Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015375.1 Kokia drynarioides strain JFW-HI SEQ_130422, 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: 122193
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 424 characters in sequence are not A, C, G, or T
Found at i:748 original size:206 final size:206
Alignment explanation
Indices: 505--892 Score: 659
Period size: 206 Copynumber: 1.9 Consensus size: 206
495 NNNNNNNNNN
*
505 GATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGA
1 GATACAAAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGA
* * *
570 CCAAATCAAACCCACGCTCGATGTGAGCAAATCTTTGAACCCCAGCTTCCTGATGAAATACCGAG
66 CCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATAAAATACCGAG
* * * *
635 AAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGT
131 AAGCAGGTCGAAACAATAAAATGGTTAGCCTCCTGATGAGACACAGAGAAGTGAACCAAATTCGT
700 CTTCTTGATGA
196 CTTCTTGATGA
*
711 GATACAAAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGA
1 GATACAAAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGA
* *
776 CCAAATCAAACCCATGCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATAAAATACTGAG
66 CCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATAAAATACCGAG
* *
841 AAGCAGGTCGAAATAATAAAATGGTTAGCCTCTTGATGAGACACAGAGAAGT
131 AAGCAGGTCGAAACAATAAAATGGTTAGCCTCCTGATGAGACACAGAGAAGT
893 ATACCAACTC
Statistics
Matches: 169, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
206 169 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.21
Consensus pattern (206 bp):
GATACAAAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGA
CCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATAAAATACCGAG
AAGCAGGTCGAAACAATAAAATGGTTAGCCTCCTGATGAGACACAGAGAAGTGAACCAAATTCGT
CTTCTTGATGA
Found at i:1357 original size:17 final size:17
Alignment explanation
Indices: 1327--1406 Score: 106
Period size: 17 Copynumber: 4.7 Consensus size: 17
1317 GGCCTAATGG
*
1327 AATTTGAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
1344 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
1361 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
*
1378 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
*
1395 AACTTAAATTTA
1 AATTTAAATTTA
1407 AATGTCCAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:1382 original size:7 final size:6
Alignment explanation
Indices: 1327--1409 Score: 52
Period size: 6 Copynumber: 14.5 Consensus size: 6
1317 GGCCTAATGG
* * * * *
1327 AATTTG AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
1372 -ATTTGA AATTTA AATTT- -ATTATA AACTTA AATTTA AAT
1 AATTT-A AATTTA AATTTA AATT-TA AATTTA AATTTA AAT
1410 GTCCAATTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
4 7 0.12
5 9 0.15
6 38 0.63
7 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:1977 original size:3 final size:3
Alignment explanation
Indices: 1969--2073 Score: 115
Period size: 3 Copynumber: 34.7 Consensus size: 3
1959 AAAAAACGAT
1969 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
2017 TGAA T-A TGA TAA TAT TAA TAA TAA CAG TAA TGAA T-T TAT TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
2062 TAA TAAA TAA TA
1 TAA T-AA TAA TA
2074 CCATTAATAA
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
2 3 0.03
3 76 0.86
4 9 0.10
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3080 original size:29 final size:29
Alignment explanation
Indices: 3037--3316 Score: 263
