Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013435.1 Kokia drynarioides strain JFW-HI SEQ_128461, 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: 109236
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 234 characters in sequence are not A, C, G, or T
Found at i:2349 original size:28 final size:29
Alignment explanation
Indices: 2306--2366 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
2296 AAAATGAGAC
2306 TTTTCGGATACTCGGGGAG-AAAATGGTAA
1 TTTTCGGATACTC-GGGAGTAAAATGGTAA
* *
2335 TTTT-GGATTCTCGGGAGTGAAATGGTAA
1 TTTTCGGATACTCGGGAGTAAAATGGTAA
2363 TTTT
1 TTTT
2367 AGGAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.17
28 20 0.69
29 4 0.14
ACGTcount: A:0.26, C:0.08, G:0.30, T:0.36
Consensus pattern (29 bp):
TTTTCGGATACTCGGGAGTAAAATGGTAA
Found at i:2590 original size:59 final size:59
Alignment explanation
Indices: 2412--2696 Score: 371
Period size: 59 Copynumber: 4.9 Consensus size: 59
2402 ATCCGGGGGT
* * * * *
2412 AAAATGGTAATTTTGGAAGTTCGGGGGTAAAAACGGAATTTTAGGAAGTTTC-A-GTGT-
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGT-TA
* * *
2469 AAAATGGGATTTTTGGAAGTTCAAGGGT-AAAATGGAATTTTTGGAAGTTTCGGGGTTT
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTTA
* * *
2527 AAAATGGGTTTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTA
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTTA
* * *
2586 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTTA
* * *
2645 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAAACGAAATTTTTGGACAGTTT
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGA-AGTTT
2697 AGGGACCTCC
Statistics
Matches: 203, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
56 21 0.10
57 25 0.12
58 27 0.13
59 125 0.62
60 5 0.02
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.35
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTTA
Found at i:2700 original size:29 final size:29
Alignment explanation
Indices: 2408--2700 Score: 294
Period size: 29 Copynumber: 10.1 Consensus size: 29
2398 GGACATCCGG
* *
2408 GGGT-AAAATGGTAA-TTTTGGAAGTTCGG
1 GGGTAAAAATGG-AATTTTTGGAAGTTTGA
* * *
2436 GGGTAAAAACGGAATTTTAGGAAGTTTCA
1 GGGTAAAAATGGAATTTTTGGAAGTTTGA
* * **
2465 GTGT-AAAATGGGATTTTTGGAAGTTCAA
1 GGGTAAAAATGGAATTTTTGGAAGTTTGA
2493 GGGT-AAAATGGAATTTTTGGAAGTTTCG-
1 GGGTAAAAATGGAATTTTTGGAAGTTT-GA
* ** * *
2521 GGGTTTAAAATGGGTTTTTTGGAAGTTCGG
1 GGG-TAAAAATGGAATTTTTGGAAGTTTGA
2551 GGGTAAAAATGGAATTTTTGGAAGTTTTGA
1 GGGTAAAAATGGAATTTTTGGAAG-TTTGA
* *
2581 GGTTAAAAATGGGATTTTTGGAAGTTTGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTGA
*
2610 GGGTAAAAATGAAATTTTTGGAAGTTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTT-GA
*
2640 -GGTCAAAAATGGGATTTTTGGAAGTTTGA
1 GGGT-AAAAATGGAATTTTTGGAAGTTTGA
* *
2669 GGGTAAAAACGAAATTTTTGGACAGTTT-A
1 GGGTAAAAATGGAATTTTTGGA-AGTTTGA
2698 GGG
1 GGG
2701 ACCTCCGGGG
Statistics
