTTAAGGAGTTTCGAGGAC
* * * * * *
23646 GAAAATGGAGTCTTCGAACATCCGGGGGTAAAATGGTAATTTTAAGGAGTTTCGAGGAC
1 AAAAATGGATTTTTAG-ACATTCGGGGGTAAAAGGGTAATTTTAAGGAGTTTCGAGGAC
*
23705 AAAAATGGGATTTTTGGA-ACTTCGGGGGTAAAA
1 AAAAAT-GGATTTTTAGACA-TTCGGGGGTAAAA
23738 ATGGAATTTT
Statistics
Matches: 74, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
57 5 0.07
58 32 0.43
59 30 0.41
60 7 0.09
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (58 bp):
AAAAATGGATTTTTAGACATTCGGGGGTAAAAGGGTAATTTTAAGGAGTTTCGAGGAC
Found at i:23712 original size:59 final size:58
Alignment explanation
Indices: 23612--23747 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 58
23602 TAGACATTCA
* * * *
23612 GGGGTAAAAGGGTAATTTTGAGAGTTTCGAGGTCGAAAAT-GGAGTCTTCGAACATCCG
1 GGGGTAAAATGGTAATTTTAAGAGTTTCGAGGACAAAAATGGGAGTCTTCGAAC-TCCG
* * * *
23670 GGGGTAAAATGGTAATTTTAAGGAGTTTCGAGGACAAAAATGGGATTTTTGGAACTTCG
1 GGGGTAAAATGGTAATTTTAA-GAGTTTCGAGGACAAAAATGGGAGTCTTCGAACTCCG
23729 GGGGTAAAAATGG-AATTTT
1 GGGGT-AAAATGGTAATTTT
23748 TGGAAATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
58 19 0.28
59 31 0.46
60 17 0.25
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.29
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTAAGAGTTTCGAGGACAAAAATGGGAGTCTTCGAACTCCG
Found at i:23737 original size:29 final size:29
Alignment explanation
Indices: 23705--23915 Score: 217
Period size: 29 Copynumber: 7.2 Consensus size: 29
23695 TTTCGAGGAC
* *
23705 AAAAATGGGATTTTTGGAACTTCGGGGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
* * * ***
23734 AAAAATGGAATTTTTGGAAATTTTAGAATT
1 AAAAATGGGATTTTTGG-AAGTTTGGGGGT
*
23764 AAAAATGGGATTTTTGGAAGTTTGGGGGA
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
* *
23793 AAAAATGGAATTTTTGGAAGTTTTGGGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
* *
23822 CAAAAATGGGATTTTTAGAAGTTTGAGGGT
1 -AAAAATGGGATTTTTGGAAGTTTGGGGGT
* **
23852 AAAAATGGAATTTTTGGAAGTTTTAGGG-
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
* *
23880 ACAAAGATGGGATTTTTGGAAGTTCGAGGGT
1 A-AAA-ATGGGATTTTTGGAAGTTTGGGGGT
23911 AAAAA
1 AAAAA
23916 CAAATTTTTT
Statistics
Matches: 150, Mismatches: 27, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
28 1 0.01
29 77 0.51
30 71 0.47
31 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (29 bp):
AAAAATGGGATTTTTGGAAGTTTGGGGGT
Found at i:23769 original size:30 final size:30
Alignment explanation
Indices: 23733--23903 Score: 161
Period size: 30 Copynumber: 5.8 Consensus size: 30
23723 ACTTCGGGGG
* *
23733 TAAAAATGGAATTTTTGGAAATTTTAGAAT
1 TAAAAATGGAATTTTTGGAAGTTTTAGGAT
* **
23763 TAAAAATGGGATTTTTGGAAGTTTGGGGGA-
1 TAAAAATGGAATTTTTGGAAGTTT-TAGGAT
* *
23793 -AAAAATGGAATTTTTGGAAGTTTTGGGGT
1 TAAAAATGGAATTTTTGGAAGTTTTAGGAT
* * * * *
23822 CAAAAATGGGATTTTTAGAAGTTTGAGG-G
1 TAAAAATGGAATTTTTGGAAGTTTTAGGAT
23851 TAAAAATGGAATTTTTGGAAGTTTTAGGGA-
1 TAAAAATGGAATTTTTGGAAGTTTTA-GGAT
* * *
23881 CAAAGATGGGATTTTTGGAAGTT
1 TAAAAATGGAATTTTTGGAAGTT
23904 CGAGGGTAAA
Statistics
Matches: 116, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
28 3 0.03
29 44 0.38
30 67 0.58
31 2 0.02
ACGTcount: A:0.35, C:0.01, G:0.29, T:0.36
Consensus pattern (30 bp):
TAAAAATGGAATTTTTGGAAGTTTTAGGAT
Found at i:23925 original size:59 final size:59
Alignment explanation
Indices: 23701--23940 Score: 297
Period size: 59 Copynumber: 4.1 Consensus size: 59
23691 GGAGTTTCGA
* * *
23701 GGACAAAAATGGGATTTTTGGAACTTCGGGGGTAAAAATGGAATTTTTGGAAATTTTA-
1 GGACAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAG
* * * * * *
23759 GAATTAAAAATGGGATTTTTGGAAGTTTGGGGGAAAAAATGGAATTTTTGGAAGTTTTGG
1 GGA-CAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAG
* * *
23819 GGTCAAAAATGGGATTTTTAGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTTAG
1 GGACAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAG
* **
23878 GGACAAAGATGGGATTTTTGGAAGTTCGAGGGTAAAAA-CAAATTTTTTGGATAG-TTTAG
1 GGACAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAA-TTTTTGGA-AGTTTTAG
23937 GGAC
1 GGAC
23941 CTCCAGAGTA
Statistics
Matches: 158, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
58 4 0.03
59 151 0.96
60 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (59 bp):
GGACAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAG
Found at i:24993 original size:22 final size:22
Alignment explanation
Indices: 24950--25000 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
24940 TTTCCCTTTT
*
24950 TTATTA-TTAAAACATTATTTA
1 TTATTATTTAAAAAATTATTTA
24971 TTATTATTTAAAAAAATTA-TTA
1 TTATTATTT-AAAAAATTATTTA
24993 TTATTATT
1 TTATTATT
25001 AATATATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 6 0.22
22 13 0.48
23 8 0.30
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATTATTTAAAAAATTATTTA
Done.