Period size: 29 Copynumber: 9.7 Consensus size: 29
3027 CCCTAAATGT
**
3037 CCCT-GAACTTCCAAAAATTCTGTTTTTA
1 CCCTCGAACTTCCAAAAATTCCATTTTTA
* *
3065 CCCTCGAACTTTC-AAAATCCCATTTTTGA
1 CCCTCGAACTTCCAAAAATTCCATTTTT-A
*
3094 CCC-CGAAACTTCCAAAAATCCCATTTTTA
1 CCCTCG-AACTTCCAAAAATTCCATTTTTA
* * * *
3123 CCCTCAAATTTCC-AAAATCCCGTTTTTGA
1 CCCTCGAACTTCCAAAAATTCCATTTTT-A
*
3152 -CCTCGAAACTTCCAAAAATTTCATTTTTA
1 CCCTCG-AACTTCCAAAAATTCCATTTTTA
* * * *
3181 CCCTCAAACTTCTAAAAATCCCAATTTTGA
1 CCCTCGAACTTCCAAAAATTCC-ATTTTTA
***
3211 -CCTCGGAACTTCC-AAAATTATGTTTTTA
1 CCCTC-GAACTTCCAAAAATTCCATTTTTA
3239 CCC-CGAACTTCCAAAAATTCCATTTTTA
1 CCCTCGAACTTCCAAAAATTCCATTTTTA
*
3267 CCCCCGAACTTCCAAAAATTCCATTTTTTA
1 CCCTCGAACTTCCAAAAATTCCA-TTTTTA
3297 CCC-CGAAACTTCCAAAAATT
1 CCCTCG-AACTTCCAAAAATT
3317 ACTATTTTGC
Statistics
Matches: 208, Mismatches: 28, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
27 8 0.04
28 55 0.26
29 80 0.38
30 65 0.31
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (29 bp):
CCCTCGAACTTCCAAAAATTCCATTTTTA
Found at i:3139 original size:58 final size:58
Alignment explanation
Indices: 3042--3313 Score: 302
Period size: 58 Copynumber: 4.7 Consensus size: 58
3032 AATGTCCCTG
** * *
3042 AACTTCCAAAAATTCTGTTTTTACCCTCGAACTTTCAAAATCCCATTTTTGACCCCGA
1 AACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAATCCCATTTTTGACCCCGA
* * * *
3100 AACTTCCAAAAATCCCATTTTTACCCTCAAATTTCCAAAATCCCGTTTTTGACCTCGA
1 AACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAATCCCATTTTTGACCCCGA
* * * * *
3158 AACTTCCAAAAATTTCATTTTTACCCTCAAACTTCTAAAAATCCCAATTTTGACCTCGG
1 AACTTCCAAAAATTCCATTTTTACCCTCAAACTTC-CAAAATCCCATTTTTGACCCCGA
*** * *
3217 AACTTCC-AAAATTATGTTTTTACCC-CGAACTTCCAAAAATTCCATTTTT-ACCCCCG-
1 AACTTCCAAAAATTCCATTTTTACCCTCAAACTTCC-AAAATCCCATTTTTGA-CCCCGA
3273 AACTTCCAAAAATTCCATTTTTTACCC-CGAAACTTCCAAAA
1 AACTTCCAAAAATTCCA-TTTTTACCCTC-AAACTTCCAAAA
3314 ATTACTATTT
Statistics
Matches: 181, Mismatches: 27, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
56 8 0.04
57 29 0.16
58 111 0.61
59 33 0.18
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.33
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAATCCCATTTTTGACCCCGA
Found at i:3267 original size:86 final size:85
Alignment explanation
Indices: 3042--3313 Score: 307
Period size: 86 Copynumber: 3.1 Consensus size: 85
3032 AATGTCCCTG
* *
3042 AACTTCCAAAAATTCTGTTTTTACCCTCGAACTTTC-AAAATCCCATTTTTGACCCCGAAACTTC
1 AACTTCC-AAAATTCTGTTTTTACCC-CGAACTTCCAAAAATTCCATTTTT-ACCCC-AAACTTC
3106 CAAAAATCCC-ATTTTTACCCTC-A
62 CAAAAATCCCAATTTTTA-CCTCGA
* * * * * *
3129 AATTTCCAAAATCCCGTTTTTGACCTCGAAACTTCCAAAAATTTCATTTTTACCCTCAAACTTCT
1 AACTTCCAAAATTCTGTTTTT-ACCCCG-AACTTCCAAAAATTCCATTTTTACCC-CAAACTTCC
* *
3194 AAAAATCCCAATTTTGACCTCGG
63 AAAAATCCCAATTTTTACCTCGA
* *
3217 AACTTCCAAAATTATGTTTTTACCCCGAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAA
1 AACTTCCAAAATTCTGTTTTTACCCCGAACTTCCAAAAATTCCATTTTTA-CCCCAAACTTCCAA
* * *
3282 AAATTCCATTTTTTACCCCGA
65 AAATCCCAATTTTTACCTCGA
3303 AACTTCCAAAA
1 AACTTCCAAAA
3314 ATTACTATTT
Statistics
Matches: 155, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
86 72 0.46
87 47 0.30
88 36 0.23
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.33
Consensus pattern (85 bp):
AACTTCCAAAATTCTGTTTTTACCCCGAACTTCCAAAAATTCCATTTTTACCCCAAACTTCCAAA
AATCCCAATTTTTACCTCGA
Found at i:3340 original size:59 final size:59
Alignment explanation
Indices: 3158--3383 Score: 166