Matches: 221, Mismatches: 33, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
28 51 0.23
29 92 0.42
30 78 0.35
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTGA
Found at i:4384 original size:16 final size:16
Alignment explanation
Indices: 4348--4384 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4338 TATTTGGGTC
*
4348 ATTTGTAATTGGGCCG
1 ATTTGTAATTGGGCCA
*
4364 TTTTGTAATTGGGCCA
1 ATTTGTAATTGGGCCA
4380 ATTTG
1 ATTTG
4385 ATCTGTACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.27, T:0.43
Consensus pattern (16 bp):
ATTTGTAATTGGGCCA
Found at i:4437 original size:7 final size:6
Alignment explanation
Indices: 4418--4479 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
4408 AATTGGACAT
* *
4418 TTTAAA TTTAAA TTTCAAA --TAAA TTTAAA TTTAAA -ATAAA CTT-AA
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
4463 TTTAAA AATAAA TTTAA
1 TTTAAA TTTAAA TTTAA
4480 TTTCCAATAG
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
4 3 0.07
5 9 0.20
6 29 0.66
7 3 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:4442 original size:17 final size:16
Alignment explanation
Indices: 4420--4482 Score: 81
Period size: 17 Copynumber: 3.8 Consensus size: 16
4410 TTGGACATTT
*
4420 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTAAAA
4437 TAAATTTAAATTTAAAA
1 TAAATTT-AATTTAAAA
*
4454 TAAACTTAATTTAAAAA
1 TAAATTTAATTT-AAAA
4471 TAAATTTAATTT
1 TAAATTTAATTT
4483 CCAATAGGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
16 5 0.12
17 37 0.88
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTAATTTAAAA
Found at i:6233 original size:22 final size:23
Alignment explanation
Indices: 6205--6250 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
6195 CAAACAGAAG
6205 TTACCAATCATA-TTTTCATTTT
1 TTACCAATCATATTTTTCATTTT
*
6227 TTACCAATCGTATTTTTCATTTT
1 TTACCAATCATATTTTTCATTTT
6250 T
1 T
6251 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.24, C:0.17, G:0.02, T:0.57
Consensus pattern (23 bp):
TTACCAATCATATTTTTCATTTT
Found at i:11581 original size:17 final size:19
Alignment explanation
Indices: 11556--11601 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
11546 CTTGTTTAAG
*
11556 AATAATTTTAT-TCT-AAA
1 AATATTTTTATATCTCAAA
11573 AATATTTTT-TATCTCAAA
1 AATATTTTTATATCTCAAA
11591 AATACTTTTTA
1 AATA-TTTTTA
11602 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 11 0.46
18 7 0.29
19 5 0.21
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTTTTATATCTCAAA
Found at i:11584 original size:18 final size:18
Alignment explanation
Indices: 11561--11601 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
11551 TTAAGAATAA
*
11561 TTTTAT-TCTAAAAATATT
1 TTTTATCTC-AAAAATACT
11579 TTTTATCTCAAAAATACT
1 TTTTATCTCAAAAATACT
11597 TTTTA
1 TTTTA
11602 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTATCTCAAAAATACT
Found at i:17752 original size:3 final size:3
Alignment explanation
