Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010882.1 Kokia drynarioides strain JFW-HI SEQ_125850, 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: 41607
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:608 original size:29 final size:29
Alignment explanation
Indices: 590--673 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
580 TCTGCATCCG
*
590 TAACTGTACCTGTGACATGATTGTATCTA
1 TAACTGTATCTGTGACATGATTGTATCTA
*
619 TAACTGTATCTGTAACATGATTGTATCTA
1 TAACTGTATCTGTGACATGATTGTATCTA
*
648 TAACTGTATCTGTGACATGACTGTAT
1 TAACTGTATCTGTGACATGATTGTAT
674 ATGTAATTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (29 bp):
TAACTGTATCTGTGACATGATTGTATCTA
Found at i:1046 original size:227 final size:227
Alignment explanation
Indices: 651--1105 Score: 892
Period size: 227 Copynumber: 2.0 Consensus size: 227
641 GTATCTATAA
*
651 CTGTATCTGTGACATGACTGTATATGTAATTTATTTGTATTATTTCTATATCGAGATCTTGTATT
1 CTGTATCTGTGACATGACTGTATATGTAATTTATTTGTATTATTTCTATACCGAGATCTTGTATT
716 TGTATTATCTAACCTTCTTCTATGTGTCTAAAATGAATCTGTCTCTGCTATAGTGGTTATGTGTT
66 TGTATTATCTAACCTTCTTCTATGTGTCTAAAATGAATCTGTCTCTGCTATAGTGGTTATGTGTT
781 TGTCTGTTTATTGAGATTTAAAGTGATATTGAGTCCAACTTCACGTAGCATTCCTTTGGTTCGTA
131 TGTCTGTTTATTGAGATTTAAAGTGATATTGAGTCCAACTTCACGTAGCATTCCTTTGGTTCGTA
846 ATTTGACAACTCTACGATACTCTGGAACTGTT
196 ATTTGACAACTCTACGATACTCTGGAACTGTT
878 CTGTATCTGTGACATGACTGTATATGTAATTTATTTGTATTATTTCTATACCGAGATCTTGTATT
1 CTGTATCTGTGACATGACTGTATATGTAATTTATTTGTATTATTTCTATACCGAGATCTTGTATT
*
943 TGTATTATCTAACCTTCTTCTATGTGTCTGAAATGAATCTGTCTCTGCTATAGTGGTTATGTGTT
66 TGTATTATCTAACCTTCTTCTATGTGTCTAAAATGAATCTGTCTCTGCTATAGTGGTTATGTGTT
1008 TGTCTGTTTATTGAGATTTAAAGTGATATTGAGTCCAACTTCACGTAGCATTCCTTTGGTTCGTA
131 TGTCTGTTTATTGAGATTTAAAGTGATATTGAGTCCAACTTCACGTAGCATTCCTTTGGTTCGTA
1073 ATTTGACAACTCTACGATACTCTGGAACTGTT
196 ATTTGACAACTCTACGATACTCTGGAACTGTT
1105 C
1 C
1106 AGTACCAATT
Statistics
Matches: 226, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
227 226 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (227 bp):
CTGTATCTGTGACATGACTGTATATGTAATTTATTTGTATTATTTCTATACCGAGATCTTGTATT
TGTATTATCTAACCTTCTTCTATGTGTCTAAAATGAATCTGTCTCTGCTATAGTGGTTATGTGTT
TGTCTGTTTATTGAGATTTAAAGTGATATTGAGTCCAACTTCACGTAGCATTCCTTTGGTTCGTA
ATTTGACAACTCTACGATACTCTGGAACTGTT
Found at i:1814 original size:7 final size:7
Alignment explanation
Indices: 1802--1826 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1792 CAAACACTAC
1802 CCTAAAA
1 CCTAAAA
1809 CCTAAAA
1 CCTAAAA
1816 CCTAAAA
1 CCTAAAA
1823 CCTA
1 CCTA
1827 CTAAAATCCT
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:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (7 bp):
CCTAAAA
Found at i:5148 original size:26 final size:26
Alignment explanation
Indices: 5095--5153 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
5085 GTAATTTTTA
* * * *
5095 TATTATTTTAATTTAATCCTTTATTT
1 TATTTTTTTAATTTAAGCCTCTAATT
*
5121 TATTTTTTTAATTTTAGCCTCTAATT
1 TATTTTTTTAATTTAAGCCTCTAATT
5147 TATTTTT
1 TATTTTT
5154 AATTTTTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.66
Consensus pattern (26 bp):
TATTTTTTTAATTTAAGCCTCTAATT
Found at i:5323 original size:25 final size:24
Alignment explanation
Indices: 5274--5325 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
5264 TCTATTTCTA
*
5274 TTTGTTTATTTATTTCTTTTCATT
1 TTTGTTTATTTATTTCTTATCATT
*
5298 TTTGTTTTTTTATATTCTTAAT-ATT
1 TTTGTTTATTTAT-TTCTT-ATCATT
5323 TTT
1 TTT
5326 ATATTATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.50
25 11 0.46
26 1 0.04
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTGTTTATTTATTTCTTATCATT
Found at i:5470 original size:3 final size:3
Alignment explanation
Indices: 5464--5523 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
5454 ATGGGTTGAC
5464 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5512 ATT ATT ATT ATT
