Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010692.1 Kokia drynarioides strain JFW-HI SEQ_125639, 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: 64231
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:7416 original size:11 final size:11
Alignment explanation
Indices: 7400--7424 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7390 AATAACATTA
7400 AAAAAAAAAAG
1 AAAAAAAAAAG
7411 AAAAAAAAAAG
1 AAAAAAAAAAG
7422 AAA
1 AAA
7425 GGGTTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:12858 original size:20 final size:20
Alignment explanation
Indices: 12825--12863 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12815 TGTGCCATAT
* *
12825 ACTCATTAATAATCTAATCC
1 ACTCATTAACAATCAAATCC
*
12845 ACTCATTAGCAATCAAATC
1 ACTCATTAACAATCAAATC
12864 AAAGAAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.31
Consensus pattern (20 bp):
ACTCATTAACAATCAAATCC
Found at i:15143 original size:97 final size:97
Alignment explanation
Indices: 14977--15170 Score: 388
Period size: 97 Copynumber: 2.0 Consensus size: 97
14967 GGAACTGTCA
14977 ACTTAAACACGAGTACTACGCTCAACTAACAACATATTCCTTACAGCATCAAGAGGCTCTGAAAA
1 ACTTAAACACGAGTACTACGCTCAACTAACAACATATTCCTTACAGCATCAAGAGGCTCTGAAAA
15042 CAAGTAGACATTGCCTACATCACTCGAACTTG
66 CAAGTAGACATTGCCTACATCACTCGAACTTG
15074 ACTTAAACACGAGTACTACGCTCAACTAACAACATATTCCTTACAGCATCAAGAGGCTCTGAAAA
1 ACTTAAACACGAGTACTACGCTCAACTAACAACATATTCCTTACAGCATCAAGAGGCTCTGAAAA
15139 CAAGTAGACATTGCCTACATCACTCGAACTTG
66 CAAGTAGACATTGCCTACATCACTCGAACTTG
15171 TTTTGGTCAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (97 bp):
ACTTAAACACGAGTACTACGCTCAACTAACAACATATTCCTTACAGCATCAAGAGGCTCTGAAAA
CAAGTAGACATTGCCTACATCACTCGAACTTG
Found at i:17742 original size:19 final size:19
Alignment explanation
Indices: 17715--17754 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
17705 AATTTGAATC
*
17715 CTAAATTAGATCAAAATAA
1 CTAAATTAGACCAAAATAA
*
17734 CTAAGTTAGACCAAAATAA
1 CTAAATTAGACCAAAATAA
17753 CT
1 CT
17755 CAATATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (19 bp):
CTAAATTAGACCAAAATAA
Found at i:20193 original size:2 final size:2
Alignment explanation
Indices: 20181--20239 Score: 109
Period size: 2 Copynumber: 29.0 Consensus size: 2
20171 AACAATAATC
20181 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20224 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
20240 TTGATTCTCC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 54 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21020 original size:29 final size:29
Alignment explanation
Indices: 20958--21014 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
20948 AAACAATAAT
*
20958 ATAAATGACTAAAACGTAACATTTCAAAC
1 ATAAATGACTAAAACGTAACATTTAAAAC
*
20987 ATAAATGACTAAAATGT-A-ATTTAAAAC
1 ATAAATGACTAAAACGTAACATTTAAAAC
21014 A
1 A
21015 AATAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 9 0.35
28 1 0.04
29 16 0.62
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.26
Consensus pattern (29 bp):
ATAAATGACTAAAACGTAACATTTAAAAC
Found at i:21750 original size:2 final size:2
Alignment explanation
Indices: 21743--21784 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
21733 CTACCCCATA