Period size: 59 Copynumber: 3.9 Consensus size: 59
3148 TTGACCTCGA
* * * ** * * *
3158 AACTTCCAAAAATTTCA-TTTTTACCCTC-AAACTTCTAAAAATCCCAATTTTGACCTCGG
1 AACTTCCAAAAACTCCATTTTTTACCC-CGAAACTTCCAAAAATTACTATTTT-ACCCCCG
* *
3217 AACTTCC-AAAA-T-TATGTTTTTACCCCG-AACTTCCAAAAATT-CCATTTTTACCCCCG
1 AACTTCCAAAAACTCCAT-TTTTTACCCCGAAACTTCCAAAAATTACTA-TTTTACCCCCG
* * *
3273 AACTTCCAAAAATTCCATTTTTTACCCCGAAACTTCCAAAAATTACTATTTTGCTCCCG
1 AACTTCCAAAAACTCCATTTTTTACCCCGAAACTTCCAAAAATTACTATTTTACCCCCG
* ** * *
3332 GA-TGTCCAAAAACTCCATTTTCAACCTCGAAAC-TCTC-AAAATTACTCTTTTA
1 AACT-TCCAAAAACTCCATTTTTTACCCCGAAACTTC-CAAAAATTACTATTTTA
3384 ACCCTAAATT
Statistics
Matches: 139, Mismatches: 17, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
56 15 0.11
57 22 0.16
58 41 0.29
59 59 0.42
60 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (59 bp):
AACTTCCAAAAACTCCATTTTTTACCCCGAAACTTCCAAAAATTACTATTTTACCCCCG
Found at i:6310 original size:61 final size:61
Alignment explanation
Indices: 6236--6357 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
6226 ATTTATGCTA
6236 ACATATTCGACTCTAGCTAAACAGCTCTAGCTAAATGAGGAGAGAAATAAATGATTAGCAT
1 ACATATTCGACTCTAGCTAAACAGCTCTAGCTAAATGAGGAGAGAAATAAATGATTAGCAT
6297 ACATATTCGACTCTAGCTAAACAGCTCTAGCTAAATGAGGAGAGAAATAAATGATTAGCAT
1 ACATATTCGACTCTAGCTAAACAGCTCTAGCTAAATGAGGAGAGAAATAAATGATTAGCAT
6358 TCTCATATTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (61 bp):
ACATATTCGACTCTAGCTAAACAGCTCTAGCTAAATGAGGAGAGAAATAAATGATTAGCAT
Found at i:23404 original size:106 final size:106
Alignment explanation
Indices: 23219--23432 Score: 410
Period size: 106 Copynumber: 2.0 Consensus size: 106
23209 GTAACTTAGA
*
23219 TCATAGAAGGTTATGGTTTGAATGGTTATGTATTTGGCCCTCTAGAGATCCCTGCTCAGTTTGTT
1 TCATAGAAGGTTATGGTTTGAATGGTTATATATTTGGCCCTCTAGAGATCCCTGCTCAGTTTGTT
23284 CAAAGAGACAGCAGTCAGTTAGTTGAGAATTCAACCTTTGT
66 CAAAGAGACAGCAGTCAGTTAGTTGAGAATTCAACCTTTGT
23325 TCATAGAAGGTTATGGTTTGAATGGTTATATATTTGGCCCTCTAGAGATCCCTGCTCAGTTTGTT
1 TCATAGAAGGTTATGGTTTGAATGGTTATATATTTGGCCCTCTAGAGATCCCTGCTCAGTTTGTT
*
23390 CAAAGAGACGGCAGTCAGTTAGTTGAGAATTCAACCTTTGT
66 CAAAGAGACAGCAGTCAGTTAGTTGAGAATTCAACCTTTGT
23431 TC
1 TC
23433 TTTATAGACA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (106 bp):
TCATAGAAGGTTATGGTTTGAATGGTTATATATTTGGCCCTCTAGAGATCCCTGCTCAGTTTGTT
CAAAGAGACAGCAGTCAGTTAGTTGAGAATTCAACCTTTGT
Found at i:25632 original size:20 final size:20
Alignment explanation
Indices: 25590--25634 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
25580 GCATCATAAT
25590 TTTACTTTAGTTTTTATTTAA
1 TTTACTTTA-TTTTTATTTAA
*
25611 TTTACTTT-TTTTTTTTTCAA
1 TTTACTTTATTTTTATTT-AA
25631 TTTA
1 TTTA
25635 ATCCTTTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 6 0.27
21 8 0.36
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTACTTTATTTTTATTTAA
Found at i:31509 original size:30 final size:30
Alignment explanation
Indices: 31448--31509 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
31438 GAAATGGTTG
* *
31448 ATTTTTTAAAATGATAAATTTTTAATTTAA
1 ATTTTTTAAAATGATAAAATTTTAATATAA
* *
31478 ATTTTTTATAATTTATAAAATTTTAA-ATAA
1 ATTTTTTA-AAATGATAAAATTTTAATATAA
31508 AT
1 AT
31510 AATGATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATTTTTTAAAATGATAAAATTTTAATATAA
Found at i:33496 original size:51 final size:52
Alignment explanation
Indices: 33441--33538 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 52
33431 TATTTTCGTG
