Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015371.1 Kokia drynarioides strain JFW-HI SEQ_130418, 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: 141638
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:6182 original size:19 final size:19
Alignment explanation
Indices: 6160--6221 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
6150 TTTTATAATA
*
6160 AATTTAGATTTAAAAAAAT
1 AATTTAGATTTTAAAAAAT
** * *
6179 AATTTACTTTTTATAATAT
1 AATTTAGATTTTAAAAAAT
6198 -ATTTAGATTTTAAAAAAT
1 AATTTAGATTTTAAAAAAT
6216 AATTTA
1 AATTTA
6222 CTAAGTTATT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
18 14 0.42
19 19 0.58
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (19 bp):
AATTTAGATTTTAAAAAAT
Found at i:6195 original size:37 final size:37
Alignment explanation
Indices: 6149--6223 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
6139 TTATTTATAA
6149 TTTTTATAATAAATTTAGATTTAAAAAAATAATTTAC
1 TTTTTATAATAAATTTAGATTTAAAAAAATAATTTAC
* *
6186 TTTTTATAATATATTTAGATTTTAAAAAATAATTTAC
1 TTTTTATAATAAATTTAGATTTAAAAAAATAATTTAC
6223 T
1 T
6224 AAGTTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (37 bp):
TTTTTATAATAAATTTAGATTTAAAAAAATAATTTAC
Found at i:6208 original size:18 final size:18
Alignment explanation
Indices: 6150--6209 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
6140 TATTTATAAT
*
6150 TTTTATAATAAATTTAGA
1 TTTTATAATATATTTAGA
* * * **
6168 TTTAAAAAAATAATTTACT
1 TTTTATAATAT-ATTTAGA
6187 TTTTATAATATATTTAGA
1 TTTTATAATATATTTAGA
6205 TTTTA
1 TTTTA
6210 AAAAATAATT
Statistics
Matches: 30, Mismatches: 11, Indels: 2
0.70 0.26 0.05
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (18 bp):
TTTTATAATATATTTAGA
Found at i:17347 original size:18 final size:19
Alignment explanation
Indices: 17317--17372 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
17307 TAAAAATATA
*
17317 AATTTTGGAATTTTGTAAAT
1 AATTTT-GAATTTTATAAAT
*
17337 -ATTTTGAATTTTAAAAAT
1 AATTTTGAATTTTATAAAT
* *
17355 AATTTTAAATTTTTTAAA
1 AATTTTGAATTTTATAAA
17373 ATTAATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (19 bp):
AATTTTGAATTTTATAAAT
Found at i:17371 original size:21 final size:21
Alignment explanation
Indices: 17344--17391 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
17334 AATATTTTGA
17344 ATTTTAAAAATAATTTTAAATT
1 ATTTTAAAAATAA-TTTAAATT
*
17366 -TTTTAAAATTAATTTAAATT
1 ATTTTAAAAATAATTTAAATT
17386 ATTTTA
1 ATTTTA
17392 TATTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTAAAAATAATTTAAATT
Found at i:17373 original size:20 final size:20
Alignment explanation
Indices: 17333--17391 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
17323 GGAATTTTGT
* *
17333 AAAT-ATTTTGAA-TTTTAA
1 AAATAATTTTAAATTTTTTA
17351 AAATAATTTTAAATTTTTTA
1 AAATAATTTTAAATTTTTTA
17371 AAATTAA-TTTAAATTATTTTA
1 AAA-TAATTTTAAATT-TTTTA
17392 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 4 0.11
19 7 0.20
20 16 0.46
21 8 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATAATTTTAAATTTTTTA
Found at i:19520 original size:22 final size:22
Alignment explanation
Indices: 19488--19531 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19478 TGGCCCTTTA
*
19488 AGGTTGGCTTATACATTGAAAG
1 AGGTTGACTTATACATTGAAAG
19510 AGGTTGACTTATACATTGAAAG
1 AGGTTGACTTATACATTGAAAG
19532 CCTGAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (22 bp):
AGGTTGACTTATACATTGAAAG
Found at i:23270 original size:25 final size:23
Alignment explanation
Indices: 23230--23280 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
23220 TATAATATTT
* *
23230 TATTACATATTTTATTTTTATGA
1 TATTACATATTTTATTATTATAA
23253 TATTACTATTATTTTATTATTATAA