21743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21785 GTTCATCCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27235 original size:12 final size:12
Alignment explanation
Indices: 27218--27244 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
27208 ATTTGGGGGA
27218 AAAATCACATCT
1 AAAATCACATCT
27230 AAAATCACATCT
1 AAAATCACATCT
27242 AAA
1 AAA
27245 CGCGCACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATCACATCT
Found at i:27484 original size:295 final size:295
Alignment explanation
Indices: 26948--27822 Score: 1642
Period size: 295 Copynumber: 3.0 Consensus size: 295
26938 ACTATTTGAC
26948 AACGCACACACACCTTACACACGTAGACGCTCGAACCCGATATCCCTAAGATAAACAACATCATT
1 AACGCACACACACCTTACACACGTAGACGCTCGAACCCGATATCCCTAAGATAAACAACATCATT
*
27013 TTTTCCACTGGAATCATTTGTTGAGTTCAGAACAATATGATTATTAAAAAAACAATTTTTTATAG
66 TTTTCCACTGGAATCACTTGTTGAGTTCAGAACAATATGATTATTAAAAAAACAATTTTTTATAG
*
27078 TAATATTTTTATCACATGCTAATGAAAAAAATAGATTAATTATCGTCACATGCAACTTTATTATT
131 TAATATTTTTATCACATGCTAATGGAAAAAATAGATTAATTATCGTCACATGCAACTTTATTATT
27143 AAGAAAAGTAACATCAAAACAACAATCAACATCAACCATCTTACTTGAAGAGATAAGTTGGCTTT
196 AAGAAAAGTAACATCAAAACAACAATCAACATCAACCATCTTACTTGAAGAGATAAGTTGGCTTT
27208 ATTTGGGGGAAAAATCACATCTAAAATCACATCTA
261 ATTTGGGGGAAAAATCACATCTAAAATCACATCTA
*
27243 AACGCGCACACACCTTACACACGTAGACGCTCGAACCCGATATCCCTAAGATAAACAACATCATT
1 AACGCACACACACCTTACACACGTAGACGCTCGAACCCGATATCCCTAAGATAAACAACATCATT
* * *
27308 TTTTCCACTGAAATCACTTGTTGAGTTCAAAACAATATGATTATTAAAAAACCAATTTTTTATAG
66 TTTTCCACTGGAATCACTTGTTGAGTTCAGAACAATATGATTATTAAAAAAACAATTTTTTATAG
27373 TAATATTTTTATCACATGCTAATGGAAAAAATAGATTAATTATCGTCACATGCAACTTTATTATT
131 TAATATTTTTATCACATGCTAATGGAAAAAATAGATTAATTATCGTCACATGCAACTTTATTATT
*
27438 AAGAAAAGTAACATCAAAACAACAATCAACATCAACCATCTTACTTGAAGAGATAAGTTGACTTT
196 AAGAAAAGTAACATCAAAACAACAATCAACATCAACCATCTTACTTGAAGAGATAAGTTGGCTTT
27503 ATTTGGGGGAAAAATCACATCTAAAATCACATCTA
261 ATTTGGGGGAAAAATCACATCTAAAATCACATCTA
* *
27538 AACGCACACACCCCTTACACACGTAGACGCTCGAACCCGATATCCCTAAGATAAACAATATCATT
1 AACGCACACACACCTTACACACGTAGACGCTCGAACCCGATATCCCTAAGATAAACAACATCATT
* *
27603 TTTTCCATTGGAATCACTTGTTGAATTCAGAACAATATGATTATTAAAAAAACAATTTTTTATAG
66 TTTTCCACTGGAATCACTTGTTGAGTTCAGAACAATATGATTATTAAAAAAACAATTTTTTATAG
27668 TAATATTTTTATCACATGCTAATGGAAAAAATAGATTAATTATCGTCACATGCAACTTTATTATT
131 TAATATTTTTATCACATGCTAATGGAAAAAATAGATTAATTATCGTCACATGCAACTTTATTATT
*
27733 AAGAAAAGTAACATCAAAACAACAATCAACATCAACCATCTTACTTAAAGAGATAAGTTGGCTTT
196 AAGAAAAGTAACATCAAAACAACAATCAACATCAACCATCTTACTTGAAGAGATAAGTTGGCTTT
27798 ATTTGGGGGAAAAATCACATCTAAA
261 ATTTGGGGGAAAAATCACATCTAAA
27823 CTCCCCCACA
Statistics
Matches: 563, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
295 563 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (295 bp):
AACGCACACACACCTTACACACGTAGACGCTCGAACCCGATATCCCTAAGATAAACAACATCATT
TTTTCCACTGGAATCACTTGTTGAGTTCAGAACAATATGATTATTAAAAAAACAATTTTTTATAG
TAATATTTTTATCACATGCTAATGGAAAAAATAGATTAATTATCGTCACATGCAACTTTATTATT
AAGAAAAGTAACATCAAAACAACAATCAACATCAACCATCTTACTTGAAGAGATAAGTTGGCTTT
ATTTGGGGGAAAAATCACATCTAAAATCACATCTA
Found at i:27530 original size:12 final size:12
Alignment explanation
Indices: 27513--27539 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