Indices: 17744--17775 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
17734 TTATTTTTAT
17744 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17776 TTTTAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:19570 original size:33 final size:35
Alignment explanation
Indices: 19505--19570 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
19495 CAAAAAATTC
* * *
19505 AAAATATTTATAAAAATTTCAAAATTTATATTTAA
1 AAAATATATAAAAAAAATTCAAAATTTATATTTAA
19540 AAAATATATAAAAAAAATT-AAAATTT-TATTT
1 AAAATATATAAAAAAAATTCAAAATTTATATTT
19571 CTCTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 7 0.25
35 16 0.57
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (35 bp):
AAAATATATAAAAAAAATTCAAAATTTATATTTAA
Found at i:29393 original size:2 final size:2
Alignment explanation
Indices: 29386--29413 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29376 GCTTTGGAGA
29386 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
29414 TCCTTCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30215 original size:26 final size:26
Alignment explanation
Indices: 30179--30228 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
30169 TGCTCACTGT
* *
30179 TTTGGAGTCTAATTTTTTTTCATGGC
1 TTTGAAGTCTAATTTCTTTTCATGGC
30205 TTTGAAGTCTAATTTCTTTTCATG
1 TTTGAAGTCTAATTTCTTTTCATG
30229 TGGCCTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.12, G:0.16, T:0.54
Consensus pattern (26 bp):
TTTGAAGTCTAATTTCTTTTCATGGC
Found at i:32867 original size:22 final size:20
Alignment explanation
Indices: 32842--32915 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 20
32832 AAAAATTATA
*
32842 TTGTTGTTTTGATTGCTATTTT
1 TTGTTGTTTT-AGTGCT-TTTT
*
32864 TTGTTGTTTTAGTGTTGTGTTT
1 TTGTTGTTTTAGTGCT-T-TTT
**
32886 TTACTGTTTTAGTGCTTTTT
1 TTGTTGTTTTAGTGCTTTTT
32906 TTGTTGTTTT
1 TTGTTGTTTT
32916 GATTGTTGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 11 0.26
21 6 0.14
22 26 0.60
ACGTcount: A:0.07, C:0.04, G:0.20, T:0.69
Consensus pattern (20 bp):
TTGTTGTTTTAGTGCTTTTT
Found at i:32921 original size:12 final size:12
Alignment explanation
Indices: 32906--32930 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32896 AGTGCTTTTT
32906 TTGTTGTTTTGA
1 TTGTTGTTTTGA
32918 TTGTTGTTTTGA
1 TTGTTGTTTTGA
32930 T
1 T
32931 GCTATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (12 bp):
TTGTTGTTTTGA
Found at i:32986 original size:24 final size:23
Alignment explanation
Indices: 32924--33009 Score: 66
Period size: 24 Copynumber: 3.7 Consensus size: 23
32914 TTGATTGTTG
* *
32924 TTTTGATGCTATTTTTTTTACTA-
1 TTTTGTTGCTA-TTTTTTTATTAT
* * * *
32947 TTTTGGTGCTGCTTTTATTGTTAT
1 TTTTGTTGCT-ATTTTTTTATTAT
*
32971 TTTTGTTGCTATTTTTTCTATTCT
1 TTTTGTTGCTATTTTTT-TATTAT
*
32995 TTTTGCTGCTATTTT
1 TTTTGTTGCTATTTT
33010 GGTTGTTATT
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
23 22 0.45
24 27 0.55
ACGTcount: A:0.10, C:0.10, G:0.13, T:0.66