** * * *
33441 TAAAAAATAGGATAAAATTAA-ATAATGTGTAAATATTGATGATTAATTTTT
1 TAAAAAATAAAATAAAATTAACACAATCTGTAAATATTGAAGATTAATTTTT
* *
33492 TAAAAATTAAAATTAAATTAACACAATCTGTAAATATTGAAGATTAA
1 TAAAAAATAAAATAAAATTAACACAATCTGTAAATATTGAAGATTAA
33539 ATTTATTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
51 17 0.44
52 22 0.56
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (52 bp):
TAAAAAATAAAATAAAATTAACACAATCTGTAAATATTGAAGATTAATTTTT
Found at i:33899 original size:41 final size:41
Alignment explanation
Indices: 33842--33926 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
33832 TTTTCACCCA
33842 ACTGCTCATTGAACTCCATTTGCAACCCTACTCAGACTCTT
1 ACTGCTCATTGAACTCCATTTGCAACCCTACTCAGACTCTT
33883 ACTGCTCATTGAACTCCATTTGCAACCCTACTCAGACTCTT
1 ACTGCTCATTGAACTCCATTTGCAACCCTACTCAGACTCTT
33924 ACT
1 ACT
33927 TCCAAACCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.25, C:0.34, G:0.09, T:0.32
Consensus pattern (41 bp):
ACTGCTCATTGAACTCCATTTGCAACCCTACTCAGACTCTT
Found at i:38764 original size:24 final size:24
Alignment explanation
Indices: 38686--38771 Score: 122
Period size: 24 Copynumber: 3.6 Consensus size: 24
38676 TTCAAAAAAT
*
38686 TTAGCTCATACGAGCCCAG-ATAGG
1 TTAGCTCTTACGAGCCCAGAAT-GG
* *
38710 TTAACTCTTACAAGCCCAGAAT-G
1 TTAGCTCTTACGAGCCCAGAATGG
38733 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
38757 TTAGCTCTTACGAGC
1 TTAGCTCTTACGAGC
38772 TCAAAATAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 21 0.38
24 32 0.58
25 2 0.04
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:49271 original size:16 final size:15
Alignment explanation
Indices: 49245--49290 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
49235 GTTAACAAAT
* *
49245 AATTCAAAAATTATA
1 AATTAAAAAAATATA
*
49260 AATTAAAAAAATAAA
1 AATTAAAAAAATATA
49275 AATTAAAAAAAATATA
1 AATT-AAAAAAATATA
49291 TAAAAAGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AATTAAAAAAATATA
Found at i:50888 original size:27 final size:25
Alignment explanation
Indices: 50849--50916 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
50839 ACAAACTAAG
* * *
50849 AATAATTACTTAATTTCTTATAAGAAT
1 AATATTTACTTAATTT-TGATAA-AAA
*
50876 AATATTTAATTAATTTTGATAAAAA
1 AATATTTACTTAATTTTGATAAAAA
50901 ATATATTTACTTAATT
1 A-ATATTTACTTAATT
50917 AAATAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 3 0.09
26 18 0.51
27 14 0.40
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (25 bp):
AATATTTACTTAATTTTGATAAAAA
Found at i:50991 original size:25 final size:25
Alignment explanation
Indices: 50935--50994 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
50925 TTAACTATGA
50935 AATAAGATTTAATAAATAAAATTTTG
1 AATAA-ATTTAATAAATAAAATTTTG
* *
50961 ATTAAATATTAATAAATAGAA-TTTG
1 AATAAAT-TTAATAAATAAAATTTTG
50986 AATAAATTT
1 AATAAATTT
50995 CTGGTACCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 2 0.07
25 12 0.40
26 16 0.53
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (25 bp):
AATAAATTTAATAAATAAAATTTTG
Found at i:54779 original size:51 final size:51
Alignment explanation
Indices: 54703--54855 Score: 270
Period size: 51 Copynumber: 3.0 Consensus size: 51
54693 AGAGTTAGAA
54703 GAATGCTGATGGGTTGGTGAGTGCAGTCAATCTTCTCTGTACATGTCTTAT
1 GAATGCTGATGGGTTGGTGAGTGCAGTCAATCTTCTCTGTACATGTCTTAT
* *
54754 GAATGCTGATGGGTTGGTCAGTGCAGTCAATCTTCTCTGTACATTTCTTAT
1 GAATGCTGATGGGTTGGTGAGTGCAGTCAATCTTCTCTGTACATGTCTTAT
* *
54805 GAATGCTGATGGGTTGGTGAGTGCAGTCGATCTTCTTTGTACATGTCTTAT