1 ATT ATT ATT ATT
5524 TCTTTATTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6399 original size:17 final size:16
Alignment explanation
Indices: 6368--6401 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6358 AAAAAAGATA
*
6368 TAAAATTATTAAATAT
1 TAAAATAATTAAATAT
6384 TAAAATAATATAAATAT
1 TAAAATAAT-TAAATAT
6401 T
1 T
6402 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATAATTAAATAT
Found at i:8607 original size:80 final size:80
Alignment explanation
Indices: 8498--8714 Score: 326
Period size: 80 Copynumber: 2.7 Consensus size: 80
8488 ATGGCACCCG
* * ** * ** *
8498 GTGCCTAACGGATAAACCGTGATAGGTGAGCCCAGCTCTAGTTGGATTAACCAACAAAGTCTGTT
1 GTGCCTAGCAGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGATTAACCAACAAAGTCCATC
8563 AATTCCTGACACCTA
66 AATTCCTGACACCTA
*
8578 GTGCCTAGCAGATAAACCGCAATATGTGAGCCCAGCTCTAGTTGGATTAACCAACAAAGTCCATC
1 GTGCCTAGCAGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGATTAACCAACAAAGTCCATC
*
8643 AATTCCTGGCACCTA
66 AATTCCTGACACCTA
* *
8658 GTGCCTAGCAGATAAACCGCAATAAGTGAGCCTAGCTCTAGTTGGATTAAGCAACAA
1 GTGCCTAGCAGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGATTAACCAACAA
8715 TTTTGCGTCC
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 125 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (80 bp):
GTGCCTAGCAGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGATTAACCAACAAAGTCCATC
AATTCCTGACACCTA
Found at i:10305 original size:82 final size:82
Alignment explanation
Indices: 10195--10367 Score: 294
Period size: 82 Copynumber: 2.1 Consensus size: 82
10185 AAGTAGTTCG
* * *
10195 ACCAAAGCT-AAAATGACCACAAAAATATAATGATCAATAAAAATGGAGCTCAAAACACCTACCA
1 ACCAAACCTCAAAATGACCACAAAAATATAAAGATCAATAAAAATAGAGCTCAAAACACCTACCA
10259 TGCAAGGGTTTAGCTCA
66 TGCAAGGGTTTAGCTCA
* *
10276 ACCAAACCTCAAAATGACCACAAATATATAAAGATCAATAAAAATAGAGCTCAAAACACGTACCA
1 ACCAAACCTCAAAATGACCACAAAAATATAAAGATCAATAAAAATAGAGCTCAAAACACCTACCA
10341 TGCAAGGGTTTAGCTCA
66 TGCAAGGGTTTAGCTCA
10358 ACCAAACCTC
1 ACCAAACCTC
10368 CTCTCCCTCT
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
81 8 0.09
82 78 0.91
ACGTcount: A:0.47, C:0.23, G:0.12, T:0.18
Consensus pattern (82 bp):
ACCAAACCTCAAAATGACCACAAAAATATAAAGATCAATAAAAATAGAGCTCAAAACACCTACCA
TGCAAGGGTTTAGCTCA
Found at i:11845 original size:15 final size:15
Alignment explanation
Indices: 11825--11854 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11815 TCTATTAACC
11825 ATTTTTCATTCTGTT
1 ATTTTTCATTCTGTT
11840 ATTTTTCATTCTGTT
1 ATTTTTCATTCTGTT
11855 TTCACAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (15 bp):
ATTTTTCATTCTGTT
Found at i:12001 original size:43 final size:43
Alignment explanation
Indices: 11954--12038 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
11944 TCCTAGCGGC
11954 GTTTGTGAAAAAAGCGCCGCTAAAGATCATGTTCTATAGCGAG
1 GTTTGTGAAAAAAGCGCCGCTAAAGATCATGTTCTATAGCGAG
** *
11997 GTTTGTGGGAAAAGCGCCGCTAATGATCATGTTCTATAGCGA
1 GTTTGTGAAAAAAGCGCCGCTAAAGATCATGTTCTATAGCGA
12039 CATTTTCCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (43 bp):
GTTTGTGAAAAAAGCGCCGCTAAAGATCATGTTCTATAGCGAG
Found at i:14111 original size:16 final size:17
Alignment explanation
Indices: 14083--14132 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
14073 AAAATAAATC
14083 TAAAAA-ATAAAAAAAA
1 TAAAAACATAAAAAAAA
* * *
14099 TATAAA-TTAAAAAAGA
1 TAAAAACATAAAAAAAA
14115 TAAAAACATAAAAAAAA
1 TAAAAACATAAAAAAAA
14132 T
1 T
14133 TCTCCCTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (17 bp):
TAAAAACATAAAAAAAA
Found at i:14119 original size:24 final size:23
Alignment explanation
Indices: 14072--14126 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
14062 AAAAATATTC
*
14072 AAAAATAAATCTAAAAAATAAAA
1 AAAAATAAATCTAAAAAAGAAAA
*
14095 AAAATATAAAT-TAAAAAAGATAA
1 AAAA-ATAAATCTAAAAAAGAAAA