Consensus pattern (23 bp):
TTTTGTTGCTATTTTTTTATTAT
Found at i:33019 original size:12 final size:12
Alignment explanation
Indices: 33004--33028 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32994 TTTTTGCTGC
33004 TATTTTGGTTGT
1 TATTTTGGTTGT
33016 TATTTTGGTTGT
1 TATTTTGGTTGT
33028 T
1 T
33029 TGGATGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (12 bp):
TATTTTGGTTGT
Found at i:33021 original size:24 final size:23
Alignment explanation
Indices: 32924--33021 Score: 65
Period size: 24 Copynumber: 4.1 Consensus size: 23
32914 TTGATTGTTG
*
32924 TTTTGATGCTATTTT-TT-TTACT
1 TTTTGCTGCTATTTTGTTGTTA-T
* * *
32946 ATTTTGGTGCTGCTTTTATTGTTAT
1 -TTTTGCTGCT-ATTTTGTTGTTAT
* * * *
32971 TTTTGTTGCTATTTTTTCTATTCT
1 TTTTGCTGCTATTTTGT-TGTTAT
32995 TTTTGCTGCTATTTTGGTTGTTAT
1 TTTTGCTGCTATTTT-GTTGTTAT
33019 TTT
1 TTT
33022 GGTTGTTTGG
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
23 14 0.24
24 38 0.64
25 4 0.07
26 3 0.05
ACGTcount: A:0.10, C:0.09, G:0.14, T:0.66
Consensus pattern (23 bp):
TTTTGCTGCTATTTTGTTGTTAT
Found at i:46945 original size:18 final size:17
Alignment explanation
Indices: 46903--46945 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
46893 ATTTTAAGTT
*
46903 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
46920 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
46938 TATAATTT
1 TATAATTT
46946 AAAACACACA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:49253 original size:26 final size:26
Alignment explanation
Indices: 49213--49280 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
49203 TAGATTAATG
*
49213 AACAGAGTTCCTGTCACAAGGTTATT
1 AACAGAGTTCTTGTCACAAGGTTATT
* *
49239 AACAGAGTTCTTGTCATAATGTTATT
1 AACAGAGTTCTTGTCACAAGGTTATT
* *
49265 ATCAAAGTTCTTGTCA
1 AACAGAGTTCTTGTCA
49281 ATCACAGCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (26 bp):
AACAGAGTTCTTGTCACAAGGTTATT
Found at i:49644 original size:26 final size:26
Alignment explanation
Indices: 49615--49700 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 26
49605 TAATCATTTG
*
49615 CTCAAAGCCTGACAGATAAACATCGA
1 CTCAAAGCCTGATAGATAAACATCGA
* * * * * *
49641 CTCAAAGCATGTTAAATAATCACCAA
1 CTCAAAGCCTGATAGATAAACATCGA
* *
49667 CTCAAATCCTGATAGATAAACATTGA
1 CTCAAAGCCTGATAGATAAACATCGA
49693 CTCAAAGC
1 CTCAAAGC
49701 TTGCTAAATA
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (26 bp):
CTCAAAGCCTGATAGATAAACATCGA
Found at i:49671 original size:52 final size:52
Alignment explanation
Indices: 49615--49716 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
49605 TAATCATTTG
*
49615 CTCAAAGCCTGACAGATAAACATCGACTCAAAGCATGTTAAATAATCACCAA
1 CTCAAAGCCTGACAGATAAACATCGACTCAAAGCATGCTAAATAATCACCAA
* * * *
49667 CTCAAATCCTGATAGATAAACATTGACTCAAAGCTTGCTAAATAATCACC
1 CTCAAAGCCTGACAGATAAACATCGACTCAAAGCATGCTAAATAATCACC
49717 GGCTTAAGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.23
Consensus pattern (52 bp):
