Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013029.1 Kokia drynarioides strain JFW-HI SEQ_128047, 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: 29596
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:3090 original size:14 final size:14
Alignment explanation
Indices: 3071--3104 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3061 AATAAAAGGG
3071 AAAAAAATTAAATC
1 AAAAAAATTAAATC
*
3085 AAAAAAATTAAATT
1 AAAAAAATTAAATC
3099 AAAAAA
1 AAAAAA
3105 GCAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAAAATTAAATC
Found at i:3122 original size:18 final size:18
Alignment explanation
Indices: 3101--3158 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
3091 ATTAAATTAA
3101 AAAAGCAAATAATAAAAT
1 AAAAGCAAATAATAAAAT
**
3119 AAAAATAAATAATAAAA-
1 AAAAGCAAATAATAAAAT
**
3136 AATGGCTAAATAATAGAAAT
1 AAAAGC-AAATAATA-AAAT
3156 AAA
1 AAA
3159 GTTTTCCTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 2 0.07
18 23 0.77
19 3 0.10
20 2 0.07
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (18 bp):
AAAAGCAAATAATAAAAT
Found at i:3794 original size:15 final size:15
Alignment explanation
Indices: 3774--3812 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
3764 GCACATCAAA
*
3774 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
3789 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
3803 CAAGAATTAA
1 CAAGAATTAA
3813 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:9176 original size:16 final size:17
Alignment explanation
Indices: 9135--9170 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
9125 GAGTTAGAAC
9135 ATTTAGAATTATATTTA
1 ATTTAGAATTATATTTA
9152 A-TTAGAATTA-ATTTA
1 ATTTAGAATTATATTTA
9167 ATTT
1 ATTT
9171 TAAATTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.33
16 11 0.61
17 1 0.06
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTTAGAATTATATTTA
Found at i:11700 original size:82 final size:82
Alignment explanation
Indices: 11556--11707 Score: 205
Period size: 82 Copynumber: 1.9 Consensus size: 82
11546 ACTAATTTCA
* * **
11556 TTTTAACTCTTGTAGGGAAGCCAATGAGTTATGTCTATTCATTAGGATCTAAAGTAGTTGAAAAG
1 TTTTAACTCTTATAGGGAAGCCAATGAGTCATGTCTATTCATTAGGATCTAAAGTAACTGAAAAG
11621 ACATGACAATTTCATTT
66 ACATGACAATTTCATTT
* * * * * *
11638 TTTTAACTCTTATAGTGAAGCTAATTAGTCATGTCTCTTCATTAGGATCTGATGTAACTGAAAAG
1 TTTTAACTCTTATAGGGAAGCCAATGAGTCATGTCTATTCATTAGGATCTAAAGTAACTGAAAAG
*
11703 GCATG
66 ACATG
11708 TCATTTCTCC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
82 59 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (82 bp):
TTTTAACTCTTATAGGGAAGCCAATGAGTCATGTCTATTCATTAGGATCTAAAGTAACTGAAAAG
ACATGACAATTTCATTT
Found at i:12269 original size:96 final size:96
Alignment explanation
Indices: 12159--12333 Score: 305
Period size: 96 Copynumber: 1.8 Consensus size: 96
12149 CATTGAGCAG
* *
12159 AGATGCATTTAACAAACAAAACATTTAATAATGCAGATTACTAAATAAAGATGCATTTAACAAAC
1 AGATGCATTAAACAAACAAAACATTTAATAATGCAGATTACTAAACAAAGATGCATTTAACAAAC
12224 AAAACACTTAATGATTTAGATTATTAATCAA
66 AAAACACTTAATGATTTAGATTATTAATCAA
* *
12255 AGATGCATTAAACAAACAAAACATTTAATGATGCAGATTATTAAACAAAGATGCATTTAACAAAC
1 AGATGCATTAAACAAACAAAACATTTAATAATGCAGATTACTAAACAAAGATGCATTTAACAAAC
*
12320 AATACACTTAATGA