*
14118 AAACATAAA
1 AAAAATAAA
14127 AAAAATTCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.18
23 17 0.61
24 6 0.21
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAATAAATCTAAAAAAGAAAA
Found at i:14370 original size:30 final size:28
Alignment explanation
Indices: 14336--14398 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 28
14326 TTTTTACCTT
14336 ATTTTTATG-ATTATTTTTAATGATTTTTGA
1 ATTTTTATGAATT-TTTTTAAT-ATTTTT-A
14366 ATTTTTATGAATTTTTTTAATATTTTTA
1 ATTTTTATGAATTTTTTTAATATTTTTA
14394 ATTTT
1 ATTTT
14399 ATAATGGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 6 0.19
29 6 0.19
30 17 0.53
31 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (28 bp):
ATTTTTATGAATTTTTTTAATATTTTTA
Found at i:14396 original size:18 final size:18
Alignment explanation
Indices: 14336--14398 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
14326 TTTTTACCTT
*
14336 ATTTTTATGATTATTTTTA
1 ATTTTT-TGAATATTTTTA
14355 ATGATTTTTGAAT-TTTTATGA
1 AT--TTTTTGAATATTTT-T-A
*
14376 ATTTTTTTAATATTTTTA
1 ATTTTTTGAATATTTTTA
14394 ATTTT
1 ATTTT
14399 ATAATGGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
18 6 0.16
19 15 0.41
20 9 0.24
21 7 0.19
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
ATTTTTTGAATATTTTTA
Found at i:14469 original size:16 final size:15
Alignment explanation
Indices: 14442--14486 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
14432 CATTAATAAA
14442 TTATTTTCTCTTTTT
1 TTATTTTCTCTTTTT
14457 TTATTTATCTC--TTT
1 TTATTT-TCTCTTTTT
14471 TTATTTTCT-TTTTT
1 TTATTTTCTCTTTTT
14485 TT
1 TT
14487 TTTCATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.11
14 14 0.52
15 6 0.22
16 4 0.15
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTTCTCTTTTT
Found at i:14745 original size:10 final size:10
Alignment explanation
Indices: 14732--14772 Score: 82
Period size: 10 Copynumber: 4.1 Consensus size: 10
14722 GTTAACTTAT
14732 TCTAACTCAG
1 TCTAACTCAG
14742 TCTAACTCAG
1 TCTAACTCAG
14752 TCTAACTCAG
1 TCTAACTCAG
14762 TCTAACTCAG
1 TCTAACTCAG
14772 T
1 T
14773 TAGCTCACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (10 bp):
TCTAACTCAG
Found at i:16651 original size:22 final size:22
Alignment explanation
Indices: 16626--16668 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16616 TTAAAATCCA
*
16626 ATTTTATTTATTTTAT-ATTTTT
1 ATTTTACTTA-TTTATCATTTTT
16648 ATTTTACTTATTTATCATTTT
1 ATTTTACTTATTTATCATTTT
16669 AAAAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (22 bp):
ATTTTACTTATTTATCATTTTT
Found at i:17533 original size:30 final size:30
Alignment explanation
Indices: 17460--17733 Score: 171
Period size: 30 Copynumber: 9.3 Consensus size: 30
17450 AAAATTATTG
* **
17460 TTTGA-CCCCTAACTTTCCAAAAATTCTTA
1 TTTGACCCCCAAACTTTCCAAAAATTCAAA
* * * *
17489 TTTTACCTCTAAACTTTCTAAAAATTCAAA
1 TTTGACCCCCAAACTTTCCAAAAATTCAAA
* * *
17519 TTTGACCCCCAAACTTTCTATAAATTTAAA
1 TTTGACCCCCAAACTTTCCAAAAATTCAAA
* * **
17549 GTTGACCCCTAAACTTT-CAAAAATTTGAA
1 TTTGACCCCCAAACTTTCCAAAAATTCAAA
* * * * *
17578 TTTAACCACCAAACTTTCCATAAGTTCCAA
1 TTTGACCCCCAAACTTTCCAAAAATTCAAA
*** *
17608 TTTGACCCTTGAAC-TTCCAAAAATCCAAA
1 TTTGACCCCCAAACTTTCCAAAAATTCAAA
* * **
17637 TGTGA-CCCTAAACTTTCCAAAAATTTGAA
1 TTTGACCCCCAAACTTTCCAAAAATTCAAA
* * * *
17666 TTTTACCACCAAACTTTCCATATATTCCAAA
1 TTTGACCCCCAAACTTTCCAAAAATT-CAAA
*** * *
17697 -TTGACCCTTGAACTATCCAAAAATCCAAA
1 TTTGACCCCCAAACTTTCCAAAAATTCAAA
*
17726 TGTGACCC
1 TTTGACCC
17734 GGTTTTAATG
Statistics
Matches: 181, Mismatches: 58, Indels: 11
0.72 0.23 0.04
Matches are distributed among these distances:
28 6 0.03
29 60 0.33
30 113 0.62
31 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.32
Consensus pattern (30 bp):
TTTGACCCCCAAACTTTCCAAAAATTCAAA
Found at i:17571 original size:59 final size:59
Alignment explanation
Indices: 17497--17662 Score: 172