27503 ATTTGGGGGA
27513 AAAATCACATCT
1 AAAATCACATCT
27525 AAAATCACATCT
1 AAAATCACATCT
27537 AAA
1 AAA
27540 CGCACACACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATCACATCT
Found at i:28014 original size:3 final size:3
Alignment explanation
Indices: 28006--28041 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
27996 AGCCCTTTTG
28006 TTC TTC TTCC TT- TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC
28042 ACTTCATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:28019 original size:15 final size:15
Alignment explanation
Indices: 27999--28041 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
27989 CCCAATAAGC
*
27999 CCTTTTGTTCTTCTT
1 CCTTTTCTTCTTCTT
28014 CCTTTTCTTCTTCTT
1 CCTTTTCTTCTTCTT
28029 -CTTCTTCTTCTTC
1 CCTT-TTCTTCTTC
28042 ACTTCATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (15 bp):
CCTTTTCTTCTTCTT
Found at i:33553 original size:33 final size:32
Alignment explanation
Indices: 33516--33591 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 32
33506 AAGAAGTGGT
33516 GGTAGCTTTGGGATTGGGATTGAAGGCAATGGA
1 GGTAG-TTTGGGATTGGGATTGAAGGCAATGGA
*
33549 GGTA-----GGTTTGGGATTGAAGGCAATGGA
1 GGTAGTTTGGGATTGGGATTGAAGGCAATGGA
33576 GGTAGGTTTGGGATTG
1 GGTA-GTTTGGGATTG
33592 AAGGCAATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
27 26 0.74
33 9 0.26
ACGTcount: A:0.22, C:0.04, G:0.45, T:0.29
Consensus pattern (32 bp):
GGTAGTTTGGGATTGGGATTGAAGGCAATGGA
Found at i:33559 original size:27 final size:27
Alignment explanation
Indices: 33529--33660 Score: 162
Period size: 27 Copynumber: 4.9 Consensus size: 27
33519 AGCTTTGGGA
33529 TTGGGATTGAAGGCAATGGAGGTAGGT
1 TTGGGATTGAAGGCAATGGAGGTAGGT
33556 TTGGGATTGAAGGCAATGGAGGTAGGT
1 TTGGGATTGAAGGCAATGGAGGTAGGT
33583 TTGGGATTGAAGGCAATGGAGGTATGG-
1 TTGGGATTGAAGGCAATGGAGGTA-GGT
* ** * **
33610 -TGGGCAAT-CCGGGAATTGTTGGTAGGT
1 TTGGG-ATTGAAGGCAA-TGGAGGTAGGT
33637 TTGGGATTGAAGGCAATGGAGGTA
1 TTGGGATTGAAGGCAATGGAGGTA
33661 TGGTAGTAGG
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
26 10 0.11
27 67 0.77
28 10 0.11
ACGTcount: A:0.25, C:0.05, G:0.43, T:0.27
Consensus pattern (27 bp):
TTGGGATTGAAGGCAATGGAGGTAGGT
Found at i:34272 original size:59 final size:59
Alignment explanation
Indices: 34180--34314 Score: 171
Period size: 59 Copynumber: 2.3 Consensus size: 59
34170 TTAATAAAAC
* * * * * * *
34180 ATTTGGTACCTAAACTTGACATTTTTTCTTAATTTGGTTCCTGAGCTTTTTTCGACTCA
1 ATTTGGTACCTAAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTAGACTCA
* * *
34239 ATTTGGTATCTAAATTTGACACTTTTTCCTAATTTGGTACCTAAATTTTTTTAGATTCA
1 ATTTGGTACCTAAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTAGACTCA
*
34298 ATTTGGTACCGAAATTT
1 ATTTGGTACCTAAATTT
34315 ATTAAATATT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (59 bp):
ATTTGGTACCTAAATTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTAGACTCA
Found at i:34536 original size:58 final size:58
Alignment explanation
Indices: 34450--34559 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 58
34440 ATTAATATTA
* * *
34450 AAAAAGCTTAGGTATCAAATTAAGAAAAAATGTCAAGTTCAGATACCAAATTGACCTC
1 AAAAAGCTTAAGTACCAAATTAAAAAAAAATGTCAAGTTCAGATACCAAATTGACCTC
* * * * *
34508 AAAAAGTTTAAGTACCAACTTAAAAAAAAGTGTCAAGTTTAGATATCAAATT