1 TATTAC-A-TATTTTATTATTATAA
23278 TAT
1 TAT
23281 GATGATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 1 0.04
25 17 0.71
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTACATATTTTATTATTATAA
Found at i:26633 original size:10 final size:10
Alignment explanation
Indices: 26618--26671 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
26608 AGGGGAAGAG
*
26618 CAAATCAAAT
1 CAAAGCAAAT
* *
26628 CAAATCAATT
1 CAAAGCAAAT
*
26638 CAAAGAAAAT
1 CAAAGCAAAT
*
26648 CAAAGCAAAG
1 CAAAGCAAAT
*
26658 CAAAGCAAAG
1 CAAAGCAAAT
26668 CAAA
1 CAAA
26672 TTAAACAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.61, C:0.19, G:0.09, T:0.11
Consensus pattern (10 bp):
CAAAGCAAAT
Found at i:26656 original size:15 final size:15
Alignment explanation
Indices: 26638--26671 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
26628 CAAATCAATT
*
26638 CAAAGAAAATCAAAG
1 CAAAGAAAAGCAAAG
*
26653 CAAAGCAAAGCAAAG
1 CAAAGAAAAGCAAAG
26668 CAAA
1 CAAA
26672 TTAAACAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.18, G:0.15, T:0.03
Consensus pattern (15 bp):
CAAAGAAAAGCAAAG
Found at i:27593 original size:18 final size:21
Alignment explanation
Indices: 27554--27599 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
27544 TTTGAAACTT
27554 TTTTTTAGATAATTATATTTA
1 TTTTTTAGATAATTATATTTA
27575 TTTTTTA-A-AATTA-ATTTA
1 TTTTTTAGATAATTATATTTA
*
27593 TTATTTA
1 TTTTTTA
27600 TTTTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 11 0.46
19 5 0.21
20 1 0.04
21 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTTAGATAATTATATTTA
Found at i:27597 original size:25 final size:29
Alignment explanation
Indices: 27569--27631 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
27559 TAGATAATTA
27569 TATTTATTTT-TTAAAATT-A-ATTT-AT
1 TATTTATTTTATTAAAATTCACATTTAAT
**
27594 TATTTATTTTATTAATTTTCACATTTAAT
1 TATTTATTTTATTAAAATTCACATTTAAT
27623 TATTTATTT
1 TATTTATTT
27632 GACATATCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 10 0.31
26 6 0.19
27 1 0.03
28 4 0.12
29 11 0.34
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (29 bp):
TATTTATTTTATTAAAATTCACATTTAAT
Found at i:41422 original size:37 final size:37
Alignment explanation
Indices: 41381--41464 Score: 141
Period size: 37 Copynumber: 2.3 Consensus size: 37
41371 TCAGTCAAAA
* *
41381 GTAATTTGCTATTTCATATAACTAATAAGTATAGTTG
1 GTAATTTGCTATTTCATATAACTAATAAATAAAGTTG
*
41418 GTAATTTGCTATTTCGTATAACTAATAAATAAAGTTG
1 GTAATTTGCTATTTCATATAACTAATAAATAAAGTTG
41455 GTAATTTGCT
1 GTAATTTGCT
41465 TTAATCATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (37 bp):
GTAATTTGCTATTTCATATAACTAATAAATAAAGTTG
Found at i:45270 original size:37 final size:35
Alignment explanation
Indices: 45187--45272 Score: 138
Period size: 35 Copynumber: 2.4 Consensus size: 35
45177 ATATCCAAAA
*
45187 TTCATAGTATATATATCTATGAAAATAATAGTGATT
1 TTCA-AGTATATATATCTATGAAAATAATAGTGATG
45223 TTCAAGTATATATATCTATGAAAATAATAGTGATG
1 TTCAAGTATATATATCTATGAAAATAATAGTGATG
45258 TTCAAG-ATTATATAT
1 TTCAAGTA-TATATAT
45273 TCATATTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
34 1 0.02
35 43 0.90
36 4 0.08
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.41
Consensus pattern (35 bp):
TTCAAGTATATATATCTATGAAAATAATAGTGATG
Found at i:48718 original size:15 final size:16
Alignment explanation
Indices: 48680--48712 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
48670 TTTTGAACAA
48680 TTTAA-TTTTTTTTCT
1 TTTAACTTTTTTTTCT
48695 TTTAACTTTTTTTT-T
1 TTTAACTTTTTTTTCT
48710 TTT
1 TTT
48713 CTCTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTAACTTTTTTTTCT
Found at i:54935 original size:28 final size:28