Period size: 59 Copynumber: 2.8 Consensus size: 59
17487 TATTTTACCT
*
17497 CTAAACTTTCTAAAAATTCAAATTTGACCCCCAAACTTTCTATAAATTTAAAGTTGACCC
1 CTAAACTTTC-AAAAATTCAAATTTGACCCCCAAACTTTCCATAAATTTAAAGTTGACCC
** * * * ** *
17557 CTAAACTTTCAAAAATTTGAATTTAACCACCAAACTTTCCATAAGTTCCAATTTGACCC
1 CTAAACTTTCAAAAATTCAAATTTGACCCCCAAACTTTCCATAAATTTAAAGTTGACCC
* * * * * * *
17616 TTGAACTTCCAAAAATCCAAATGTGA-CCCTAAACTTTCCAAAAATTT
1 CTAAACTTTCAAAAATTCAAATTTGACCCCCAAACTTTCCATAAATTT
17663 GAATTTTACC
Statistics
Matches: 84, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
58 16 0.19
59 58 0.69
60 10 0.12
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (59 bp):
CTAAACTTTCAAAAATTCAAATTTGACCCCCAAACTTTCCATAAATTTAAAGTTGACCC
Found at i:17674 original size:88 final size:88
Alignment explanation
Indices: 17555--17733 Score: 308
Period size: 88 Copynumber: 2.0 Consensus size: 88
17545 TAAAGTTGAC
*
17555 CCCTAAACTTTCAAAAATTTGAATTTAACCACCAAACTTTCCATA-AGTTCCAATTTGACCCTTG
1 CCCTAAACTTTCAAAAATTTGAATTTAACCACCAAACTTTCCATATA-TTCCAAATTGACCCTTG
17619 AACT-TCCAAAAATCCAAATGTGA
65 AACTATCCAAAAATCCAAATGTGA
*
17642 CCCTAAACTTTCCAAAAATTTGAATTTTACCACCAAACTTTCCATATATTCCAAATTGACCCTTG
1 CCCTAAACTTT-CAAAAATTTGAATTTAACCACCAAACTTTCCATATATTCCAAATTGACCCTTG
17707 AACTATCCAAAAATCCAAATGTGA
65 AACTATCCAAAAATCCAAATGTGA
17731 CCC
1 CCC
17734 GGTTTTAATG
Statistics
Matches: 87, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
87 11 0.13
88 53 0.61
89 23 0.26
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (88 bp):
CCCTAAACTTTCAAAAATTTGAATTTAACCACCAAACTTTCCATATATTCCAAATTGACCCTTGA
ACTATCCAAAAATCCAAATGTGA
Found at i:18656 original size:17 final size:17
Alignment explanation
Indices: 18634--18667 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18624 CCTTACCTTG
18634 TACAAAAAGATAGTACA
1 TACAAAAAGATAGTACA
18651 TACAAAAAGATAGTACA
1 TACAAAAAGATAGTACA
18668 GATCCAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.18
Consensus pattern (17 bp):
TACAAAAAGATAGTACA
Found at i:18844 original size:7 final size:7
Alignment explanation
Indices: 18834--18859 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18824 GGTGTTTTAG
18834 TTTTTCT
1 TTTTTCT
18841 TTTTTCT
1 TTTTTCT
18848 TTTTTCT
1 TTTTTCT
18855 TTTTT
1 TTTTT
18860 ATAACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:21661 original size:23 final size:23
Alignment explanation
Indices: 21629--21677 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
21619 TATCAAATTT
*
21629 TCATAATCAATCTCATTTTCTTTC
1 TCATAATCAATCTCA-TTTCATTC
*
21653 TCAT-ATCAATTTCATTTCATTC
1 TCATAATCAATCTCATTTCATTC
21675 TCA
1 TCA
21678 CTTCCATCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 9 0.39
24 4 0.17
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.49
Consensus pattern (23 bp):
TCATAATCAATCTCATTTCATTC
Found at i:23698 original size:6 final size:6
Alignment explanation
Indices: 23675--23774 Score: 79
Period size: 6 Copynumber: 17.5 Consensus size: 6
23665 GTATAAATTG
* * *
23675 ATTTAAA ATTTAT TTTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTAT
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA
* * *
23723 CTTT-- -TTTAA ATTTAA ATTT-A CTTTAA ATTTAA ATTT-A ATTAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
23766 ATTTAA ATT
1 ATTTAA ATT
23775 GATTTAAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
3 3 0.04
4 2 0.03
5 10 0.13
6 54 0.72
7 6 0.08
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (6 bp):
ATTTAA
Found at i:23732 original size:38 final size:38
Alignment explanation
Indices: 23687--23759 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
23677 TTAAAATTTA
23687 TTTTTAAATTTAAATTTA-TCTTAAATTTAAATTTATCT
1 TTTTTAAATTTAAATTTACT-TTAAATTTAAATTTATCT
23725 TTTTTAAATTTAAATTTACTTTAAATTTAAATTTA
1 TTTTTAAATTTAAATTTACTTTAAATTTAAATTTA