1 GAATGCTGATGGGTTGGTGAGTGCAGTCAATCTTCTCTGTACATGTCTTAT
54856 CAGTCCCTCC
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 96 1.00
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.39
Consensus pattern (51 bp):
GAATGCTGATGGGTTGGTGAGTGCAGTCAATCTTCTCTGTACATGTCTTAT
Found at i:55670 original size:29 final size:31
Alignment explanation
Indices: 55644--55707 Score: 62
Period size: 30 Copynumber: 2.1 Consensus size: 31
55634 TTAATATATA
* *
55644 TAATAA-AATCAAAAT-TAAAATTT-TATATT
1 TAATAATAAT-AAAATAAAAAATTTGTATATA
* *
55673 TAAAAATAATTAAATAAAAAATTTGTATATA
1 TAATAATAATAAAATAAAAAATTTGTATATA
55704 TAAT
1 TAAT
55708 TGTACAAGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
29 9 0.33
30 10 0.37
31 8 0.30
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (31 bp):
TAATAATAATAAAATAAAAAATTTGTATATA
Found at i:71677 original size:16 final size:16
Alignment explanation
Indices: 71606--71677 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 16
71596 CGTTTGGTTC
71606 GCTGTAATGAAATAAA
1 GCTGTAATGAAATAAA
* * *
71622 ACTGTAATGGAATAGA
1 GCTGTAATGAAATAAA
* * *
71638 GTTATAATGGAATAGAA
1 GCTGTAATGAAATA-AA
71655 -CTGTAATGAAATAAA
1 GCTGTAATGAAATAAA
*
71670 GCTCTAAT
1 GCTGTAAT
71678 CGATAATTCA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
15 2 0.05
16 40 0.93
17 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (16 bp):
GCTGTAATGAAATAAA
Found at i:71745 original size:44 final size:44
Alignment explanation
Indices: 71690--71797 Score: 180
Period size: 44 Copynumber: 2.5 Consensus size: 44
71680 ATAATTCAGT
* *
71690 TGTTTGGTTGAATGGAATGGAATAGAGCTGTAATAATATTCTTG
1 TGTTTGATTGAATGGAATGGAATAAAGCTGTAATAATATTCTTG
*
71734 TGTTTGATTGAATGGAATGAAATAAAGCTGTAATAATATTCTTG
1 TGTTTGATTGAATGGAATGGAATAAAGCTGTAATAATATTCTTG
*
71778 TGTTTGATTGAATGTAATGG
1 TGTTTGATTGAATGGAATGG
71798 TGTTGTAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.31, C:0.04, G:0.25, T:0.40
Consensus pattern (44 bp):
TGTTTGATTGAATGGAATGGAATAAAGCTGTAATAATATTCTTG
Found at i:75975 original size:20 final size:22
Alignment explanation
Indices: 75952--75994 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
75942 ACAATATAAT
*
75952 TATTTTTAT-TATG-TTTTAAA
1 TATTTTTATATAGGTTTTTAAA
75972 TATTTTTATATAGGTTTTTAAA
1 TATTTTTATATAGGTTTTTAAA
75994 T
1 T
75995 TTAAAACAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
TATTTTTATATAGGTTTTTAAA
Found at i:77221 original size:5 final size:5
Alignment explanation
Indices: 77211--77243 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
77201 TTTCGTTATT
77211 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
77244 TGTTAGGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:79053 original size:5 final size:5
Alignment explanation
Indices: 79046--79097 Score: 68
Period size: 5 Copynumber: 10.4 Consensus size: 5
79036 ACTTACTAAA
* * * *
79046 AAATA AAATA AAATA AAATC AAATT AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT
79096 AA
1 AA
79098 CGAAACTTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (5 bp):
AAATT
Found at i:79452 original size:13 final size:14
Alignment explanation
Indices: 79422--79454 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
79412 ATTTATTACA
*
79422 TTTCTCTCCTCTTC
1 TTTCTTTCCTCTTC
79436 TTTCTTTCCTC-TC
1 TTTCTTTCCTCTTC
79449 TTTCTT
1 TTTCTT
79455 CCTTCTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTCTTTCCTCTTC
Found at i:79466 original size:11 final size:11
Alignment explanation
Indices: 79432--79477 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
79422 TTTCTCTCCT
79432 CTTCTTTCTTTC
1 CTTCTTTC-TTC
79444 CTCTCTTTCTTC
1 CT-TCTTTCTTC
*
79456 CTTCTTGCTTC
1 CTTCTTTCTTC
*
79467 TTTCTTTCTTC
1 CTTCTTTCTTC
79478 TCTAGTGCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 17 0.57
12 7 0.23
13 6 0.20
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.63
Consensus pattern (11 bp):
CTTCTTTCTTC
Found at i:80032 original size:15 final size:15
Alignment explanation
Indices: 79986--80033 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
79976 TTGATAAACC
*
79986 GAAAAATTAAGTATC
1 GAAAAATTAAGTATT
*
80001 GAAAAGA-TAAGTGTT
1 GAAAA-ATTAAGTATT
*
80016 GAAAATTTAAGTATT
1 GAAAAATTAAGTATT
80031 GAA
1 GAA
80034 TTTATATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.19, T:0.29
Consensus pattern (15 bp):
GAAAAATTAAGTATT
Found at i:80193 original size:18 final size:18
Alignment explanation
Indices: 80170--80205 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
80160 AATTTTATTC
80170 TAAACA-AAAATCAAACTT
1 TAAACATAAAAT-AAACTT
80188 TAAACATAAAATAAACTT
1 TAAACATAAAATAAACTT
80206 GGACTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAACATAAAATAAACTT
Found at i:80590 original size:16 final size:16
Alignment explanation
Indices: 80569--80603 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
80559 TTTTATTTTG
80569 ATAATAAATTTTAAA-A
1 ATAAT-AATTTTAAATA
80585 ATAATAATTTTAAATA
1 ATAATAATTTTAAATA
80601 ATA
1 ATA
80604 TTATTCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATAATTTTAAATA
Found at i:80656 original size:15 final size:15
Alignment explanation
Indices: 80636--80691 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
80626 ATTCAATATT
80636 AATATTTTAATAATA
1 AATATTTTAATAATA
*
80651 AATATTATTACAATTATA
1 AATATT-TT--AATAATA
*
80669 AATATATTAATAATA
1 AATATTTTAATAATA
*
80684 AATGTTTT
1 AATATTTT
80692 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 18 0.55
16 2 0.06
17 2 0.06
18 11 0.33
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:102116 original size:5 final size:5
Alignment explanation
Indices: 102106--102130 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
102096 GTTAAAAATA
102106 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
102131 TTAAATTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:102555 original size:20 final size:21
Alignment explanation
Indices: 102522--102563 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
102512 TTACCTCAAA
*
102522 CCCCAAATTATTTTACTCCTC
1 CCCCAAAATATTTTACTCCTC
102543 CCCCAAAAT-TTTTACTCCTC
1 CCCCAAAATATTTTACTCCTC
102563 C
1 C
102564 TCACATTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (21 bp):
CCCCAAAATATTTTACTCCTC
Found at i:106474 original size:15 final size:15
Alignment explanation
Indices: 106424--106475 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
106414 ATGGATTTAG
*
106424 ATAATTTTGAATTTT
1 ATAATTTTGAATATT
* *
106439 ATAAGTTATAAATATT
1 ATAA-TTTTGAATATT
* *
106455 TTAATTTTGAATATA
1 ATAATTTTGAATATT
106470 ATAATT
1 ATAATT
106476 CGTTTTATTT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
ATAATTTTGAATATT
Found at i:106580 original size:19 final size:18
Alignment explanation
Indices: 106541--106581 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
106531 TATAAAAAAC
**
106541 ATAAATTATTTATATTTA