66 AAAACACTTAATGA
12334 AGCATAATTA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 74 1.00
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.27
Consensus pattern (96 bp):
AGATGCATTAAACAAACAAAACATTTAATAATGCAGATTACTAAACAAAGATGCATTTAACAAAC
AAAACACTTAATGATTTAGATTATTAATCAA
Found at i:12332 original size:48 final size:48
Alignment explanation
Indices: 12159--12333 Score: 260
Period size: 48 Copynumber: 3.6 Consensus size: 48
12149 CATTGAGCAG
* * * *
12159 AGATGCATTTAACAAACAAAACATTTAATAATGCAGATTACTAAATAA
1 AGATGCATTTAACAAACAAAACACTTAATGATGCAGATTATTAAACAA
** *
12207 AGATGCATTTAACAAACAAAACACTTAATGATTTAGATTATTAATCAA
1 AGATGCATTTAACAAACAAAACACTTAATGATGCAGATTATTAAACAA
* *
12255 AGATGCATTAAACAAACAAAACATTTAATGATGCAGATTATTAAACAA
1 AGATGCATTTAACAAACAAAACACTTAATGATGCAGATTATTAAACAA
*
12303 AGATGCATTTAACAAACAATACACTTAATGA
1 AGATGCATTTAACAAACAAAACACTTAATGA
12334 AGCATAATTA
Statistics
Matches: 112, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 112 1.00
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.27
Consensus pattern (48 bp):
AGATGCATTTAACAAACAAAACACTTAATGATGCAGATTATTAAACAA
Found at i:15292 original size:29 final size:28
Alignment explanation
Indices: 15244--15313 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
15234 CCGTTTTACA
*
15244 AATTTTATAGTTATGCCACTATTTTTCAT
1 AATTTTATAGTTATGCCACTAGTTTTC-T
*
15273 AATTTTATAGCTT-TGTCACTAGTTTTCT
1 AATTTTATAG-TTATGCCACTAGTTTTCT
*
15301 ATATTTTACAGTT
1 A-ATTTTATAGTT
15314 CAGGTACTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.11
29 30 0.83
30 2 0.06
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.53
Consensus pattern (28 bp):
AATTTTATAGTTATGCCACTAGTTTTCT
Found at i:15385 original size:41 final size:39
Alignment explanation
Indices: 15322--15407 Score: 91
Period size: 40 Copynumber: 2.2 Consensus size: 39
15312 TTCAGGTACT
* * *
15322 ATTTTTTTCAGATTTTAGAGTTTCGTCACTGGTTTTCCAA
1 ATTTTTTACAGATTTTACAGTTTCGCCA-TGGTTTTCCAA
* * *
15362 ATTTTTTACAGTTCTTTACAGTTTTGCCATTGTTTTCCAA
1 ATTTTTTACAGAT-TTTACAGTTTCGCCATGGTTTTCCAA
*
15402 AATTTT
1 ATTTTT
15408 ACATTGCCAC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 26 0.68
41 12 0.32
ACGTcount: A:0.21, C:0.15, G:0.12, T:0.52
Consensus pattern (39 bp):
ATTTTTTACAGATTTTACAGTTTCGCCATGGTTTTCCAA
Found at i:15516 original size:28 final size:28
Alignment explanation
Indices: 15485--15547 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
15475 TGGTTTTTCA
15485 AACTATTTTTCAAAATTTACAATTTTGC
1 AACTATTTTTCAAAATTTACAATTTTGC
* * * *
15513 AACTATTTTTTAGATTTTACAGTTTTGC
1 AACTATTTTTCAAAATTTACAATTTTGC
*
15541 CACTATT
1 AACTATT
15548 CTTAAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.49
Consensus pattern (28 bp):
AACTATTTTTCAAAATTTACAATTTTGC
Found at i:16023 original size:31 final size:32
Alignment explanation
Indices: 15988--16059 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 32
15978 GAATGATATC
*
15988 ATGATCATTTATAAAATATGATTGCTT-AGGA
1 ATGATCATTAATAAAATATGATTGCTTAAGGA
* * * * *
16019 ATGATTATCAATGATATATGTTTGCTTAAGGA
1 ATGATCATTAATAAAATATGATTGCTTAAGGA
*
16051 ATGACCATT
1 ATGATCATT
16060 CTAATTCATG
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (32 bp):
ATGATCATTAATAAAATATGATTGCTTAAGGA