1 AAAAAGCTTAAGTACCAAATTAAAAAAAAATGTCAAGTTCAGATACCAAATT
34560 AGAAAAAAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (58 bp):
AAAAAGCTTAAGTACCAAATTAAAAAAAAATGTCAAGTTCAGATACCAAATTGACCTC
Found at i:34547 original size:31 final size:31
Alignment explanation
Indices: 34511--34589 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
34501 TGACCTCAAA
* **
34511 AAGTTTAAGTACCAACTTAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTACC
* *
34542 AAGTTT-AGATATCAAATTAGAAAAAAGTACC
1 AAGTTTAAG-TACCAAATTAAAAAAAAGTACC
34573 AAGTTTATA-TACCAAAT
1 AAGTTTA-AGTACCAAAT
34590 ATTATATCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
30 2 0.05
31 36 0.92
33 1 0.03
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAGTACC
Found at i:35682 original size:21 final size:22
Alignment explanation
Indices: 35640--35682 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
35630 ACAAATTCAG
*
35640 AAAAATATCAAATAAATTGAAA
1 AAAAATATCAAATAAATGGAAA
* *
35662 AAAAATAT-ATATATATGGAAA
1 AAAAATATCAAATAAATGGAAA
35683 GCTTTAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (22 bp):
AAAAATATCAAATAAATGGAAA
Found at i:40270 original size:20 final size:20
Alignment explanation
Indices: 40220--40270 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
40210 TAAAACCATT
*
40220 AAAAATA-TAGAAAATCATAA
1 AAAAATATTA-AAAATCAAAA
* * *
40240 AAATATTTTAAAAATTAAAA
1 AAAAATATTAAAAATCAAAA
40260 AAAAATATTAA
1 AAAAATATTAA
40271 TTCTTTCATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAATATTAAAAATCAAAA
Found at i:41280 original size:20 final size:21
Alignment explanation
Indices: 41257--41305 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
41247 AAAAAATCTC
*
41257 AAATTTTTTAAAAATCCAAA-
1 AAATTTTATAAAAATCCAAAT
* * *
41277 AAATTATATAAAATTCTAAAT
1 AAATTTTATAAAAATCCAAAT
41298 AAATTTTA
1 AAATTTTA
41306 GAAATATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTTTATAAAAATCCAAAT
Found at i:41542 original size:11 final size:11
Alignment explanation
Indices: 41526--41550 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41516 CAACAAATTC
41526 AAAAAAATAAA
1 AAAAAAATAAA
41537 AAAAAAATAAA
1 AAAAAAATAAA
41548 AAA
1 AAA
41551 TATGGAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:42051 original size:24 final size:24
Alignment explanation
Indices: 42000--42052 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
41990 CTGAGCTAAA
* *
42000 TTTTATTTATATTTTAAATGAATG
1 TTTTACTTATATTTTAAATAAATG
*
42024 TTTTACTTATATTTTTAATAAGAT-
1 TTTTACTTATATTTTAAATAA-ATG
42048 TTTTA
1 TTTTA
42053 TACAAACCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTACTTATATTTTAAATAAATG
Found at i:43340 original size:18 final size:19
Alignment explanation
Indices: 43296--43340 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
43286 GGTGTTTTAA
43296 ATTTAAAACCATTAAAGAT
1 ATTTAAAACCATTAAAGAT
** *
43315 ATAAAAAATCA-TAAAGAT
1 ATTTAAAACCATTAAAGAT
43333 ATTTAAAA
1 ATTTAAAA
43341 ATTACGAAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (19 bp):
ATTTAAAACCATTAAAGAT
Found at i:43407 original size:20 final size:19
Alignment explanation
Indices: 43356--43398 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
43346 GAAAGTTATA
*
43356 AAATTATAAAAAATAGTAT