CTCAAAGCCTGACAGATAAACATCGACTCAAAGCATGCTAAATAATCACCAA
Found at i:49711 original size:26 final size:26
Alignment explanation
Indices: 49596--49711 Score: 83
Period size: 26 Copynumber: 4.5 Consensus size: 26
49586 GTACATAGTA
* *
49596 CCTGCTAAATAATCATTTG-CTCAAAG
1 CCTGCTAAATAAACA-TCGACTCAAAG
*
49622 CCTGAC-AGATAAACATCGACTCAAAG
1 CCTG-CTAAATAAACATCGACTCAAAG
* * * * * *
49648 CATGTTAAATAATCACCAACTCAAAT
1 CCTGCTAAATAAACATCGACTCAAAG
* * *
49674 CCTGATAGATAAACATTGACTCAAAG
1 CCTGCTAAATAAACATCGACTCAAAG
*
49700 CTTGCTAAATAA
1 CCTGCTAAATAA
49712 TCACCGGCTT
Statistics
Matches: 66, Mismatches: 21, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
25 2 0.03
26 63 0.95
27 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.25
Consensus pattern (26 bp):
CCTGCTAAATAAACATCGACTCAAAG
Found at i:54154 original size:61 final size:60
Alignment explanation
Indices: 54089--54435 Score: 357
Period size: 61 Copynumber: 5.6 Consensus size: 60
54079 TAAAATTATT
*
54089 TTTTTCTTTATTTTTTTTCATATAATATATTTTAACTTTTTAACTTTAAATAAATATTTCC
1 TTTTTCTTT-TTTTTTTTCATATCATATATTTTAACTTTTTAACTTTAAATAAATATTTCC
* * ** *
54150 TTTTT-TATTTATTTTTTCATATCATATATTATAACTTTAAATATTTATATAATAAAATTATTT-
1 TTTTTCT-TTTTTTTTTTCATATCATATATTTTAACTTTTTA-ACTT-TA-AAT-AAA-TATTTC
54213 C
60 C
*
54214 TTTCTT-TATTTTTTTTTCATATCATATATTTTAACTTTTATAACTTTAAATAAATATTTCC
1 TTT-TTCTTTTTTTTTTTCATATCATATATTTTAACTTTT-TAACTTTAAATAAATATTTCC
* * * ** *
54275 TTTTTATTTCTTTTTTTAATATCATATATTTTAACTTTAAATATTTATATAATAAA-ATTAT--
1 TTTTTCTTTTTTTTTTTCATATCATATATTTTAACTTTTTA-ACTT-TA-AATAAATATT-TCC
* *
54336 TTCTTTCTTTATTTTTTCCATATCATATATTTTAACTTTTTAACTTTAAATAAATATTTCC
1 TT-TTTCTTTTTTTTTTTCATATCATATATTTTAACTTTTTAACTTTAAATAAATATTTCC
*
54397 TTTTT-TATTTCTTTTTTTCATATAATATATTTTAACTTT
1 TTTTTCT-TTT-TTTTTTTCATATCATATATTTTAACTTT
54436 AAATATTTAT
Statistics
Matches: 238, Mismatches: 28, Indels: 40
0.78 0.09 0.13
Matches are distributed among these distances:
59 8 0.03
60 46 0.19
61 82 0.34
62 43 0.18
63 12 0.05
64 38 0.16
65 9 0.04
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (60 bp):
TTTTTCTTTTTTTTTTTCATATCATATATTTTAACTTTTTAACTTTAAATAAATATTTCC
Found at i:54297 original size:125 final size:124
Alignment explanation
Indices: 54077--54451 Score: 648
Period size: 123 Copynumber: 3.0 Consensus size: 124
54067 TTGAACATTA
* *
54077 AATAAAATTATTTTTTTCTTTATTTTTTTTCATATAATATATTTTAACTTTTTAACTTTAAATAA
1 AATAAAATTATTTCTTTCTTTATTTTTTTTCATATCATATATTTTAACTTTTTAACTTTAAATAA
* *
54142 ATATTTCCTTTTTTATTT-ATTTTTTCATATCATATATTATAACTTTAAATATTTATAT
66 ATATTTCCTTTTTTATTTCTTTTTTTCATATCATATATTTTAACTTTAAATATTTATAT
54200 AATAAAATTATTTCTTTCTTTATTTTTTTTTCATATCATATATTTTAACTTTTATAACTTTAAAT
1 AATAAAATTATTTCTTTCTTTA-TTTTTTTTCATATCATATATTTTAACTTTT-TAACTTTAAAT
*
54265 AAATATTTCC-TTTTTATTTCTTTTTTTAATATCATATATTTTAACTTTAAATATTTATAT
64 AAATATTTCCTTTTTTATTTCTTTTTTTCATATCATATATTTTAACTTTAAATATTTATAT