Found at i:16572 original size:56 final size:57
Alignment explanation
Indices: 16506--16635 Score: 192
Period size: 56 Copynumber: 2.3 Consensus size: 57
16496 CAGATTTTAT
*
16506 AGTTTTGCCATTGGTTTTCTAGATTTTACAGTTCTACCATTATTTT-CAAAAATTAC
1 AGTTTTGCCATTGGTTTTCCAGATTTTACAGTTCTACCATTATTTTCCAAAAATTAC
* * * **
16562 AGTTTTGCCATTAGCTTTCCAGATTTTACAGTTCTACCATTATTTTCCAGATTTTAC
1 AGTTTTGCCATTGGTTTTCCAGATTTTACAGTTCTACCATTATTTTCCAAAAATTAC
16619 AGTTTTGCCA-TGGTTTT
1 AGTTTTGCCATTGGTTTT
16636 TCAAAATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
56 48 0.74
57 17 0.26
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (57 bp):
AGTTTTGCCATTGGTTTTCCAGATTTTACAGTTCTACCATTATTTTCCAAAAATTAC
Found at i:16629 original size:28 final size:28
Alignment explanation
Indices: 16491--16629 Score: 145
Period size: 29 Copynumber: 4.9 Consensus size: 28
16481 TAAGTATTTT
* * *
16491 TTTTTCAGATTTTATAGTTTTGCCATTGG
1 TTTTCCAGATTTTACAGTTTTGCCATT-A
* * *
16520 TTTTCTAGATTTTACAGTTCTACCATTA
1 TTTTCCAGATTTTACAGTTTTGCCATTA
* **
16548 TTTT-CAAAAATTACAGTTTTGCCATTA
1 TTTTCCAGATTTTACAGTTTTGCCATTA
* * *
16575 GCTTTCCAGATTTTACAGTTCTACCATTA
1 -TTTTCCAGATTTTACAGTTTTGCCATTA
16604 TTTTCCAGATTTTACAGTTTTGCCAT
1 TTTTCCAGATTTTACAGTTTTGCCAT
16630 GGTTTTTCAA
Statistics
Matches: 87, Mismatches: 21, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
27 17 0.20
28 30 0.34
29 40 0.46
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (28 bp):
TTTTCCAGATTTTACAGTTTTGCCATTA
Found at i:16635 original size:28 final size:28
Alignment explanation
Indices: 16491--16635 Score: 121
Period size: 28 Copynumber: 5.1 Consensus size: 28
16481 TAAGTATTTT
* *
16491 TTTTTCAGATTTTATAGTTTTGCCATTGG
1 TTTTCCAGATTTTACAGTTTTGCCA-TGG
* * * **
16520 TTTTCTAGATTTTACAGTTCTACCATTA
1 TTTTCCAGATTTTACAGTTTTGCCATGG
* ** *
16548 TTTT-CAAAAATTACAGTTTTGCCATTAG
1 TTTTCCAGATTTTACAGTTTTGCCA-TGG
* * * **
16576 CTTTCCAGATTTTACAGTTCTACCATTA
1 TTTTCCAGATTTTACAGTTTTGCCATGG
16604 TTTTCCAGATTTTACAGTTTTGCCATGG
1 TTTTCCAGATTTTACAGTTTTGCCATGG
16632 TTTT
1 TTTT
16636 TCAAAATTTT
Statistics
Matches: 86, Mismatches: 28, Indels: 5
0.72 0.24 0.04
Matches are distributed among these distances:
27 14 0.16
28 37 0.43
29 35 0.41
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.49
Consensus pattern (28 bp):
TTTTCCAGATTTTACAGTTTTGCCATGG
Found at i:16656 original size:85 final size:85
Alignment explanation
Indices: 16496--16676 Score: 186
Period size: 85 Copynumber: 2.1 Consensus size: 85
16486 ATTTTTTTTT
* * * * *
16496 CAGATTTTATAGTTTTGCCATTGGTTTTCTAGATTTTACAGTTCTACCATTATTTTCAAAAATTA
1 CAGATTTTACAGTTCTACCATTGATTTTCCAGATTTTACAGTTCTACCATTATTTTCAAAAATTA
** * *
16561 CAGTTTTGCCATTAGCTTTC
66 CAACTCTGCCACTAGCTTTC
* * *
16581 CAGATTTTACAGTTCTACCATT-ATTTTCCAGATTTTACAGTTTTGCCATGGT-TTTTCAAAATT
1 CAGATTTTACAGTTCTACCATTGATTTTCCAGATTTTACAGTTCTACCAT--TATTTTCAAAAAT
* **
16644 TTCAACTCTGCCACTATTTTTC
64 TACAACTCTGCCACTAGCTTTC
*
16666 TAGATTTTACA
1 CAGATTTTACA
16677 ATTTTGCTTC
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
84 23 0.29
85 54 0.69
86 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.46
Consensus pattern (85 bp):
CAGATTTTACAGTTCTACCATTGATTTTCCAGATTTTACAGTTCTACCATTATTTTCAAAAATTA