1 ATAAATTATTTATATAAA
106559 ATAAAGTTATTTATATAAA
1 ATAAA-TTATTTATATAAA
106578 ATAA
1 ATAA
106582 TTGAAATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATAAATTATTTATATAAA
Found at i:107055 original size:26 final size:24
Alignment explanation
Indices: 107016--107085 Score: 70
Period size: 30 Copynumber: 2.7 Consensus size: 24
107006 ATATCTTTTA
107016 TTATA-ATCTATAATATAATAATAG
1 TTATATAT-TATAATATAATAATAG
107040 TTATATATGTATTAATATTTTTAATAATAG
1 TTATATAT-TA-TAATA----TAATAATAG
107070 TTATATATTATAATAT
1 TTATATATTATAATAT
107086 TATTTTATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
24 6 0.15
25 4 0.10
26 5 0.13
28 5 0.13
29 2 0.05
30 17 0.44
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (24 bp):
TTATATATTATAATATAATAATAG
Found at i:107092 original size:30 final size:30
Alignment explanation
Indices: 107031--107086 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
107021 ATCTATAATA
107031 TAATAATAGTTATATATGTATTAATATTTT
1 TAATAATAGTTATATATGTATTAATATTTT
107061 TAATAATAGTTATATAT-TA-TAATATT
1 TAATAATAGTTATATATGTATTAATATT
107087 ATTTTATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 7 0.27
29 2 0.08
30 17 0.65
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (30 bp):
TAATAATAGTTATATATGTATTAATATTTT
Found at i:107597 original size:26 final size:26
Alignment explanation
Indices: 107568--107617 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
107558 TATTAAGTTA
107568 TAAAAAAT-ATTATATTAATTATATGC
1 TAAAAAATAATTATA-TAATTATATGC
* *
107594 TAAATAATAATTATATATTTATAT
1 TAAAAAATAATTATATAATTATAT
107618 TTATATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
TAAAAAATAATTATATAATTATATGC
Found at i:110604 original size:39 final size:39
Alignment explanation
Indices: 110560--110637 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
110550 AAGTAATAAG
110560 AATGTAAATTTGAATCCAAAAAACAAAGCAATAAAAACT
1 AATGTAAATTTGAATCCAAAAAACAAAGCAATAAAAACT
110599 AATGTAAATTTGAATCCAAAAAACAAAGCAATAAAAACT
1 AATGTAAATTTGAATCCAAAAAACAAAGCAATAAAAACT
110638 TGCAACAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.21
Consensus pattern (39 bp):
AATGTAAATTTGAATCCAAAAAACAAAGCAATAAAAACT
Found at i:113956 original size:14 final size:14
Alignment explanation
Indices: 113937--113982 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
113927 TAAATAATGC
113937 TTTCTTCCCATGTT
1 TTTCTTCCCATGTT
** *
113951 TTTCTT-TAATG-C
1 TTTCTTCCCATGTT
113963 TTTCTTCCCATGTT
1 TTTCTTCCCATGTT
113977 TTTCTT
1 TTTCTT
113983 TCTTTTAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
14 12 0.50
ACGTcount: A:0.09, C:0.24, G:0.07, T:0.61
Consensus pattern (14 bp):
TTTCTTCCCATGTT
Found at i:113960 original size:26 final size:26
Alignment explanation
Indices: 113931--113983 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
113921 TTGTGTTAAA
113931 TAATGCTTTCTTCCCATGTTTTTCTT
1 TAATGCTTTCTTCCCATGTTTTTCTT
113957 TAATGCTTTCTTCCCATGTTTTTCTT
1 TAATGCTTTCTTCCCATGTTTTTCTT
113983 T
1 T
113984 CTTTTAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.11, C:0.23, G:0.08, T:0.58
Consensus pattern (26 bp):
TAATGCTTTCTTCCCATGTTTTTCTT
Found at i:120810 original size:3 final size:3
Alignment explanation
Indices: 120802--120839 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
120792 TGAAATTAGG
120802 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
120840 TTAGGTTAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.