23760 ATTAAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (38 bp):
TTTTTAAATTTAAATTTACTTTAAATTTAAATTTATCT
Found at i:23762 original size:11 final size:11
Alignment explanation
Indices: 23693--23771 Score: 58
Period size: 11 Copynumber: 7.2 Consensus size: 11
23683 TTTATTTTTA
23693 AATTTAAATTT
1 AATTTAAATTT
23704 -ATCTTAAATTT
1 AAT-TTAAATTT
**
23715 AAATTTATCTTT
1 -AATTTAAATTT
23727 --TTTAAATTT
1 AATTTAAATTT
*
23736 AAATTT-ACTTT
1 -AATTTAAATTT
23747 AAATTTAAATTT
1 -AATTTAAATTT
*
23759 AATTAAAATTT
1 AATTTAAATTT
23770 AA
1 AA
23772 ATTGATTTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
9 7 0.13
10 2 0.04
11 30 0.56
12 13 0.24
13 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:23783 original size:17 final size:16
Alignment explanation
Indices: 23675--23782 Score: 99
Period size: 17 Copynumber: 6.1 Consensus size: 16
23665 GTATAAATTG
23675 ATTTAAAATTTATTTTTAA
1 ATTT-AAATTTA--TTTAA
23694 ATTTAAATTTATCTTAA
1 ATTTAAATTTAT-TTAA
23711 ATTTAAATTTATCTTTTTTAA
1 ATTTAAATTTA-----TTTAA
23732 ATTTAAATTTACTTTAA
1 ATTTAAATTTA-TTTAA
*
23749 ATTTAAATTTAATTAAA
1 ATTTAAATTT-ATTTAA
*
23766 ATTTAAATTGATTTAA
1 ATTTAAATTTATTTAA
23782 A
1 A
23783 AATTAGTATT
Statistics
Matches: 78, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
16 7 0.09
17 43 0.55
18 8 0.10
19 4 0.05
21 15 0.19
22 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.54
Consensus pattern (16 bp):
ATTTAAATTTATTTAA
Found at i:25623 original size:29 final size:28
Alignment explanation
Indices: 25577--26008 Score: 357
Period size: 29 Copynumber: 14.8 Consensus size: 28
25567 ACTTAAATTA
*
25577 TCCAGAAAATTATATTTTTACACCCAAACT
1 TCCA-AAAATTACATTTTTAC-CCCAAACT
* * *
25607 TCCAAAAATTCCATTTTGACCCAAGAACT
1 TCCAAAAATTACATTTTTACCCCA-AACT
*
25636 TTCAAAAATTACATTTTTACCCCTAAACT
1 TCCAAAAATTACATTTTTACCCC-AAACT
25665 TCCAAAAATTACA-TTTTACCCCTAAAACT
1 TCCAAAAATTACATTTTTACCCC--AAACT
** **
25694 TTTAAAAATTACATTTTTACCCTTGAACT
1 TCCAAAAATTACATTTTTACCC-CAAACT
* *
25723 TCCAAAAATTCCATTTTTAACCCTAAAACT
1 TCCAAAAATTACATTTTT-ACCC-CAAACT
*
25753 TTCAAAAATTACATTTTTACCCCCAAACT
1 TCCAAAAATTACATTTTTA-CCCCAAACT
* * **
25782 TCCAAAAATTCCATTTTGACCATGAAACT
1 TCCAAAAATTACATTTTTACC-CCAAACT
* *
25811 T-CAAAAATTACATTTTAACCCTCGAACT
1 TCCAAAAATTACATTTTTACCC-CAAACT
** *
25839 TCCAAAAATTTTATTTTTGACTCCGAAACT
1 TCCAAAAATTACATTTTT-AC-CCCAAACT
* *
25869 TCTAAAACTTACATTTTTACCCTCAAACT
1 TCCAAAAATTACATTTTTACCC-CAAACT
** * *
25898 TTTAAAAATTCCATTTTTAACCCTAAAACT
1 TCCAAAAATTACATTTTT-ACCC-CAAACT
***
25928 TTTGAAAATTACATTTTTACCCCCAAACT
1 TCCAAAAATTACATTTTTA-CCCCAAACT
* * *
25957 TCCAAAAATTCCATTTTGACCTCAAAACT
1 TCCAAAAATTACATTTTTACC-CCAAACT
*
25986 TTCAAAAATTACCA-TTTTACCCC
1 TCCAAAAATTA-CATTTTTACCCC
26009 TGAATGTCCA
Statistics
Matches: 326, Mismatches: 59, Indels: 36
0.77 0.14 0.09
Matches are distributed among these distances:
28 41 0.13
29 191 0.59
30 92 0.28
31 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (28 bp):
TCCAAAAATTACATTTTTACCCCAAACT
Found at i:25672 original size:58 final size:57
Alignment explanation
Indices: 25582--26031 Score: 486
Period size: 58 Copynumber: 7.7 Consensus size: 57
25572 AATTATCCAG
*
25582 AAAATTATATTTTTACACCC-AAACTTCCAAAAATTCCATTTTGACCCAAGAACTTTCA
1 AAAATTACATTTTTAC-CCCTAAACTTCCAAAAATTCCATTTTGACCCAA-AACTTTCA
* *
25640 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTT-ACCCCTAAAACTTTTA
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGA-CCC-AAAACTTTCA
* * *
25698 AAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTAACCCTAAAACTTTCA
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCA-TTTTGACCC-AAAACTTTCA
*
25757 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGA-CCATGAAAC-TTCA
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCCA--AAACTTTCA
* * ** *
25814 AAAATTACA-TTTTAACCCTCGAACTTCCAAAAATTTTATTTTTGACTCCGAAAC-TTCTA
