Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015348.1 Kokia drynarioides strain JFW-HI SEQ_130395, 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: 119902
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 217 characters in sequence are not A, C, G, or T
Found at i:1187 original size:23 final size:22
Alignment explanation
Indices: 1157--1233 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 22
1147 ACGCTAGCGC
1157 GCTTACTGTTCGGCACTGT-GTGT
1 GCTTACTGTTC-GCACT-TCGTGT
*
1180 GCTTACTGTTTCGTACTTCGTGT
1 GCTTACTG-TTCGCACTTCGTGT
* *
1203 GCTTACTGTTTCGCACCTCGAGT
1 GCTTACTG-TTCGCACTTCGTGT
*
1226 GCCTACTG
1 GCTTACTG
1234 ATTTGAGCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.02
23 43 0.91
24 3 0.06
ACGTcount: A:0.10, C:0.26, G:0.25, T:0.39
Consensus pattern (22 bp):
GCTTACTGTTCGCACTTCGTGT
Found at i:1274 original size:22 final size:22
Alignment explanation
Indices: 1224--1301 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 22
1214 CGCACCTCGA
** *
1224 GTGCCTACTGATTTGAGCTATGT
1 GTGCCTACTGATTACA-CTGTGT
*
1247 GCGCCTACTGATTACACTGTGT
1 GTGCCTACTGATTACACTGTGT
* *
1269 GTGCCTACTGAATTGCACTGCGT
1 GTGCCTACTG-ATTACACTGTGT
*
1292 GTGCTTACTG
1 GTGCCTACTG
1302 TTTCCCCAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 14 0.30
23 32 0.70
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.35
Consensus pattern (22 bp):
GTGCCTACTGATTACACTGTGT
Found at i:22167 original size:17 final size:18
Alignment explanation
Indices: 22136--22173 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
22126 ATTTTAAATT
*
22136 TTTTTTATAACTTTTATA
1 TTTTTTATAACTTTTAAA
*
22154 TTTTTT-TAATTTTTAAA
1 TTTTTTATAACTTTTAAA
22171 TTT
1 TTT
22174 AAAAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTATAACTTTTAAA
Found at i:24438 original size:21 final size:22
Alignment explanation
Indices: 24408--24450 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
24398 TTTAATCGAT
* *
24408 TGAATCTTAAT-TTAATTTATA
1 TGAATATTAATGTTAATGTATA
24429 TGAATATTAATGTTAATGTATA
1 TGAATATTAATGTTAATGTATA
24451 AAAATATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (22 bp):
TGAATATTAATGTTAATGTATA
Found at i:24456 original size:22 final size:21
Alignment explanation
Indices: 24414--24469 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
24404 CGATTGAATC
* **
24414 TTAATTTAATTTATATGAATA
1 TTAATTTAATGTATAAAAATA
24435 TTAATGTTAATGTATAAAAATA
1 TTAAT-TTAATGTATAAAAATA
*
24457 TGAATTTGAATGT
1 TTAATTT-AATGT
24470 CTTAAAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (21 bp):
TTAATTTAATGTATAAAAATA
Found at i:28284 original size:30 final size:30
Alignment explanation
Indices: 28258--28628 Score: 332
Period size: 30 Copynumber: 12.1 Consensus size: 30
28248 AAACATGATT
* *
28258 TGCAGTCACACGAGCAGCATTTACATGAAC
1 TGCAGTCGCACGAGCTGCATTTACATGAAC
* * **
28288 AGCAGTCACATAAACTGCTGCATTTACATGAAC
1 TGCAGTCGCA-CGA--GCTGCATTTACATGAAC
* * *
28321 TGCAGTTGCATGAGCTGCATTTACAAGAAC
1 TGCAGTCGCACGAGCTGCATTTACATGAAC
**
28351 TGCAGTCGCATAAACTGCTGCATTTACATGAAC
1 TGCAGTCGCA-CGA--GCTGCATTTACATGAAC
* *
28384 TGCAGTTGCATGAGCTGCATTTACATGAAC
1 TGCAGTCGCACGAGCTGCATTTACATGAAC
* *
28414 TGCAGTTGCATGAGCTGCATTTACATGAAC
1 TGCAGTCGCACGAGCTGCATTTACATGAAC
* **
28444 TGCAGTCACATAAACTGCTGCATTTACATGAAC
1 TGCAGTCGCA-CGA--GCTGCATTTACATGAAC
* * * * *
28477 TACAGTCACACGAGCTGCATTTACACGGAT
1 TGCAGTCGCACGAGCTGCATTTACATGAAC
*
28507 TGCAGTCGCACGAGCTGCATTTACATTG-AT
1 TGCAGTCGCACGAGCTGCATTTACA-TGAAC
* *
28537 TGCAGTCGCACGAACTGCATTTACATGAAG
1 TGCAGTCGCACGAGCTGCATTTACATGAAC
* *
28567 TGCAATCACACGAGCTGCATTTACATGAA-
1 TGCAGTCGCACGAGCTGCATTTACATGAAC
* ** * *
28596 GGCAGGTTACACGAGCTGCATTTGCACGAAC
1 TGCA-GTCGCACGAGCTGCATTTACATGAAC
28627 TG
1 TG
28629 TGTTCCGATG
Statistics
Matches: 287, Mismatches: 41, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
29 5 0.02
30 200 0.70
31 5 0.02
32 3 0.01
33 74 0.26
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (30 bp):
TGCAGTCGCACGAGCTGCATTTACATGAAC
Found at i:28325 original size:63 final size:61
Alignment explanation
Indices: 28258--28595 Score: 333
Period size: 63 Copynumber: 5.5 Consensus size: 61
28248 AAACATGATT
* * *
28258 TGCAGTCACACGAGCAGCATTTACATGAACAGCAGTCACATAAACTGCTGCATTTACATGAAC
1 TGCAGTCACACGAGCTGCATTTACATGAACTGCAGTCGCATAAA--GCTGCATTTACATGAAC