CAACTCTGCCACTAGCTTTC
Found at i:16717 original size:28 final size:29
Alignment explanation
Indices: 16558--16718 Score: 98
Period size: 28 Copynumber: 5.7 Consensus size: 29
16548 TTTTCAAAAA
* * ** *
16558 TTACAGTTTTGCCATTAGCTTTCCAGATT
1 TTACAATTTTGCCACTATTTTTCGAGATT
* * * * *
16587 TTACAGTTCTACCATTA-TTTTCCAGATT
1 TTACAATTTTGCCACTATTTTTCGAGATT
* * * *
16615 TTACAGTTTTGCCA-TGGTTTTTCAAAATT
1 TTACAATTTTGCCACT-ATTTTTCGAGATT
* * *
16644 TT-CAACTCTGCCACTATTTTTCTAGATT
1 TTACAATTTTGCCACTATTTTTCGAGATT
**
16672 TTACAATTTTGCTTCTATTTTT-GAGATT
1 TTACAATTTTGCCACTATTTTTCGAGATT
16700 TTACAA-TTTGTCCACTATT
1 TTACAATTTTG-CCACTATT
16719 CTTAAAAAAA
Statistics
Matches: 106, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
27 5 0.05
28 59 0.56
29 42 0.40
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (29 bp):
TTACAATTTTGCCACTATTTTTCGAGATT
Found at i:18858 original size:40 final size:40
Alignment explanation
Indices: 18814--18891 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
18804 TCAATTGAAA
*
18814 AATCGATACCGAAACAACATTTTGTTTCTCGATTAAAACC
1 AATCGATACCAAAACAACATTTTGTTTCTCGATTAAAACC
*
18854 AATCGATACCAAAACAACATTTTGTTTCTCGCTTAAAA
1 AATCGATACCAAAACAACATTTTGTTTCTCGATTAAAA
18892 ATAAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (40 bp):
AATCGATACCAAAACAACATTTTGTTTCTCGATTAAAACC
Found at i:21768 original size:22 final size:22
Alignment explanation
Indices: 21695--21779 Score: 116
Period size: 22 Copynumber: 3.9 Consensus size: 22
21685 CCATGGATGT
*
21695 ATTATGCCAATATAATTGATTG
1 ATTACGCCAATATAATTGATTG
* * *
21717 ATTGCACAAATATAATTGATTG
1 ATTACGCCAATATAATTGATTG
*
21739 ATTGCGCCAATATAATTGATTG
1 ATTACGCCAATATAATTGATTG
*
21761 ATTACGCCAATATAGTTGA
1 ATTACGCCAATATAATTGA
21780 ATATTTTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (22 bp):
ATTACGCCAATATAATTGATTG
Found at i:25447 original size:13 final size:12
Alignment explanation
Indices: 25431--25478 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
25421 TTTATTTTTC
25431 TTTTTTTTCTCAA
1 TTTTTTTT-TCAA
25444 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
25456 TTTTTCTTTTCGA
1 TTTTT-TTTTCAA
*
25469 CTTTTTTTTC
1 TTTTTTTTTC
25479 TTTTTTTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
12 14 0.44
13 18 0.56
ACGTcount: A:0.10, C:0.15, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:25459 original size:25 final size:22
Alignment explanation
Indices: 25425--25485 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 22
25415 TTTTTTTTTA
*
25425 TTTTTCTTTTTTTTCTCAATTTT
1 TTTTTCTTTTTTTT-TCAACTTT
*
25448 TTTTTCAATTTTTCTTTTCGACTTT
1 TTTTTC--TTTTT-TTTTCAACTTT
25473 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
25486 CTAAACAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 2 0.06
23 11 0.33
25 17 0.52
26 3 0.09
ACGTcount: A:0.08, C:0.13, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTTCTTTTTTTTTCAACTTT
Found at i:25485 original size:12 final size:12
Alignment explanation
Indices: 25419--25485 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
25409 TTGTCCTTTT
25419 TTTTTATTTTTC-
1 TTTTT-TTTTTCA
*
25431 TTTTTTTTCTCA
1 TTTTTTTTTTCA
*
25443 ATTTTTTTTTCAA
1 TTTTTTTTTTC-A
*
25456 TTTTTCTTTTCGA
1 TTTTTTTTTTC-A
*
25469 -CTTTTTTTTC-