1 AAATGATAAAAAATAGTAT
43375 AAATGATACAAAAACTA-TAT
1 AAATGATA-AAAAA-TAGTAT
43395 AAAT
1 AAAT
43399 TGTTAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 12 0.57
21 2 0.10
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (19 bp):
AAATGATAAAAAATAGTAT
Found at i:43487 original size:20 final size:20
Alignment explanation
Indices: 43450--43487 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43440 AAATATATAT
*
43450 AAATTAAAAAAGATAAAAGA
1 AAATTAAAAAAGAAAAAAGA
43470 AAATGTAAAAAA-AAAAAA
1 AAAT-TAAAAAAGAAAAAA
43488 ATTAAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (20 bp):
AAATTAAAAAAGAAAAAAGA
Found at i:43488 original size:21 final size:20
Alignment explanation
Indices: 43450--43488 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
43440 AAATATATAT
* *
43450 AAATTAAAAAAGATAAAAGA
1 AAATTAAAAAAAAAAAAAGA
43470 AAATGTAAAAAAAAAAAAA
1 AAAT-TAAAAAAAAAAAAA
43489 TTAAAACTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (20 bp):
AAATTAAAAAAAAAAAAAGA
Found at i:43595 original size:17 final size:17
Alignment explanation
Indices: 43573--43619 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
43563 GCAGTTTTAG
*
43573 ATTTTAAATTTTAATTC
1 ATTTTAAATTTAAATTC
* *
43590 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTC
*
43607 ATTGTAAATTTAA
1 ATTTTAAATTTAA
43620 GCTTATTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTC
Found at i:43615 original size:34 final size:33
Alignment explanation
Indices: 43577--43643 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
43567 TTTTAGATTT
*
43577 TAAATTTTAA-TTCATTTTAAGTTTAAATTTATTG
1 TAAA-TTTAACTT-ATTTGAAGTTTAAATTTATTG
*
43611 TAAATTTAAGCTTATTTGGAGTTTAAATTTATT
1 TAAATTTAA-CTTATTTGAAGTTTAAATTTATT
43644 TTGAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.17
34 22 0.76
35 2 0.07
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (33 bp):
TAAATTTAACTTATTTGAAGTTTAAATTTATTG
Found at i:43786 original size:15 final size:15
Alignment explanation
Indices: 43761--43797 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
43751 CCCATTACAC
43761 CCCAAACCTAATTGA
1 CCCAAACCTAATTGA
* *
43776 GCCAAATCTAATTGA
1 CCCAAACCTAATTGA
43791 CCCAAAC
1 CCCAAAC
43798 AGGCCCAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.32, G:0.08, T:0.19
Consensus pattern (15 bp):
CCCAAACCTAATTGA
Found at i:44415 original size:3 final size:3
Alignment explanation
Indices: 44409--44451 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
44399 ATAAATTCAT
*
44409 TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA -AA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
44452 TTATTATTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:44790 original size:28 final size:28
Alignment explanation
Indices: 44751--44808 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
44741 TTTTAAGAGG
44751 AAAAAGAAAGAGCAAATAAAGAGAATCA
1 AAAAAGAAAGAGCAAATAAAGAGAATCA
44779 AAAAAGAAAGAGCAAATAAAGAGAATCA
1 AAAAAGAAAGAGCAAATAAAGAGAATCA
44807 AA
1 AA
44809 CGTTTTTCAA
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:0.69, C:0.07, G:0.17, T:0.07
Consensus pattern (28 bp):
AAAAAGAAAGAGCAAATAAAGAGAATCA
Found at i:45687 original size:29 final size:27
Alignment explanation