1 AAAATTACATTTTTACCCCT-AAACTTCCAAAAATTCCA-TTTTGAC-CCAAAACTTTC-A
* ** * **
25873 AAACTTACATTTTTA-CCCTCAAACTTTTAAAAATTCCATTTTTAACCCTAAAACTTTTG
1 AAAATTACATTTTTACCCCT-AAACTTCCAAAAATTCCA-TTTTGACCC-AAAACTTTCA
*
25932 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCTCAAAACTTTCA
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGACC-CAAAACTTTCA
* *
25990 AAAATTACCA-TTTTACCCCTGAA-TGTCCAAAAATTCCGTTTT
1 AAAATTA-CATTTTTACCCCTAAACT-TCCAAAAATTCCATTTT
26032 TGATCTTGAT
Statistics
Matches: 336, Mismatches: 37, Indels: 38
0.82 0.09 0.09
Matches are distributed among these distances:
56 9 0.03
57 35 0.10
58 154 0.46
59 125 0.37
60 13 0.04
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (57 bp):
AAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCCAAAACTTTCA
Found at i:25883 original size:175 final size:175
Alignment explanation
Indices: 25582--26129 Score: 625
Period size: 175 Copynumber: 3.1 Consensus size: 175
25572 AATTATCCAG
* * *
25582 AAAATTATATTTTTACACCCAAACTTCCAAAAATTCCATTTTGACCCAAG-AACTTTCAAAAATT
1 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGA-CCATGAAACTTTCAAAAATT
* * * * * *
25646 ACATTTTTACCC-CTAAACTTCCAAAAATTACA-TTTT-ACCCCTAAAACTTTTAAAAATTACAT
65 ACATTTTAACCCTC-GAACTTCCAAAAATTACATTTTTGACTCC-GAAACTTCTAAAACTTACAT
*
25708 TTTTACCCTTGAACTTCCAAAAATTCCATTTTTAACCCTAAAACTTTCA
128 TTTTACCCTCGAACTT-CAAAAATTCCATTTTTAACCCTAAAACTTTCA
25757 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCATGAAAC-TTCAAAAATTA
1 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCATGAAACTTTCAAAAATTA
**
25821 CATTTTAACCCTCGAACTTCCAAAAATTTTATTTTTGACTCCGAAACTTCTAAAACTTACATTTT
66 CATTTTAACCCTCGAACTTCCAAAAATTACATTTTTGACTCCGAAACTTCTAAAACTTACATTTT
* * **
25886 TACCCTCAAACTTTTAAAAATTCCATTTTTAACCCTAAAACTTTTG
131 TACCCTCGAAC-TTCAAAAATTCCATTTTTAACCCTAAAACTTTCA
*
25932 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACC-TCAAAACTTTCAAAAATT
1 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCAT-GAAACTTTCAAAAATT
* * * * ***
25996 ACCATTTTACCCCT-GAA-TGTCCAAAAATTCCGTTTTTGA-TCTTGATTTTTCTAAAACTTATC
65 A-CATTTTAACCCTCGAACT-TCCAAAAATTACATTTTTGACTC-CGAAACTTCTAAAACTTA-C
* * * * *
26058 ATTTTT-CCCTCGGA-TGTCTAAAATTCCATTTTTAACCCCAAAATTTTCCT
126 ATTTTTACCCTCGAACT-TCAAAAATTCCATTTTTAACCCTAAAACTTT-CA
*
26108 AAAATTAC-TATTTTGCCCCCAA
1 AAAATTACAT-TTTTACCCCCAA
26130 GAGTCCAAAA
Statistics
Matches: 325, Mismatches: 34, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
174 42 0.13
175 189 0.58
176 76 0.23
177 18 0.06
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (175 bp):
AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCATGAAACTTTCAAAAATTA
CATTTTAACCCTCGAACTTCCAAAAATTACATTTTTGACTCCGAAACTTCTAAAACTTACATTTT
TACCCTCGAACTTCAAAAATTCCATTTTTAACCCTAAAACTTTCA
Found at i:29757 original size:21 final size:21
Alignment explanation
Indices: 29711--29758 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
29701 TTTGGTTTTA
*
29711 CACCCGTGTACCACCAGGTTC
1 CACCGGTGTACCACCAGGTTC
29732 CACCGGTGTACCACCAGGTTC
1 CACCGGTGTACCACCAGGTTC
29753 CACCGG
1 CACCGG
29759 AAACAAACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.17
Consensus pattern (21 bp):
CACCGGTGTACCACCAGGTTC
Found at i:37729 original size:50 final size:49
Alignment explanation
Indices: 37599--37831 Score: 152
Period size: 50 Copynumber: 4.7 Consensus size: 49
37589 TAACATCGTG
* * * *
37599 AAACACGACAGGAAAGATCTAAGACCGCAACGACCGAATCC-AGTACCGT-A
1 AAACACGACGGGAAAGATCTAAGACCGCAACG-GCGGA-CCGTGTACC-TCA
* * * * *
37649 AAGATACAAAAGGGAAAGGTCTAAG-TCGCAACGGCGGACCGTGTACCTCA
1 AA-ACAC-GACGGGAAAGATCTAAGACCGCAACGGCGGACCGTGTACCTCA
* * ** *
37699 GAAACACGACGGGAAAGATTTAAGACCGCAACGACGGATCC-AATACCGCA
1 -AAACACGACGGGAAAGATCTAAGACCGCAACGGCGGA-CCGTGTACCTCA
* * * * *
37749 AAGATACAAAAGGGAAAGGTCTAAG-TCGCAACGGCGGACCGTGTACCTCAA