** * *
28321 TGCAGTTGCATGAGCTGCATTTACAAGAACTGCAGTCGCATAAACTGCTGCATTTACATGAAC
1 TGCAGTCACACGAGCTGCATTTACATGAACTGCAGTCGCATAAA--GCTGCATTTACATGAAC
** * * *
28384 TGCAGTTGCATGAGCTGCATTTACATGAACTGCAGTTGCAT-GAGCTGCATTTACATGAAC
1 TGCAGTCACACGAGCTGCATTTACATGAACTGCAGTCGCATAAAGCTGCATTTACATGAAC
** * * ** * * *
28444 TGCAGTCACATAAACTGCTGCATTTACATGAACTACAGTCACA-CGAGCTGCATTTACACGGAT
1 TGCAGTCACA-CGA--GCTGCATTTACATGAACTGCAGTCGCATAAAGCTGCATTTACATGAAC
* * ** *
28507 TGCAGTCGCACGAGCTGCATTTACATTG-ATTGCAGTCGCACGAA-CTGCATTTACATGAAG
1 TGCAGTCACACGAGCTGCATTTACA-TGAACTGCAGTCGCATAAAGCTGCATTTACATGAAC
*
28567 TGCAATCACACGAGCTGCATTTACATGAA
1 TGCAGTCACACGAGCTGCATTTACATGAA
28596 GGCAGGTTAC
Statistics
Matches: 235, Mismatches: 33, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.01
60 83 0.35
61 4 0.02
62 2 0.01
63 144 0.61
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (61 bp):
TGCAGTCACACGAGCTGCATTTACATGAACTGCAGTCGCATAAAGCTGCATTTACATGAAC
Found at i:28332 original size:15 final size:15
Alignment explanation
Indices: 28305--28461 Score: 134
Period size: 15 Copynumber: 10.3 Consensus size: 15
28295 ACATAAACTG
*
28305 CTGCATTTACATGAA
1 CTGCAGTTACATGAA
* *
28320 CTGCAGTTGCATGAG
1 CTGCAGTTACATGAA
* *
28335 CTGCATTTACAAGAA
1 CTGCAGTTACATGAA
** *
28350 CTGCAGTCGCATAAA
1 CTGCAGTTACATGAA
*
28365 CTGCTGCATTTACATGAA
1 ---CTGCAGTTACATGAA
* *
28383 CTGCAGTTGCATGAG
1 CTGCAGTTACATGAA
*
28398 CTGCATTTACATGAA
1 CTGCAGTTACATGAA
* *
28413 CTGCAGTTGCATGAG
1 CTGCAGTTACATGAA
*
28428 CTGCATTTACATGAA
1 CTGCAGTTACATGAA
* *
28443 CTGCAGTCACATAAA
1 CTGCAGTTACATGAA
28458 CTGC
1 CTGC
28462 TGCATTTACA
Statistics
Matches: 108, Mismatches: 31, Indels: 6
0.74 0.21 0.04
Matches are distributed among these distances:
15 97 0.90
18 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (15 bp):
CTGCAGTTACATGAA
Found at i:28417 original size:93 final size:93
Alignment explanation
Indices: 28274--28628 Score: 414
Period size: 93 Copynumber: 3.8 Consensus size: 93
28264 CACACGAGCA
* ** *
28274 GCATTTACATGAACAGCAGTCACATAAACTGCTGCATTTACATGAACTGCAGTTGCATGAGCTGC
1 GCATTTACATGAACTGCAGTCACA-CGA--GCTGCATTTACATGAACTGCAGTTGCACGAGCTGC
*
28339 ATTTACAAGAACTGCAGTCGCATAAACTGCT
63 ATTTACATGAACTGCAGTCGCATAAACTGCT
** * *
28370 GCATTTACATGAACTGCAGTTGCATGAGCTGCATTTACATGAACTGCAGTTGCATGAGCTGCATT
1 GCATTTACATGAACTGCAGTCACACGAGCTGCATTTACATGAACTGCAGTTGCACGAGCTGCATT
*
28435 TACATGAACTGCAGTCACATAAACTGCT
66 TACATGAACTGCAGTCGCATAAACTGCT
* * * * *
28463 GCATTTACATGAACTACAGTCACACGAGCTGCATTTACACGGATTGCAGTCGCACGAGCTGCATT
1 GCATTTACATGAACTGCAGTCACACGAGCTGCATTTACATGAACTGCAGTTGCACGAGCTGCATT
* **
28528 TACATTG-ATTGCAGTCGCACGAA---CT
66 TACA-TGAACTGCAGTCGCATAAACTGCT
* * * *
28553 GCATTTACATGAAGTGCAATCACACGAGCTGCATTTACATGAA-GGCAGGTTACACGAGCTGCAT
1 GCATTTACATGAACTGCAGTCACACGAGCTGCATTTACATGAACTGCA-GTTGCACGAGCTGCAT
* *
28617 TTGCACGAACTG
65 TTACATGAACTG
28629 TGTTCCGATG
Statistics
Matches: 225, Mismatches: 31, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
89 4 0.02
90 61 0.27
93 136 0.60
94 2 0.01
95 1 0.00
96 21 0.09
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (93 bp):
GCATTTACATGAACTGCAGTCACACGAGCTGCATTTACATGAACTGCAGTTGCACGAGCTGCATT
TACATGAACTGCAGTCGCATAAACTGCT
Found at i:28570 original size:15 final size:16
Alignment explanation
Indices: 28551--28596 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
28541 GTCGCACGAA
28551 CTGCATTTACATGAAG
1 CTGCATTTACATGAAG
* * *
28567 -TGCAATCACACG-AG
1 CTGCATTTACATGAAG
28581 CTGCATTTACATGAAG
1 CTGCATTTACATGAAG
28597 GCAGGTTACA
Statistics
Matches: 22, Mismatches: 6, Indels: 4
0.69 0.19 0.12
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (16 bp):
CTGCATTTACATGAAG
Found at i:36475 original size:5 final size:5
Alignment explanation
Indices: 36465--36493 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
36455 CTTTCTTAAC
36465 CATAG CATAG CATAG CATAG CATAG CATA
1 CATAG CATAG CATAG CATAG CATAG CATA
36494 ACCCACACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (5 bp):
CATAG
Found at i:48036 original size:24 final size:23
Alignment explanation
Indices: 47990--48047 Score: 89
Period size: 24 Copynumber: 2.5 Consensus size: 23
47980 CGTTTGTTTA
*
47990 ATGTTCACGAACATTAATCGAAC
1 ATGTTCATGAACATTAATCGAAC
*
48013 ATGTTCATGAACATATAATTGAAC