Alignment explanation
Indices: 54897--54954 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
54887 CCACGTTTTC
54897 TTCAATTGGACGGAAGGGAGGGATATTT
1 TTCAATTGGACGGAAGGGAGGGATATTT
54925 TTCAATTGGACGGAAGGGAGGGATATTT
1 TTCAATTGGACGGAAGGGAGGGATATTT
54953 TT
1 TT
54955 TATTACGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.07, G:0.34, T:0.31
Consensus pattern (28 bp):
TTCAATTGGACGGAAGGGAGGGATATTT
Found at i:56211 original size:31 final size:29
Alignment explanation
Indices: 56163--56227 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
56153 ATTCAAGTGA
* *
56163 GTTAAAAAAATTCAAATATCAAATTAAAT
1 GTTAAAAAAATTCAAATACCAAATAAAAT
*
56192 GTTAAAATCAAATTTAAATACCAAATAAAAT
1 GTTAAAA--AAATTCAAATACCAAATAAAAT
*
56223 ATTAA
1 GTTAA
56228 CCATTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.23
31 23 0.77
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (29 bp):
GTTAAAAAAATTCAAATACCAAATAAAAT
Found at i:56479 original size:31 final size:32
Alignment explanation
Indices: 56443--56509 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
56433 ATTTTTTATA
56443 ATCATTTCAAG-TTTTTCTTTGATGAGTAATG
1 ATCATTTCAAGTTTTTTCTTTGATGAGTAATG
* *
56474 ATCATTTCAAGTTTTTTTTTTTGGTGAGTAATG
1 ATCATTTCAAG-TTTTTTCTTTGATGAGTAATG
56507 ATC
1 ATC
56510 GTTGACAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 11 0.34
33 21 0.66
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.51
Consensus pattern (32 bp):
ATCATTTCAAGTTTTTTCTTTGATGAGTAATG
Found at i:57540 original size:13 final size:13
Alignment explanation
Indices: 57504--57549 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
57494 AAGCCCAAAA
*
57504 AAATTTAAATACC
1 AAATATAAATACC
* *
57517 AAATTAAAAATATC
1 AAA-TATAAATACC
57531 AAATATAAATACC
1 AAATATAAATACC
57544 AAATAT
1 AAATAT
57550 TATATTAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATATAAATACC
Found at i:64130 original size:22 final size:22
Alignment explanation
Indices: 64104--64159 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
64094 TTCCTTGTTG
* * *
64104 TTTTGTTGTTGTTTTGTTACTA
1 TTTTGTTGTTATATTGCTACTA
* *
64126 TTTTGCTATTATATTGCTACTA
1 TTTTGTTGTTATATTGCTACTA
64148 TTTTGTTGTTAT
1 TTTTGTTGTTAT
64160 TGTTTAGATA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (22 bp):
TTTTGTTGTTATATTGCTACTA
Found at i:66419 original size:14 final size:15
Alignment explanation
Indices: 66400--66428 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
66390 CAAAAATACT
66400 AAAAATTA-TAAAAA
1 AAAAATTATTAAAAA
66414 AAAAATTATTAAAAA
1 AAAAATTATTAAAAA
66429 TATACATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATTATTAAAAA
Found at i:67728 original size:36 final size:36
Alignment explanation
Indices: 67682--67752 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
67672 AGTGAGAAAG
*
67682 AAAGAAATATGAGAAAGAA-ATAGAAGGACGAGAGAA
1 AAAGAAATATGA-AAAAAAGATAGAAGGACGAGAGAA
* *
67718 AAAGAGATATGAAAAAAAGATAGAGGGACGAGAGA
1 AAAGAAATATGAAAAAAAGATAGAAGGACGAGAGA
67753 GGGAAAGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.59, C:0.03, G:0.30, T:0.08
Consensus pattern (36 bp):
AAAGAAATATGAAAAAAAGATAGAAGGACGAGAGAA
Found at i:77955 original size:2 final size:2
Alignment explanation
Indices: 77948--77981 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
77938 TGAAAGTAGC
77948 AG AG AG AG -G A- AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
77982 GAAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:82825 original size:26 final size:26
Alignment explanation
Indices: 82808--82859 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
82798 ATCATATATT
82808 ATTACCATAAATATAAATATTATTTA