1 AA-ACAC-GACGGGAAAGATCTAAGACCGCAACGGCGGACCGTGTACCTC-A
* *
37800 AAACACGACGAGAAAGATCTAAGACCGTAACG
1 AAACACGACGGGAAAGATCTAAGACCGCAACG
37832 ACAGATCCAA
Statistics
Matches: 135, Mismatches: 36, Indels: 24
0.69 0.18 0.12
Matches are distributed among these distances:
49 33 0.24
50 59 0.44
51 30 0.22
52 13 0.10
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (49 bp):
AAACACGACGGGAAAGATCTAAGACCGCAACGGCGGACCGTGTACCTCA
Found at i:37772 original size:100 final size:100
Alignment explanation
Indices: 37598--37884 Score: 457
Period size: 100 Copynumber: 2.9 Consensus size: 100
37588 TTAACATCGT
* * * *
37598 GAAACACGACAGGAAAGATCTAAGACCGCAACGACCGAATCCAGTACCGTAAAGATACAAAAGGG
1 GAAACACGACGGGAAAGATCTAAGACCGCAACGA-CGGATCCAATACCGCAAAGATACAAAAGGG
37663 AAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA
65 AAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA
*
37699 GAAACACGACGGGAAAGATTTAAGACCGCAACGACGGATCCAATACCGCAAAGATACAAAAGGGA
1 GAAACACGACGGGAAAGATCTAAGACCGCAACGACGGATCCAATACCGCAAAGATACAAAAGGGA
37764 AAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA
66 AAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA
* * * *
37799 AAAACACGACGAGAAAGATCTAAGACCGTAACGACAGATCCAATACCGCAAAGATACAAAAGGGA
1 GAAACACGACGGGAAAGATCTAAGACCGCAACGACGGATCCAATACCGCAAAGATACAAAAGGGA
* * *
37864 AAGGTTTAAGTCACAATGGCG
66 AAGGTCTAAGTCGCAACGGCG
37885 AACCTTATAC
Statistics
Matches: 173, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
100 141 0.82
101 32 0.18
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.12
Consensus pattern (100 bp):
GAAACACGACGGGAAAGATCTAAGACCGCAACGACGGATCCAATACCGCAAAGATACAAAAGGGA
AAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA
Found at i:37821 original size:49 final size:49
Alignment explanation
Indices: 37660--37822 Score: 168
Period size: 50 Copynumber: 3.3 Consensus size: 49
37650 AGATACAAAA
* *
37660 GGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAACACGAC
1 GGGAAAGATCTAAGTCGCAACGGCGGACCGTGTACCTCAAAAACACGAC
* * * ** * * *
37709 GGGAAAGATTTAAGACCGCAACGACGGATCC-AATACCGCAAAGATACA-AAA
1 GGGAAAGATCTAAG-TCGCAACGGCGGA-CCGTGTACCTCAAA-A-ACACGAC
*
37760 GGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAAAAACACGAC
1 GGGAAAGATCTAAGTCGCAACGGCGGACCGTGTACCTCAAAAACACGAC
*
37809 GAGAAAGATCTAAG
1 GGGAAAGATCTAAG
37823 ACCGTAACGA
Statistics
Matches: 87, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
48 3 0.03
49 28 0.32
50 37 0.43
51 16 0.18
52 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.27, T:0.12
Consensus pattern (49 bp):
GGGAAAGATCTAAGTCGCAACGGCGGACCGTGTACCTCAAAAACACGAC
Found at i:38371 original size:6 final size:6
Alignment explanation
Indices: 38349--38404 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
38339 GTTTAAATTG
* * *
38349 ATTTAA ATTTAT TTTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTAT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA
*
38396 CTTTAA ATT
1 ATTTAA ATT
38405 GATTTAAAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
6 33 0.85
7 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (6 bp):
ATTTAA
Found at i:38385 original size:17 final size:17
Alignment explanation
Indices: 38349--38404 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
38339 GTTTAAATTG
*
38349 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA-TCTTAA
38367 ATTTAAATTTATCTTAA
1 ATTTAAATTTATCTTAA
38384 ATTTAAATTTATCTTTAA
1 ATTTAAATTTATC-TTAA
38402 ATT
1 ATT
38405 GATTTAAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
17 18 0.50
18 18 0.50
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTAAATTTATCTTAA
Found at i:38394 original size:29 final size:28
Alignment explanation
Indices: 38340--38412 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 28
38330 TAAGATTGGG