1 ATGTTCATGAACAT-TAATCGAAC
48037 ATGTTCATGAA
1 ATGTTCATGAA
48048 TAATAAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (23 bp):
ATGTTCATGAACATTAATCGAAC
Found at i:49507 original size:12 final size:12
Alignment explanation
Indices: 49492--49550 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
49482 ATAACATCCA
49492 AACAACAAAAAT
1 AACAACAAAAAT
*
49504 AACAAC--CAA-
1 AACAACAAAAAT
*
49513 AACAACATTAAA-
1 AACAACA-AAAAT
49525 AACAACAAAAAT
1 AACAACAAAAAT
*
49537 AGCAACAAAAAT
1 AACAACAAAAAT
49549 AA
1 AA
49551 TTGCAAAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
9 6 0.16
10 2 0.05
11 3 0.08
12 27 0.71
ACGTcount: A:0.71, C:0.19, G:0.02, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:49517 original size:21 final size:21
Alignment explanation
Indices: 49482--49550 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
49472 CACATAAAGG
*
49482 ATAACATCC-AAACAACAAAA
1 ATAACAACCAAAACAACAAAA
*
49502 ATAACAACCAAAACAACATTAA
1 ATAACAACCAAAACAACA-AAA
*
49524 A-AACAACAAAAATAGCAACAAAA
1 ATAACAAC-CAAA-A-CAACAAAA
49547 ATAA
1 ATAA
49551 TTGCAAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 8 0.21
21 14 0.36
22 6 0.15
23 4 0.10
24 7 0.18
ACGTcount: A:0.68, C:0.20, G:0.01, T:0.10
Consensus pattern (21 bp):
ATAACAACCAAAACAACAAAA
Found at i:70166 original size:13 final size:13
Alignment explanation
Indices: 70148--70180 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
70138 ACATCCTATA
70148 ATATCACTGATAT
1 ATATCACTGATAT
70161 ATATCACTGATAT
1 ATATCACTGATAT
70174 ATATCAC
1 ATATCAC
70181 AATGGTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (13 bp):
ATATCACTGATAT
Found at i:73232 original size:20 final size:19
Alignment explanation
Indices: 73194--73232 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
73184 TGTTTTTATG
**
73194 GTAATTTTTTTAATTTTCA
1 GTAATTTTTTTAAAATTCA
73213 GTAATTTTTTTAAAAATTCA
1 GTAATTTTTTT-AAAATTCA
73233 ATTATCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (19 bp):
GTAATTTTTTTAAAATTCA
Found at i:75309 original size:6 final size:6
Alignment explanation
Indices: 75298--75346 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
75288 GATTCAAGGT
75298 ATATAC ATATAC --ATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
75344 ATA
1 ATA
75347 CAACGAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.10
6 37 0.90
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:75680 original size:22 final size:24
Alignment explanation
Indices: 75646--75694 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
75636 AACCAATACA
75646 TTTACTTACATATAAATGTTTGGT
1 TTTACTTACATATAAATGTTTGGT
**
75670 TTTA-TTA-ATATTTATGTTTGGT
1 TTTACTTACATATAAATGTTTGGT
75692 TTT
1 TTT
75695 TCTGAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 3 0.13
24 4 0.17
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.59
Consensus pattern (24 bp):
TTTACTTACATATAAATGTTTGGT
Found at i:77394 original size:16 final size:17
Alignment explanation
Indices: 77363--77395 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
77353 CATTTTTATT
*
77363 ACTTGCACATAAATAAA
1 ACTTGCACAGAAATAAA
77380 ACTTG-ACAGAAATAAA
1 ACTTGCACAGAAATAAA
77396 TTGATTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (17 bp):
ACTTGCACAGAAATAAA
Found at i:82324 original size:27 final size:26
Alignment explanation
Indices: 82294--82346 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
82284 ATTAAAACCC
82294 AAATTATTAATGAAAT-ATTTTATATTT
1 AAATTATTAA--AAATAATTTTATATTT
*
82321 AAATTATTAAATATAATTTTATATTT
1 AAATTATTAAAAATAATTTTATATTT
82347 TATTATTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 11 0.46
27 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AAATTATTAAAAATAATTTTATATTT
Found at i:84938 original size:33 final size:33
Alignment explanation
Indices: 84875--84951 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
84865 GTCACACAAG
* * *
84875 CTGCATTTACAAGAGCTGTAGTCGCGTAAACTA
1 CTGCATTTACAAGAGCTGCAGTCACATAAACTA
* *
84908 CTGCATTTACATG-GACTGCAGTCACATAAACTG
1 CTGCATTTACAAGAG-CTGCAGTCACATAAACTA
*
84941 TTGCATTTACA
1 CTGCATTTACA
84952 CAAACTACAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
32 1 0.03
33 36 0.97
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (33 bp):
CTGCATTTACAAGAGCTGCAGTCACATAAACTA