1 ATTACCATAAATATAAATATTATTTA
*
82834 ATTATCATAAATATAAATATTATTTA
1 ATTACCATAAATATAAATATTATTTA
82860 TCTTAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTACCATAAATATAAATATTATTTA
Found at i:85198 original size:58 final size:58
Alignment explanation
Indices: 85120--85411 Score: 244
Period size: 60 Copynumber: 4.9 Consensus size: 58
85110 ATTCGAGGGG
* *
85120 AAAATTTAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTGGGAAGTTTGGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGGAAGTTTGGGGGTC
* ** * * * * * *
85178 AAAATATGGTTTTGGAAAAGTTTAGGGTCAAAATGTAACTTTGGGAAAGTATGAGGATT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGG-AAGTTTGGGGGTC
* * * * * * ** *
85237 AAAATGTATTTTTGGAAAATTTTAGGGTTAAAAATATGATTTTAAGAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTT-AAAATGTAATTTT-GGGAAGTTTGGGGGTC
* * * * * *
85297 AAAATGTGATTTTTGAGAAGTTTAGGGGTTAAAATGTAATTTTAGGAAAGTTTGGAGGCC
1 AAAATGTAATTTTGGAAAAGTTTA-GGGTTAAAATGTAATTTT-GGGAAGTTTGGGGGTC
* * * * *
85357 AAAATGCAATTTT-AAAAAGTTTAGGATAAAAATATAATTTTGGGAAAGTTTGGGG
1 AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGG-AAGTTTGGGG
85412 ACTACCTGGT
Statistics
Matches: 184, Mismatches: 45, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
57 2 0.01
58 63 0.34
59 41 0.22
60 72 0.39
61 6 0.03
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGGAAGTTTGGGGGTC
Found at i:85225 original size:30 final size:29
Alignment explanation
Indices: 85120--85407 Score: 204
Period size: 30 Copynumber: 9.8 Consensus size: 29
85110 ATTCGAGGGG
* * *
85120 AAAATTTAATTTTAGAAAAGTTTAGGGTT
1 AAAATGTAATTTTGGGAAAGTTTAGGGTT
* *
85149 AAAATGTAATTTTGGG-AAGTTTGGGGGTC
1 AAAATGTAATTTTGGGAAAGTTT-AGGGTT
* ** * *
85178 AAAATATGGTTTTGGAAAAGTTTAGGGTC
1 AAAATGTAATTTTGGGAAAGTTTAGGGTT
* * *
85207 AAAATGTAACTTTGGGAAAGTATGAGGATT
1 AAAATGTAATTTTGGGAAAGT-TTAGGGTT
* * *
85237 AAAATGTATTTTTGGAAAATTTTAGGGTT
1 AAAATGTAATTTTGGGAAAGTTTAGGGTT
* * **
85266 AAAAATATGATTTTAAGAAAGTTTAAGGGTT
1 -AAAATGTAATTTTGGGAAAGTTT-AGGGTT
* *
85297 AAAATGTGATTTT-TGAGAAGTTTAGGGGTT
1 AAAATGTAATTTTGGGA-AAGTTTA-GGGTT
* * **
85327 AAAATGTAATTTTAGGAAAGTTTGGAGGCC
1 AAAATGTAATTTTGGGAAAGTTTAG-GGTT
* ** * *
85357 AAAATGCAATTTT-AAAAAGTTTAGGATA
1 AAAATGTAATTTTGGGAAAGTTTAGGGTT
*
85385 AAAATATAATTTTGGGAAAGTTT
1 AAAATGTAATTTTGGGAAAGTTT
85408 GGGGACTACC
Statistics
Matches: 200, Mismatches: 49, Indels: 20
0.74 0.18 0.07
Matches are distributed among these distances:
28 18 0.09
29 75 0.38
30 99 0.50
31 8 0.04
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTGGGAAAGTTTAGGGTT
Found at i:86915 original size:48 final size:48
Alignment explanation
Indices: 86844--86936 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
86834 ACTGAGTGGC
86844 TAGGGATGGGGCGGCAGGTAGCAAGTTGCTACCATTAGGGTTTTTGGT
1 TAGGGATGGGGCGGCAGGTAGCAAGTTGCTACCATTAGGGTTTTTGGT
86892 TAGGGATGGGGCGGCAGGTAGCAAGTTGCTACCATTAGGGTTTTT
1 TAGGGATGGGGCGGCAGGTAGCAAGTTGCTACCATTAGGGTTTTT
86937 CTTTTTTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.19, C:0.13, G:0.39, T:0.29
Consensus pattern (48 bp):
TAGGGATGGGGCGGCAGGTAGCAAGTTGCTACCATTAGGGTTTTTGGT
Found at i:98117 original size:16 final size:16
Alignment explanation
Indices: 98096--98155 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
98086 TCTTAATAAA
* *
98096 AAAAAAAATTATATTC
1 AAAAAAAATTAAATAC
*
98112 AAAAAATAA-TAAAAAC
1 AAAAAA-AATTAAATAC
98128 AAAAAAAATTAAATAC
1 AAAAAAAATTAAATAC
*
98144 ATTAAAAAATTA
1 A-AAAAAAATTA
98156 TAAACTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 2 0.06
16 23 0.64
17 11 0.31
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAAAATTAAATAC
Found at i:103113 original size:20 final size:20
Alignment explanation
Indices: 103075--103128 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
103065 AGTCTTCAAG
* *
103075 GTATCGATAGAAGTGGAGTT
1 GTATCGGTAGAAGTAGAGTT
*
103095 GTATCGGTAGAATTAGAGTT
1 GTATCGGTAGAAGTAGAGTT
* *
103115 CTACCGGTAGAAGT
1 GTATCGGTAGAAGT
103129 CTCACTGGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (20 bp):
GTATCGGTAGAAGTAGAGTT
Found at i:103308 original size:47 final size:45
Alignment explanation
Indices: 103257--103346 Score: 110
Period size: 47 Copynumber: 2.0 Consensus size: 45
103247 TTTATTCGAA
103257 TTTGATGTCGA-TATTGATTGTGATTTTTGATTTAGGGTTTATTTTAG
1 TTTGATGTCGATTA-TGATTGTGA-TTTTGATTTAGGG-TTATTTTAG
* * * *
103304 TTTGATTTGGATTATGATTTTTATTTTGATTTAGGGTTATTTT
1 TTTGATGTCGATTATGATTGTGATTTTGATTTAGGGTTATTTT
103347 GATTGGATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
45 7 0.18
46 13 0.34
47 16 0.42
48 2 0.05
ACGTcount: A:0.19, C:0.01, G:0.21, T:0.59
Consensus pattern (45 bp):
TTTGATGTCGATTATGATTGTGATTTTGATTTAGGGTTATTTTAG
Found at i:104924 original size:16 final size:16
Alignment explanation
Indices: 104890--104922 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
104880 TAATTTTATT
*
104890 AATATATAAATATTAA
1 AATAAATAAATATTAA
104906 AATAAATAAA-ATTAA
1 AATAAATAAATATTAA
104921 AA
1 AA
104923 ATTAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAATAAATATTAA
Found at i:105467 original size:49 final size:50
Alignment explanation
Indices: 105372--105470 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 50
105362 AATATTTAAA
* * * * *
105372 GTGACGACACTAATTAGAGGAAAATTTTATTTTAATAGGTGACAACACTT
1 GTGACGACACCAATTAGAGAAAAAATATATTTTAATAGATGACAACACTT
* *
105422 GTGACGACACCAATT-GATAAAAAATATATTTTATTAGATGACAACACTT
1 GTGACGACACCAATTAGAGAAAAAATATATTTTAATAGATGACAACACTT
105471 AAAGTTACGA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 28 0.67
50 14 0.33
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (50 bp):
GTGACGACACCAATTAGAGAAAAAATATATTTTAATAGATGACAACACTT
Found at i:122454 original size:30 final size:29
Alignment explanation
Indices: 122420--122485 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
122410 CTTACCCATA
*
122420 TTATTTT-TATTTAAAAAATTTATATAGTTT
1 TTATTTTATATTT-AAAAATTTA-ATAATTT
*
122450 TTATTTTAATATTTAATAATTTAATAATTT
1 TTATTTT-ATATTTAAAAATTTAATAATTT
122480 TTATTT
1 TTATTT
122486 ATTGAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 19 0.59
31 8 0.25
32 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (29 bp):
TTATTTTATATTTAAAAATTTAATAATTT
Found at i:123212 original size:5 final size:5
Alignment explanation
Indices: 123202--123239 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
123192 ACACATTGAA
* *
123202 AATCC AATCC AATCC AATTC AATTC AAT-C AATCC AATC
1 AATCC AATCC AATCC AATCC AATCC AATCC AATCC AATC
123240 TTCCCTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (5 bp):
AATCC
Found at i:134250 original size:2 final size:2
Alignment explanation
Indices: 134243--134273 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
134233 ATGTAAAAGA
134243 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
134274 CAAAGATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:141105 original size:28 final size:27
Alignment explanation
Indices: 141074--141129 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
141064 AACTTATTTT
*
141074 TCTCGATTTCTTATTCTCAATTCTCAAA
1 TCTCGATTTCTTATTCTAAATTCT-AAA
* *
141102 TCTCGGTTTTTTATTCTAAATTCTAAA
1 TCTCGATTTCTTATTCTAAATTCTAAA
141129 T
1 T
141130 TCTAAATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (27 bp):
TCTCGATTTCTTATTCTAAATTCTAAA
Done.