*
54325 AATAAAATTATTTCTTTCTTTA-TTTTTTCCATATCATATATTTTAACTTTTTAACTTTAAATAA
1 AATAAAATTATTTCTTTCTTTATTTTTTTTCATATCATATATTTTAACTTTTTAACTTTAAATAA
*
54389 ATATTTCCTTTTTTATTTCTTTTTTTCATATAATATATTTTAACTTTAAATATTTATAT
66 ATATTTCCTTTTTTATTTCTTTTTTTCATATCATATATTTTAACTTTAAATATTTATAT
54448 AATA
1 AATA
54452 TATTTCAATT
Statistics
Matches: 240, Mismatches: 8, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
122 21 0.09
123 101 0.42
124 38 0.16
125 80 0.33
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (124 bp):
AATAAAATTATTTCTTTCTTTATTTTTTTTCATATCATATATTTTAACTTTTTAACTTTAAATAA
ATATTTCCTTTTTTATTTCTTTTTTTCATATCATATATTTTAACTTTAAATATTTATAT
Found at i:58130 original size:2 final size:2
Alignment explanation
Indices: 58123--58151 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58113 GGATTTTAAT
58123 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58152 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60979 original size:20 final size:21
Alignment explanation
Indices: 60943--60984 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
60933 TAACCCAAAT
60943 ACGAGAAGTGAAAATCATAAA
1 ACGAGAAGTGAAAATCATAAA
*
60964 ACGAGGAGTG-AAATCATAAA
1 ACGAGAAGTGAAAATCATAAA
60984 A
1 A
60985 TTGATTTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.55, C:0.10, G:0.21, T:0.14
Consensus pattern (21 bp):
ACGAGAAGTGAAAATCATAAA
Found at i:62598 original size:28 final size:29
Alignment explanation
Indices: 62556--62627 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
62546 CAATATGATA
* *
62556 TCAGCTTATGTGAGTAA-ATTTATAAATG
1 TCAGCTTGTGTGAGTAACATTGATAAATG
* * * *
62584 TGAGCTTGTGTGAGTAACCTTGATCATTG
1 TCAGCTTGTGTGAGTAACATTGATAAATG
62613 TCAGCTTGTGTGAGT
1 TCAGCTTGTGTGAGT
62628 CCTAGTTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (29 bp):
TCAGCTTGTGTGAGTAACATTGATAAATG
Found at i:66952 original size:25 final size:23
Alignment explanation
Indices: 66914--66959 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
66904 TAATTAATAA
66914 TATTATTATAATATAATAATATTT
1 TATTATTATAATATAA-AATATTT
66938 TATTATTTATAATATAAAATAT
1 TATTA-TTATAATATAAAATAT
66960 AAAAGAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATTATAATATAAAATATTT
Found at i:71947 original size:29 final size:28
Alignment explanation
Indices: 71922--71985 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
71912 TACAAAGGAT
71922 TTTCTTTAACAGAGTCAACCAAAAAGGC
1 TTTCTTTAACAGAGTCAACCAAAAAGGC
* * *
71950 TTCCTTTAACAGAGTCTACCACAAAGGC
1 TTTCTTTAACAGAGTCAACCAAAAAGGC
71978 TTTCTTTA
1 TTTCTTTA
71986 GTAGAATCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (28 bp):
TTTCTTTAACAGAGTCAACCAAAAAGGC
Found at i:72287 original size:28 final size:28
Alignment explanation
Indices: 72224--72317 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 28
72214 GAGGTTAGTT
*
72224 ACAAAGGATTTTCTTTTAACAGAGTC-AGCC
1 ACAAAGG--TTTCCTTTAACAGAGTCTA-CC