Found at i:85013 original size:30 final size:30
Alignment explanation
Indices: 84942--85026 Score: 116
Period size: 30 Copynumber: 2.8 Consensus size: 30
84932 CATAAACTGT
** * *
84942 TGCATTTACACAAACTACAGTCGCACGAGT
1 TGCATTTACACGGATTACAGTCGCACGAGC
*
84972 TGTATTTACACGGATTACAGTCGCACGAGC
1 TGCATTTACACGGATTACAGTCGCACGAGC
*
85002 TGCATTTACACGGATTGCAGTCGCA
1 TGCATTTACACGGATTACAGTCGCA
85027 TGAATAGCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (30 bp):
TGCATTTACACGGATTACAGTCGCACGAGC
Found at i:85037 original size:30 final size:30
Alignment explanation
Indices: 84942--85041 Score: 112
Period size: 30 Copynumber: 3.3 Consensus size: 30
84932 CATAAACTGT
** * *
84942 TGCATTTACACAAACTACAGTCGCACGAGT
1 TGCATTTACACGGATTACAGTCGCACGAGA
* *
84972 TGTATTTACACGGATTACAGTCGCACGAGC
1 TGCATTTACACGGATTACAGTCGCACGAGA
* *
85002 TGCATTTACACGGATTGCAGTCGCATGA-A
1 TGCATTTACACGGATTACAGTCGCACGAGA
85031 TAGCATTTACA
1 T-GCATTTACA
85042 AGAAGGCAGG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
29 1 0.02
30 59 0.98
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (30 bp):
TGCATTTACACGGATTACAGTCGCACGAGA
Found at i:86380 original size:12 final size:13
Alignment explanation
Indices: 86363--86392 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
86353 GGGACGCAAT
86363 GAAAGGGGAAGG-
1 GAAAGGGGAAGGA
86375 GAAAGGGGAAGGA
1 GAAAGGGGAAGGA
86388 GAAAG
1 GAAAG
86393 AGAACATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (13 bp):
GAAAGGGGAAGGA
Found at i:86536 original size:17 final size:17
Alignment explanation
Indices: 86511--86544 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
86501 TTTTCTCATG
*
86511 TTTGTAAAATAATTTAC
1 TTTGGAAAATAATTTAC
*
86528 TTTGGAAAATCATTTAC
1 TTTGGAAAATAATTTAC
86545 AACCAAACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (17 bp):
TTTGGAAAATAATTTAC
Found at i:86589 original size:14 final size:14
Alignment explanation
Indices: 86570--86596 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
86560 TGAAAAGACT
86570 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
86584 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
86597 AGGTAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:89179 original size:34 final size:34
Alignment explanation
Indices: 89140--89206 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
89130 TTATTAACTT
89140 TAAATTTTTACCATTGACATCATTAACATTAATA
1 TAAATTTTTACCATTGACATCATTAACATTAATA
** * *
89174 TAAATTTTTACGTTTGACATTATTAACTTTAAT
1 TAAATTTTTACCATTGACATCATTAACATTAAT
89207 GAAAAAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.46
Consensus pattern (34 bp):
TAAATTTTTACCATTGACATCATTAACATTAATA
Found at i:93508 original size:29 final size:29
Alignment explanation
Indices: 93476--93534 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
93466 TCTCAACTTT
* * * *
93476 TCCCAGCATCTTTTTCTTCTCTTATTTTC
1 TCCCAACATATTTTTCTTCACTCATTTTC
*
93505 TCCCAACATATTTTTTTTCACTCATTTTC
1 TCCCAACATATTTTTCTTCACTCATTTTC
93534 T
1 T
93535 TTCCAACACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.15, C:0.29, G:0.02, T:0.54
Consensus pattern (29 bp):
TCCCAACATATTTTTCTTCACTCATTTTC
Found at i:93856 original size:6 final size:6
Alignment explanation
Indices: 93845--93922 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
93835 ATTTGTTTAA
* ** *
93845 AAATTT AAATTT -ATTTT AAATTT AAATTT -GTTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
93891 -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA
93923 ATTATTATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
5 16 0.29
6 36 0.64
7 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:93877 original size:35 final size:34
Alignment explanation
Indices: 93812--93938 Score: 137
Period size: 35 Copynumber: 3.6 Consensus size: 34
93802 CCAAACTCCC
* *
93812 TTTAAATTTATATTAAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTAT-TTTAAATTTAAATTTGTTT-AAAA
**
93848 TTTAAATTTATTTTAAATTTAAATTTGTTTTGAA
1 TTTAAATTTATTTTAAATTTAAATTTGTTTAAAA
* * * *
93882 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTT-GTTTAAAA
* *
93917 TTTAAAATTATTATAAATTTAA
1 TTTAAATTTATTTTAAATTTAA
93939 GCTCAAATAC
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
34 26 0.34
35 40 0.52
36 11 0.14
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTGTTTAAAA
Found at i:93936 original size:17 final size:17
Alignment explanation
Indices: 93812--93938 Score: 137
Period size: 17 Copynumber: 7.3 Consensus size: 17
93802 CCAAACTCCC
*
93812 TTTAAATTTATATTAAAA
1 TTTAAATTTAT-TTTAAA
* * *
93830 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
93848 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
93865 TTTAAATTTGTTTTGAA
1 TTTAAATTTATTTTAAA
* *
93882 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
93899 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
93917 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
93934 TTTAA
1 TTTAA
93939 GCTCAAATAC
Statistics
Matches: 92, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
17 54 0.59
18 38 0.41
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:93982 original size:19 final size:17
Alignment explanation
Indices: 93949--93983 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
93939 GCTCAAATAC
93949 AAAAAATTAAAAGGTCT
1 AAAAAATTAAAAGGTCT
93966 AAAATAATTATAAAGGTC
1 AAAA-AATTA-AAAGGTC
93984 CAAATTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (17 bp):
AAAAAATTAAAAGGTCT
Found at i:94752 original size:20 final size:21
Alignment explanation
Indices: 94711--94748 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
94701 TAATAGCATT
94711 ATTATTAATATATTAATAATA
1 ATTATTAATATATTAATAATA
94732 ATTA-TAATAT-TTAATAA
1 ATTATTAATATATTAATAA
94749 ATAACTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATTAATATATTAATAATA
Found at i:94759 original size:19 final size:20
Alignment explanation
Indices: 94716--94759 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
94706 GCATTATTAT
*
94716 TAATATATTAATAATAATTA
1 TAATATATTAATAATAACTA
94736 TAATAT-TTAATAAATAACTA
1 TAATATATTAAT-AATAACTA
94756 -AATA
1 TAATA
94760 AAAAAAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATATATTAATAATAACTA
Found at i:95099 original size:30 final size:30
Alignment explanation
Indices: 95059--95441 Score: 365
Period size: 29 Copynumber: 12.9 Consensus size: 30
95049 GGAGGTCCCT
95059 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTTGACCCCAA
* * * **
95089 AACTTTCAAAAATTCTATTTTT-ACCCCCG
1 AACTTCCAAAAATCCCATTTTTGACCCCAA
* *
95118 AACTTCAAAAAATCTCATTTTTGACCCCAAA
1 AACTTCCAAAAATCCCATTTTTGACCCC-AA
* * *
95149 AACTTCAAAAAATTCCATTTTT-ACCCTC-G
1 AACTTCCAAAAATCCCATTTTTGACCC-CAA
* *
95178 AACTTCCAAAAATCCCATTTTTGATCCCGA
1 AACTTCCAAAAATCCCATTTTTGACCCCAA
*** * *
95208 AACTTTTGAAAATTCCATTTTT-ACCCCTA
1 AACTTCCAAAAATCCCATTTTTGACCCCAA
* *
95237 AACTT-CTAAAATCCCATTTTTGACCTCAA
1 AACTTCCAAAAATCCCATTTTTGACCCCAA
* **
95266 AACTTTCAAAAAAT-CCATTTTT-ACCCCCG
1 AAC-TTCCAAAAATCCCATTTTTGACCCCAA
* *
95295 AACTTCCAAAAATCCCAATTTTGACCTCGATCGA
1 AACTTCCAAAAATCCCATTTTTGACC-C---CAA
* *
95329 AA-TTCCAAAAATCTCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTGACCCCAA
*
95358 AACTTCCAAAAATCCCA-TTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTGACCCCAA
*
95387 AACTTCCAAAAATCCCATTTTT-ACCCTC-G
1 AACTTCCAAAAATCCCATTTTTGACCC-CAA
95416 AACTTCCAAAAATCCCATTTTTGACC
1 AACTTCCAAAAATCCCATTTTTGACC
95442 TCGAAATTTC
Statistics
Matches: 290, Mismatches: 45, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
28 22 0.08
29 134 0.46
30 83 0.29
31 27 0.09
32 1 0.00
33 20 0.07
34 3 0.01
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.31
Consensus pattern (30 bp):
AACTTCCAAAAATCCCATTTTTGACCCCAA
Found at i:95156 original size:59 final size:59
Alignment explanation
Indices: 95059--95441 Score: 461
Period size: 59 Copynumber: 6.4 Consensus size: 59
95049 GGAGGTCCCT
*
95059 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCAAAAATTCTATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTTACCCCCG
* * *
95118 AACTTCAAAAAATCTCATTTTTGACCCCAAAAAC-TTCAAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTGACCCC-AAAACTTTC-AAAAATTCCATTTTTACCCCCG
* * ** **
95178 AACTTCCAAAAATCCCATTTTTGATCCCGAAACTTTTGAAAATTCCATTTTTACCCCTA
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTTACCCCCG
* * *
95237 AACTT-CTAAAATCCCATTTTTGACCTCAAAACTTTCAAAAAATCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTTACCCCCG
* * * **
95295 AACTTCCAAAAATCCCAATTTTGACCTCGATCGAAA-TTCCAAAAA-TCTCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTGACC-C---CAAAACTTTCAAAAATTC-CATTTTT-ACCCCCG
* * * *