Indices: 45640--45833 Score: 124
Period size: 29 Copynumber: 6.7 Consensus size: 27
45630 CTTCCAAAAC
45640 TTTCC-AAAATTACCATTTTACCCCTATA
1 TTTCCAAAAATTACCATTTTACCCC-A-A
*
45668 TTTCCAAAAATT-CCATTTTTGATCCCAAA
1 TTTCCAAAAATTACCA-TTTT-A-CCCCAA
* *
45697 TTCCCTAAAATTACCATTTTACCCTCGAA
1 TTTCCAAAAATTACCATTTTACCC-C-AA
** *
45726 AGTCCAAAAATT-CCATTTTTAACCTCAAA
1 TTTCCAAAAATTACCA-TTTT-ACC-CCAA
*
45755 CTTTCCTAAAATTACCATTTTACCCTCGAA
1 -TTTCCAAAAATTACCATTTTACCC-C-AA
* *
45785 TGTCCAAAAATTACTATTTTACCCTCAAA
1 TTTCCAAAAATTACCATTTTACCC-C-AA
** *
45814 CCTCCGAAAATTACCATTTT
1 TTTCCAAAAATTACCATTTT
45834 CTCCCGGGCA
Statistics
Matches: 131, Mismatches: 21, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
27 3 0.02
28 13 0.10
29 85 0.65
30 23 0.18
31 7 0.05
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (27 bp):
TTTCCAAAAATTACCATTTTACCCCAA
Found at i:45778 original size:59 final size:59
Alignment explanation
Indices: 45636--45833 Score: 246
Period size: 58 Copynumber: 3.4 Consensus size: 59
45626 CAAACTTCCA
* * *
45636 AAACTTTCC-AAAATTACCATTTTACCC-CTATATTTCCAAAAATTCCATTTTTGATCC-C
1 AAACTTTCCTAAAATTACCATTTTACCCTCGA-ATGTCCAAAAATTCCATTTTT-AACCTC
* *
45694 AAA-TTCCCTAAAATTACCATTTTACCCTCGAAAGTCCAAAAATTCCATTTTTAACCTC
1 AAACTTTCCTAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCTC
* *
45752 AAACTTTCCTAAAATTACCATTTTACCCTCGAATGTCCAAAAATTAC-TATTTTACCCTC
1 AAACTTTCCTAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCAT-TTTTAACCTC
* *
45811 AAAC-CTCCGAAAATTACCATTTT
1 AAACTTTCCTAAAATTACCATTTT
45834 CTCCCGGGCA
Statistics
Matches: 124, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
57 7 0.06
58 62 0.50
59 55 0.44
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (59 bp):
AAACTTTCCTAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCTC
Found at i:47762 original size:15 final size:16
Alignment explanation
Indices: 47727--47767 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
47717 GGTAAAAGAG
47727 TAAAAAGAAATAAAAC
1 TAAAAAGAAATAAAAC
*
47743 T-AAAAGAAATTAAA-
1 TAAAAAGAAATAAAAC
47757 TAAAAAAGAAA
1 T-AAAAAGAAA
47768 GCAATGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 12 0.55
16 9 0.41
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (16 bp):
TAAAAAGAAATAAAAC
Found at i:55737 original size:17 final size:17
Alignment explanation
Indices: 55715--55773 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
55705 ATGAGAATAG
55715 ATTTTTAATTAATTAAA
1 ATTTTTAATTAATTAAA
*
55732 ATTTTTAA--ACTTAAA
1 ATTTTTAATTAATTAAA
*
55747 TCTTATTTAATTAATTAAA
1 -ATT-TTTAATTAATTAAA
*
55766 AATTTTAA
1 ATTTTTAA
55774 ACCTAAATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 6 0.18
16 2 0.06
17 18 0.55
18 1 0.03
19 6 0.18
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTTAATTAATTAAA
Found at i:55756 original size:34 final size:34
Alignment explanation
Indices: 55718--55785 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
55708 AGAATAGATT
* *
55718 TTTAATTAATTAAAATTTTTAAACTTAAATCTTA
1 TTTAATTAATTAAAAATTTTAAACCTAAATCTTA
55752 TTTAATTAATTAAAAATTTTAAACCTAAATCTTA
1 TTTAATTAATTAAAAATTTTAAACCTAAATCTTA
55786 ACTGAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (34 bp):
TTTAATTAATTAAAAATTTTAAACCTAAATCTTA
Done.