*
72254 AAAAAGGTTTCCTTTAACAGAGTCTACC
1 ACAAAGGTTTCCTTTAACAGAGTCTACC
** * *
72282 ACAAAGACTTCCTTTAACAGAATCTCGCC
1 ACAAAGGTTTCCTTTAACAGAGTCT-ACC
72311 ACAAAGG
1 ACAAAGG
72318 CGTCTTTTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 39 0.72
29 9 0.17
30 6 0.11
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (28 bp):
ACAAAGGTTTCCTTTAACAGAGTCTACC
Found at i:72427 original size:312 final size:311
Alignment explanation
Indices: 71753--72429 Score: 1004
Period size: 311 Copynumber: 2.2 Consensus size: 311
71743 CCATAAAGGC
* * * *
71753 ATCTTTTAATAGATATAGCCACATAA-ACTTGCCTTTCAAAGTATCGCCACAAAGACATTCCTTT
1 ATCTTTGAATAGATATAGCCACA-AAGACTTGACTTTCAGAGTATAGCCACAAAGACATTCCTTT
71817 TATCAAAGAGCGTCACAAGGGCTTCTTTATAGAGGTTTGTCACACAAGCGTTCCTTTCAAGGTTT
65 TATCAAAGAGCGTCACAAGGGCTTCTTTATAGAGGTTTGTCACACAAGCGTTCCTTTCAAGGTTT
* *
71882 AGCCACAAAGGCTATCTTACAAAGTTTAGTTACAAAGGATTTTCTTTAACAGAGTCAACCAAAAA
130 AACCACAAAGGCTATCTTACAAAGGTTAGTTACAAAGGATTTTCTTTAACAGAGTCAACCAAAAA
* * **
71947 GGCTTCCTTTAACAGAGTCTACCACAAAGGCTTTCTTTAGTAGAATCTCGCCACAAAGGCGTCCT
195 GGCTTCCTTTAACAGAGTCTACCACAAAGACTTCCTTTAACAGAATCTCGCCACAAAGGCGTCCT
* ****
72012 TTGAGAGGTTCACTACAAAGGCATTCCTTTATAGAGATTTGCCACAAAGGTT
260 TTGAGAGGTTCACCACAAAGGCATTCCTTTATAGAGATTTGCCACAAAAACA
* * * *
72064 GTCTTTTAATAGATATAGCCACAAAGACTTGCCTTTCAGAGTATCGCCACAAAGACATTCCTTTT
1 ATCTTTGAATAGATATAGCCACAAAGACTTGACTTTCAGAGTATAGCCACAAAGACATTCCTTTT
*
72129 ATCAAAGAGCGTCACAAGGGCTTCTTTATAGAGGTTTGTCACATAAGCGTTCCTTTC-AGAGTTT
66 ATCAAAGAGCGTCACAAGGGCTTCTTTATAGAGGTTTGTCACACAAGCGTTCCTTTCAAG-GTTT
* *
72193 AACCACAAAGGCTATCTTACAGAGGTTAGTTACAAAGGATTTTCTTTTAACAGAGTCAGCCAAAA
130 AACCACAAAGGCTATCTTACAAAGGTTAGTTACAAAGGATTTTC-TTTAACAGAGTCAACCAAAA
* *
72258 AGGTTTCCTTTAACAGAGTCTACCACAAAGACTTCCTTTAACAGAATCTCGCCACAAAGGCGTCT
194 AGGCTTCCTTTAACAGAGTCTACCACAAAGACTTCCTTTAACAGAATCTCGCCACAAAGGCGTCC
72323 TTTGAGAGGTTCACCACAAAGGCATTCCTTTATAGAGATTTGCCACAAAAACA
259 TTTGAGAGGTTCACCACAAAGGCATTCCTTTATAGAGATTTGCCACAAAAACA
* * * * *
72376 ATCCTTTGAAT-GGT-TCGCCACACAGGCTT-ACTATTCCAGAGTTTAGCCACAAAG
1 AT-CTTTGAATAGATATAGCCACAAAGACTTGACT-TT-CAGAGTATAGCCACAAAG
72430 GTTGTCTTAC
Statistics
Matches: 333, Mismatches: 27, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
310 6 0.02
311 175 0.53
312 145 0.44
313 7 0.02
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (311 bp):
ATCTTTGAATAGATATAGCCACAAAGACTTGACTTTCAGAGTATAGCCACAAAGACATTCCTTTT
ATCAAAGAGCGTCACAAGGGCTTCTTTATAGAGGTTTGTCACACAAGCGTTCCTTTCAAGGTTTA
ACCACAAAGGCTATCTTACAAAGGTTAGTTACAAAGGATTTTCTTTAACAGAGTCAACCAAAAAG
GCTTCCTTTAACAGAGTCTACCACAAAGACTTCCTTTAACAGAATCTCGCCACAAAGGCGTCCTT
TGAGAGGTTCACCACAAAGGCATTCCTTTATAGAGATTTGCCACAAAAACA
Found at i:82054 original size:20 final size:20
Alignment explanation
Indices: 82029--82078 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
82019 TCAGAGAGAG
82029 AAATAAAAATTAAGAACTAA