95358 AACTTCCAAAAATCCCA-TTTTAACCCCAAAACTTCCAAAAATCCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTTACCCCCG
95416 AACTTCCAAAAATCCCATTTTTGACC
1 AACTTCCAAAAATCCCATTTTTGACC
95442 TCGAAATTTC
Statistics
Matches: 275, Mismatches: 36, Indels: 26
0.82 0.11 0.08
Matches are distributed among these distances:
58 74 0.27
59 97 0.35
60 53 0.19
61 3 0.01
62 22 0.08
63 26 0.09
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.31
Consensus pattern (59 bp):
AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTTACCCCCG
Found at i:96756 original size:25 final size:24
Alignment explanation
Indices: 96728--96775 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
96718 AAAAACTTTA
*
96728 TTTTTGTTAAATTTATATTAAAATG
1 TTTTTCTTAAATTTAT-TTAAAATG
* *
96753 TTTTTCTTTATTTTATTTAAAAT
1 TTTTTCTTAAATTTATTTAAAAT
96776 ATTGTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTTTCTTAAATTTATTTAAAATG
Found at i:97549 original size:12 final size:12
Alignment explanation
Indices: 97532--97611 Score: 71
Period size: 12 Copynumber: 7.1 Consensus size: 12
97522 ATAACATCTA
97532 AACAACAAAAAT
1 AACAACAAAAAT
97544 AACAAC-AAAAT
1 AACAACAAAAAT
*
97555 AACAGC---AA-
1 AACAACAAAAAT
*
97563 AACAACACAAAT
1 AACAACAAAAAT
** *
97575 AGTAACAAAAAC
1 AACAACAAAAAT
97587 AACAACAAAAAT
1 AACAACAAAAAT
*
97599 AACATCAAAAAT
1 AACAACAAAAAT
97611 A
1 A
97612 TCACTAAAAC
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
8 5 0.09
9 2 0.04
11 12 0.22
12 35 0.65
ACGTcount: A:0.70, C:0.19, G:0.03, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:97554 original size:31 final size:31
Alignment explanation
Indices: 97519--97584 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
97509 AAACGAATAA
* *
97519 AAAATAACATCTAAACAACAAAAATAACAAC
1 AAAATAACAGCAAAACAACAAAAATAACAAC
* **
97550 AAAATAACAGCAAAACAACACAAATAGTAAC
1 AAAATAACAGCAAAACAACAAAAATAACAAC
97581 AAAA
1 AAAA
97585 ACAACAACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.68, C:0.18, G:0.03, T:0.11
Consensus pattern (31 bp):
AAAATAACAGCAAAACAACAAAAATAACAAC
Found at i:97683 original size:26 final size:26
Alignment explanation
Indices: 97649--97726 Score: 81
Period size: 25 Copynumber: 3.1 Consensus size: 26
97639 AAACAACATC
*
97649 AAAACAGCAACCAAAA-AGTGAAAAAA
1 AAAAAAGCAACCAAAACAGT-AAAAAA
* *
97675 GAAGAAGC-ACCAAAACAGTAAAAAA
1 AAAAAAGCAACCAAAACAGTAAAAAA
**
97700 AAAAAAGCAA-CAAAAGGGTAAAAAA
1 AAAAAAGCAACCAAAACAGTAAAAAA
97725 AA
1 AA
97727 CAACACCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
25 34 0.79
26 9 0.21
ACGTcount: A:0.69, C:0.13, G:0.14, T:0.04
Consensus pattern (26 bp):
AAAAAAGCAACCAAAACAGTAAAAAA
Found at i:97686 original size:25 final size:25
Alignment explanation
Indices: 97649--97739 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 25
97639 AAACAACATC
*
97649 AAAACAGCAACCAAAA-AGTGAAAAAA
1 AAAAAAGC-ACCAAAACAGT-AAAAAA
* *
97675 GAAGAAGCACCAAAACAGTAAAAAA
1 AAAAAAGCACCAAAACAGTAAAAAA
* **
97700 AAAAAAGCAACAAAAGGGT-AAAAA
1 AAAAAAGCACCAAAACAGTAAAAAA
*
97724 AAACAA-CACCAAAACA
1 AAAAAAGCACCAAAACA
97740 ACAATATAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
23 7 0.13
24 10 0.19
25 27 0.52
26 8 0.15
ACGTcount: A:0.68, C:0.16, G:0.12, T:0.03
Consensus pattern (25 bp):
AAAAAAGCACCAAAACAGTAAAAAA
Found at i:113388 original size:19 final size:19
Alignment explanation
Indices: 113345--113390 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
113335 TTGTTTATTA
*
113345 TATAATTTTTATTAAATTT
1 TATAATTTTTATTAAATAT
*
113364 TA-AATTTTT-TTACATAAT
1 TATAATTTTTATTAAAT-AT
113382 TATAATTTT
1 TATAATTTT
113391 AAAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.22
18 10 0.43
19 8 0.35
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TATAATTTTTATTAAATAT
Found at i:114071 original size:9 final size:9
Alignment explanation
Indices: 114057--114089 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
114047 AAATTTTTCA
*
114057 TTTAAACAT
1 TTTAAAAAT
114066 TTTAAAAAT
1 TTTAAAAAT
114075 TTTAAAAAT
1 TTTAAAAAT
114084 TTTAAA
1 TTTAAA
114090 TTAGTAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:115365 original size:5 final size:6
Alignment explanation
Indices: 115313--115397 Score: 50
Period size: 6 Copynumber: 14.3 Consensus size: 6
115303 TTATTTTGGG
* *** *