1 TTTTTTTTTTCA
25479 TTTTTTT
1 TTTTTTT
25486 CTAAACAATA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
11 10 0.23
12 22 0.51
13 11 0.26
ACGTcount: A:0.09, C:0.12, G:0.01, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:26414 original size:5 final size:5
Alignment explanation
Indices: 26404--26456 Score: 61
Period size: 5 Copynumber: 9.8 Consensus size: 5
26394 AGTGCATAAT
*
26404 TAAAA TAAAA TTAAAAA TAAAA TAAGA TAAAA TAAAA TAAAA TTGAAAA
1 TAAAA TAAAA -T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA -T-AAAA
26453 TAAA
1 TAAA
26457 TATACTAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 30 0.71
6 4 0.10
7 8 0.19
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:26434 original size:27 final size:27
Alignment explanation
Indices: 26404--26455 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
26394 AGTGCATAAT
26404 TAAAATAAAATTAAAAAT-AAAATAAGA
1 TAAAATAAAA-TAAAAATGAAAATAAGA
*
26431 TAAAATAAAATAAAATTGAAAATAA
1 TAAAATAAAATAAAAATGAAAATAA
26456 ATATACTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (27 bp):
TAAAATAAAATAAAAATGAAAATAAGA
Found at i:26559 original size:155 final size:154
Alignment explanation
Indices: 26327--26638 Score: 615
Period size: 155 Copynumber: 2.0 Consensus size: 154
26317 TTTTCGAGCA
26327 AAAAAAAATAGACAAAGACAAGTCAAAGAGGGAGATAATTAAAAAAAACAACCATAAGAATAAAA
1 AAAAAAAATAGACAAAGACAAGTCAAAGAGGGAGATAATTAAAAAAAACAACCATAAGAATAAAA
26392 ATAGTGCATAATTAAAATAAAATTAAAAATAAAATAAGATAAAATAAAATAAAATTGAAAATAAA
66 ATAGTGCATAATTAAAATAAAATTAAAAATAAAATAAGATAAAATAAAATAAAATTGAAAATAAA
26457 TATACTAATTTTTTTGAACTTTGC
131 TATACTAATTTTTTTGAACTTTGC
26481 AAAAAAAATAGACAAAGACAAGTCAAAGAGGGAGATAATTAAAAAAAAACAACCATAAGAATAAA
1 AAAAAAAATAGACAAAGACAAGTCAAAGAGGGAGATAATT-AAAAAAAACAACCATAAGAATAAA
26546 AATAGTGCATAATTAAAATAAAATTAAAAATAAAATAAGATAAAATAAAATAAAATTGAAAATAA
65 AATAGTGCATAATTAAAATAAAATTAAAAATAAAATAAGATAAAATAAAATAAAATTGAAAATAA
26611 ATATACTAATTTTTTTGAACTTTGC
130 ATATACTAATTTTTTTGAACTTTGC
26636 AAA
1 AAA
26639 TTTTTTCAAA
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
154 40 0.25
155 117 0.75
ACGTcount: A:0.61, C:0.06, G:0.10, T:0.23
Consensus pattern (154 bp):
AAAAAAAATAGACAAAGACAAGTCAAAGAGGGAGATAATTAAAAAAAACAACCATAAGAATAAAA
ATAGTGCATAATTAAAATAAAATTAAAAATAAAATAAGATAAAATAAAATAAAATTGAAAATAAA
TATACTAATTTTTTTGAACTTTGC
Found at i:26569 original size:5 final size:5
Alignment explanation
Indices: 26559--26611 Score: 61
Period size: 5 Copynumber: 9.8 Consensus size: 5
26549 AGTGCATAAT
*
26559 TAAAA TAAAA TTAAAAA TAAAA TAAGA TAAAA TAAAA TAAAA TTGAAAA
1 TAAAA TAAAA -T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA -T-AAAA
26608 TAAA
1 TAAA
26612 TATACTAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 30 0.71
6 4 0.10
7 8 0.19
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:26589 original size:27 final size:27
Alignment explanation
Indices: 26559--26610 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
26549 AGTGCATAAT
26559 TAAAATAAAATTAAAAAT-AAAATAAGA
1 TAAAATAAAA-TAAAAATGAAAATAAGA
*
26586 TAAAATAAAATAAAATTGAAAATAA
1 TAAAATAAAATAAAAATGAAAATAA
26611 ATATACTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (27 bp):
TAAAATAAAATAAAAATGAAAATAAGA
Done.