1 AAATAAAAATTAAGAACTAA
** * *
82049 AAATAAATCTTAATAATTAA
1 AAATAAAAATTAAGAACTAA
82069 AAATAGAAAA
1 AAATA-AAAA
82079 ATAAAAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (20 bp):
AAATAAAAATTAAGAACTAA
Found at i:98940 original size:18 final size:16
Alignment explanation
Indices: 98909--98957 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
98899 AGATTTAGGT
*
98909 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
98926 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
98940 TTAAAAATTTATTCTAA
1 TTAAAAATTTATT-TAA
98957 T
1 T
98958 CCCATTTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.36
15 3 0.11
16 9 0.32
17 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:106652 original size:25 final size:25
Alignment explanation
Indices: 106615--106681 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
106605 CATCTTGAGC
*
106615 CACAGCTCGTGTGAGCATTTATATT
1 CACAGCTCATGTGAGCATTTATATT
*
106640 TACAGCTCATGTGAGCATTTATATT
1 CACAGCTCATGTGAGCATTTATATT
* *
106665 CACAACTTATGTGAGCA
1 CACAGCTCATGTGAGCA
106682 ACTCTATCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (25 bp):
CACAGCTCATGTGAGCATTTATATT
Found at i:108757 original size:31 final size:31
Alignment explanation
Indices: 108710--108848 Score: 101
Period size: 31 Copynumber: 4.5 Consensus size: 31
108700 TTAATATAAT
* * *
108710 ATTTGGTACTTGAACTTGACATTTTTTCCTA
1 ATTTGGTACCTAAACTTGGCATTTTTTCCTA
***
108741 ATTTGGTACCTAAACTT----TTTTCTGGTTAA
1 ATTTGGTACCTAAACTTGGCATTTT-TTCCT-A
*
108770 ATTTGGTA-CTCAAACTTGGCACTTTTTCCTA
1 ATTTGGTACCT-AAACTTGGCATTTTTTCCTA
* *
108801 AGTTGGTACCTAAACTTGGCACTTTTTT-TTA
1 ATTTGGTACCTAAACTTGGCA-TTTTTTCCTA
* *
108832 AGTTGGTACTTAAACTT
1 ATTTGGTACCTAAACTT
108849 TTTGGGGTTC
Statistics
Matches: 86, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
27 4 0.05
28 4 0.05
29 15 0.17
31 51 0.59
32 9 0.10
33 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGGCATTTTTTCCTA
Found at i:108897 original size:90 final size:91
Alignment explanation
Indices: 108710--108903 Score: 230
Period size: 90 Copynumber: 2.1 Consensus size: 91
108700 TTAATATAAT
* * * *
108710 ATTTGGTACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTCTGGTTAAATTTG
1 ATTTGGTACCTAAACTTGACATTTTTTCCTAAGTTGGTACCTAAACTTTTTTCGGGTTAAATTTG
*
108775 GTACTCAAACTTGGCACTTTTTCCTA
66 GTACTCAAACTTGACACTTTTTCCTA
* * * * * *
108801 AGTTGGTACCTAAACTTGGCACTTTTTT-TTAAGTTGGTACTTAAAC-TTTTTGGGGTTCAATTT
1 ATTTGGTACCTAAACTTGACA-TTTTTTCCTAAGTTGGTACCTAAACTTTTTTCGGGTTAAATTT
** *
108864 GGTACTTGAACTTGACTCTTTTTCCTA
65 GGTACTCAAACTTGACACTTTTTCCTA
*
108891 TTTTGGTACCTAA
1 ATTTGGTACCTAA
108904 TCTTTTTTTA
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
90 48 0.56
91 32 0.37
92 6 0.07
ACGTcount: A:0.22, C:0.16, G:0.15, T:0.46
Consensus pattern (91 bp):
ATTTGGTACCTAAACTTGACATTTTTTCCTAAGTTGGTACCTAAACTTTTTTCGGGTTAAATTTG
GTACTCAAACTTGACACTTTTTCCTA
Done.