115313 TTTAAA TTT-AG TTTAAA GTTTAAA CTTTTCT TTTAAG TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
115362 -TTAAG TTTAAA ATT-AA TTTGAA TTTAAA TTTTAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
115398 AATTAAAAAA
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
5 12 0.20
6 38 0.64
7 9 0.15
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:115367 original size:17 final size:17
Alignment explanation
Indices: 115345--115399 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
115335 AACTTTTCTT
115345 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAATTTAAA
* *
115362 TTAAGTTTAAAATTAAT
1 TTAAGTTTAAATTTAAA
*
115379 TTGAA-TTTAAATTTTAA
1 TT-AAGTTTAAATTTAAA
115396 TTAA
1 TTAA
115400 TTAAAAAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 2 0.06
17 28 0.88
18 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:116095 original size:3 final size:3
Alignment explanation
Indices: 116087--116165 Score: 50
Period size: 3 Copynumber: 25.7 Consensus size: 3
116077 CAATAATCTC
* * * * *
116087 AAT AAT AAT AAT AAT AAT AAAT ATT ACT AAT AAC ATT AAT AAT ACT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
116133 AAT GAC AGT AAT AAT AGT AAT AAGT ATT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA
116166 ATGTTATTAA
Statistics
Matches: 55, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
3 50 0.91
4 5 0.09
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:116265 original size:6 final size:6
Alignment explanation
Indices: 116254--116328 Score: 54
Period size: 6 Copynumber: 13.2 Consensus size: 6
116244 TGGGCCTAAC
* * * *
116254 AAATTT AAATTT -ATTTT AAAATT AAGTTT -ATTTT AAATTT --ATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
116298 AAATTT --ATTAT AAATTT AAATTT AAAATTT A
1 AAATTT AAATT-T AAATTT AAATTT -AAATTT A
116329 TTTAAATAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
4 7 0.13
5 9 0.17
6 29 0.54
7 9 0.17
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:116273 original size:11 final size:11
Alignment explanation
Indices: 116257--116335 Score: 64
Period size: 11 Copynumber: 7.6 Consensus size: 11
116247 GCCTAACAAA
116257 TTTAAATTTAT
1 TTTAAATTTAT
116268 TTTAAA---A-
1 TTTAAATTTAT
*
116275 -TTAAGTTTAT
1 TTTAAATTTAT
116285 TTTAAATTTA-
1 TTTAAATTTAT
116295 TTTAAATTTAT
1 TTTAAATTTAT
*
116306 TATAAATTTAAAT
1 TTTAAATTT--AT
*
116319 TTAAAATTTA-
1 TTTAAATTTAT
116329 TTTAAAT
1 TTTAAAT
116336 AATGCCTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
6 4 0.07
8 1 0.02
9 1 0.02
10 16 0.30
11 23 0.43
13 9 0.17
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:116283 original size:17 final size:17
Alignment explanation
Indices: 116258--116321 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
116248 CCTAACAAAT
116258 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
116275 TTAAGTTTATTTTAAATTTA
1 TTAAATTTATTTTAAA---A
* *
116295 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
116313 TTAAATTTA
1 TTAAATTTA
116322 AAATTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 24 0.62
20 1 0.03
21 14 0.36
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:116301 original size:38 final size:34
Alignment explanation
Indices: 116256--116335 Score: 97
Period size: 38 Copynumber: 2.2 Consensus size: 34
116246 GGCCTAACAA
* *
116256 ATTTAAATTTATTTTAAAATTAAGTTTATTTTAAATTT
1 ATTTAAATTTATTATAAAATTAA----ATTTAAAATTT
*
116294 ATTTAAATTTATTATAAATTTAAATTTAAAATTT
1 ATTTAAATTTATTATAAAATTAAATTTAAAATTT
116328 ATTTAAAT
1 ATTTAAAT
116336 AATGCCTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
34 18 0.46
38 21 0.54
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (34 bp):
ATTTAAATTTATTATAAAATTAAATTTAAAATTT
Found at i:116331 original size:17 final size:17
Alignment explanation
Indices: 116283--116335 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
116273 AATTAAGTTT
*
116283 ATTTTAAATTTATTTAA
1 ATTTAAAATTTATTTAA
** **
116300 ATTTATTATAAATTTAA
1 ATTTAAAATTTATTTAA
116317 ATTTAAAATTTATTTAA
1 ATTTAAAATTTATTTAA
116334 AT
1 AT
116336 AATGCCTAAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTAAAATTTATTTAA
Found at i:118117 original size:29 final size:29
Alignment explanation
Indices: 118074--118596 Score: 473
Period size: 29 Copynumber: 17.8 Consensus size: 29
118064 AGAGGTCCTT
*
118074 AAACTGTCCAAAAATTCCATTTTTACCCTT