**
38340 TTTAAATTGATTTAAATTTATTTTTAAA
1 TTTAAATTGATTTAAATTTAAATTTAAA
* **
38368 TTTAAATTTATCTTAAATTTAAATTTATC
1 TTTAAATTGAT-TTAAATTTAAATTTAAA
38397 TTTAAATTGATTTAAA
1 TTTAAATTGATTTAAA
38413 ACTTAGTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 15 0.39
29 23 0.61
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (28 bp):
TTTAAATTGATTTAAATTTAAATTTAAA
Found at i:39546 original size:29 final size:29
Alignment explanation
Indices: 39504--39868 Score: 292
Period size: 29 Copynumber: 12.7 Consensus size: 29
39494 AAATTGTCCA
* *
39504 AAAAATTACATTTTTACCCTTAAACTTCA
1 AAAAATTACATTTTTACCCTCAAACTTCT
*
39533 AAAAATT-CCTTTTTGA-CCTCGAAACTT-T
1 AAAAATTACATTTTT-ACCCTC-AAACTTCT
**
39561 TGAAATTACATTTTTACCCT-AAACTTCT
1 AAAAATTACATTTTTACCCTCAAACTTCT
* * *
39589 AAAAATTCCATTTTAACCCTAAAACTTCT
1 AAAAATTACATTTTTACCCTCAAACTTCT
*
39618 AAAAATTACATTTTTA-CCTCGAACTT-T
1 AAAAATTACATTTTTACCCTCAAACTTCT
* * * *
39645 CAAAAATTCCATTTTAACTC-CAAACTTTT
1 -AAAAATTACATTTTTACCCTCAAACTTCT
* *
39674 GAAAATTACATTTTTA-CCTCCGAAA-TTCC
1 AAAAATTACATTTTTACCCT-C-AAACTTCT
* * *
39703 AAAAATTCCATTTTTGATCCC-GAAACTTTT
1 AAAAATTACATTTTT-A-CCCTCAAACTTCT
* * * *
39733 GAAAATTACA-TTTTACCGTCGAACTTCC
1 AAAAATTACATTTTTACCCTCAAACTTCT
*
39761 AAAAATTCCATTTTTAACCC-CAAAACTTCT
1 AAAAATTACATTTTT-ACCCTC-AAACTTCT
39791 AAAAATTACATTTTTACCCTCAAACTTCT
1 AAAAATTACATTTTTACCCTCAAACTTCT
*
39820 AAAAATTCCATTTTTGA-CCTCGAAACGTTC-
1 AAAAATTACATTTTT-ACCCTC-AAAC-TTCT
39850 AAAAATTACCA-TTTTACCC
1 AAAAATTA-CATTTTTACCC
39869 CCGGATGTCC
Statistics
Matches: 266, Mismatches: 44, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
27 10 0.04
28 87 0.33
29 106 0.40
30 56 0.21
31 5 0.02
32 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCTCAAACTTCT
Found at i:39964 original size:59 final size:59
Alignment explanation
Indices: 39504--39986 Score: 392
Period size: 59 Copynumber: 8.3 Consensus size: 59
39494 AAATTGTCCA
** * * *
39504 AAAAATTACATTTTTACCCTTAAACTTCAAAAAATTCC-TTTTTGACCTCGAAACTTT-T
1 AAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACC-CCAAACTTTCT
* * * *
39562 -GAAATTACATTTTTACCCT-AAACTTCTAAAAATTCCA-TTTTAACCCTAAAAC-TTCT
1 AAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCC-CAAACTTTCT
* *
39618 AAAAATTACATTTTTA-CCTCGAACTTTCAAAAATTCCA-TTTTAACTCCAAACTTT-T
1 AAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCAAACTTTCT
* * * *
39674 GAAAATTACATTTTTA-CCTCCGAAATTCCAAAAATTCCATTTTTGATCCCGAAACTTT-T
1 AAAAATTACATTTTTACCCT-CGAACTTCCAAAAATTCCATTTTT-AACCCCAAACTTTCT
* *
39733 GAAAATTACA-TTTTACCGTCGAACTTCCAAAAATTCCATTTTTAACCCCAAAAC-TTCT
1 AAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCC-AAACTTTCT
* * * * *
39791 AAAAATTACATTTTTACCCTCAAACTTCTAAAAATTCCATTTTTGACCTCGAAACGTTC-
1 AAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACC-CCAAACTTTCT
* * * * * *** **
39850 AAAAATTACCA-TTTTACCCCCGGA-TGTCCAAAAATTCCGTTTTTGATCTTGATTTTTCT
1 AAAAATTA-CATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTAACCCCAAACTTTCT
* ** * *
39909 AAAAATTTCCGTTTTACCCTCGAA-TGTCC-AAAATTCCATTTTTAACCCCAAATTTTTT
1 AAAAATTACATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTAACCCCAAACTTTCT
*
39967 CCAAAATTACCA-TTTTACCC
1 -AAAAATTA-CATTTTTACCC
39987 CTAAGAGTCC
Statistics
Matches: 351, Mismatches: 53, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
55 3 0.01
56 54 0.15
57 80 0.23
58 73 0.21
59 134 0.38
60 7 0.02
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.37
Consensus pattern (59 bp):
AAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCAAACTTTCT
Found at i:41443 original size:3 final size:3
Alignment explanation
Indices: 41435--41465 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
41425 TGAATGTTTA
41435 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41466 TATTTGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Done.