1 AAACT-TCCAAAAATTCCATTTTTACCCTC
* *
118104 AAACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* * *
118134 AAACTTCTAAAAATTCAATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* * * *
118163 GAGCTTCCAAAAATCCCATTTTGACCC-C
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* *
118191 AAAACTTCTAAAAATTTCATTTTTACCCTC
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* *
118221 GAACTTCCAAAAATCCCATTTTTGA-CCTC
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* **
118250 GAAACTTCTAAAAATTATATTTTTACACCT-
1 -AAACTTCCAAAAATTCCATTTTTAC-CCTC
*
118280 AAACTTCCAAAAATCCCATTTTTGACCC-C
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* * * *
118309 AAAACTTCAAAAAATTCTATTTTTGCCCCC
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* *
118339 AAACTTCCAAAAA-TCCTATTTTTAACCTTA
1 AAACTTCCAAAAATTCC-ATTTTT-ACCCTC
*
118369 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
*
118398 AAACTTCCAAAAAATCCCATTTTTACCCTC
1 AAACTTCC-AAAAATTCCATTTTTACCCTC
118428 AAACTTCCAAAAATTCCATTTTTAGCCC-C
1 AAACTTCCAAAAATTCCATTTTTA-CCCTC
*
118457 AAACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
118487 AAACTTCC-AAAATTACCA-TTTTA-CCTC
1 AAACTTCCAAAAATT-CCATTTTTACCCTC
* *
118514 AGAA-TGTCCAAAAACTCCATTTTCGA-CCTC
1 A-AACT-TCCAAAAATTCCATTTT-TACCCTC
*
118544 GAAAC-TCTC-AAAATTACC-CTTTTACCCTC
1 -AAACTTC-CAAAAATT-CCATTTTTACCCTC
*
118573 AAA-TGTCCAAAAATTCTATTTTTA
1 AAACT-TCCAAAAATTCCATTTTTA
118597 ACTTCGAATT
Statistics
Matches: 403, Mismatches: 57, Indels: 67
0.76 0.11 0.13
Matches are distributed among these distances:
27 5 0.01
28 18 0.04
29 227 0.56
30 146 0.36
31 7 0.02
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCTC
Found at i:118175 original size:59 final size:59
Alignment explanation
Indices: 118074--118508 Score: 545
Period size: 59 Copynumber: 7.4 Consensus size: 59
118064 AGAGGTCCTT
**
118074 AAACTGTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACT-TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTA
* * * * * *
118134 AAACTTCTAAAAATTCAATTTTTACCCCCGAGCTTCCAAAAATCCCA-TTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTA
* * * * * *
118192 AAACTTCTAAAAATTTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA-CCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCT-A
* ** * * * *
118251 AAACTTCTAAAAATTATATTTTTACACCTAAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTA
* * * * *
118310 AAACTTCAAAAAATTCTATTTTTGCCCCCAAACTTCCAAAAATCCTATTTTTAACCTTA
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTA
*
118369 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAAATCCCATTTTT-ACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCC-AAAAATCCCATTTTTAACCCTA
* *
118428 AAACTTCCAAAAATTCCATTTTTAGCCCCAAACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTA
118487 AAACTTCC-AAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
118509 ACCTCAGAAT
Statistics
Matches: 329, Mismatches: 40, Indels: 13
0.86 0.10 0.03
Matches are distributed among these distances:
58 74 0.22
59 234 0.71
60 21 0.06
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTA
Found at i:118604 original size:58 final size:57
Alignment explanation
Indices: 118344--118630 Score: 189
Period size: 58 Copynumber: 4.9 Consensus size: 57
118334 CCCCCAAACT
** *
118344 TCCAAAAA-TCCTATTTTTAACCTTAAAACTTCCAAAAATT-CCATTTTTACCCCCA-AACT-
1 TCCAAAAATTCC-ATTTTTAA-CTCGAAACTTCC-AAAATTACCA-TTTTA-CCTCAGAA-TG
* * *
118403 TCCAAAAAATCCCATTTTTACCCTC-AAACTTCCAAAAATT-CCATTTTTAGCCCCA-AACT-
1 TCC-AAAAATTCCATTTTTA-ACTCGAAACTTCC-AAAATTACCA-TTTTA-CCTCAGAA-TG
* *
118462 TCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAATTACCATTTTACCTCAGAATG
1 TCCAAAAATTCCATTTTTAACTC-GAAACTTCCAAAATTACCATTTTACCTCAGAATG
* * * *
118520 TCCAAAAACTCCATTTTCGACCTCGAAAC-TCTCAAAATTACCCTTTTACCCTCA-AATG
1 TCCAAAAATTCCATTTT-TAACTCGAAACTTC-CAAAATTACCATTTTA-CCTCAGAATG
* ** * *
118578 TCCAAAAATTCTATTTTTAACTTCGAATTTTCTAAAAATTACCATTTCACCTC
1 TCCAAAAATTCCATTTTTAAC-TCGAAACTTC-CAAAATTACCATTTTACCTC
118631 TCGAGAATAA
Statistics
Matches: 192, Mismatches: 23, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
57 11 0.06
58 91 0.47
59 74 0.39
60 14 0.07
61 2 0.01
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (57 bp):
TCCAAAAATTCCATTTTTAACTCGAAACTTCCAAAATTACCATTTTACCTCAGAATG
Done.