Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005734.1 Kokia drynarioides strain JFW-HI SEQ_119972, 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: 42639
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:758 original size:24 final size:24
Alignment explanation
Indices: 723--784 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
713 CAAACCCGAG
*
723 GAAAA-TCTCTCAGCTAAAAACTAT-
1 GAAAATTC-CTCAG-TAAAAACCATC
* *
747 GAAAATTCCTCAGTCAATACCATC
1 GAAAATTCCTCAGTAAAAACCATC
771 GAAAATTCCTCAGT
1 GAAAATTCCTCAGT
785 CGCAAACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 7 0.21
24 24 0.73
25 2 0.06
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (24 bp):
GAAAATTCCTCAGTAAAAACCATC
Found at i:6155 original size:29 final size:29
Alignment explanation
Indices: 6113--6303 Score: 194
Period size: 29 Copynumber: 6.4 Consensus size: 29
6103 ACAGGATCGA
*
6113 AAAATG-AAGTTTTGGAGAA-TTTAGGGTT
1 AAAATGTAA-TTTTGGAAAAGTTTAGGGTT
* * * *
6141 AAAATGTAATTTTTGAAAAAAAAATTAAGAGTT
1 AAAATGTAA-TTTTG---GAAAAGTTTAGGGTT
*
6174 AAAATGTAATTTTAGG-AAA-TTTTGGGTT
1 AAAATGTAATTTT-GGAAAAGTTTAGGGTT
* *
6202 AAAATGTGATTTTGGAAAAGTTTGAGGGTG
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTT
6232 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTA-GGGTT
6262 AAAATGTAATTTT-GAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTA-GGGTT
6291 AAAATGTAATTTT
1 AAAATGTAATTTT
6304 TGAATAAAGT
Statistics
Matches: 139, Mismatches: 14, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.01
28 27 0.19
29 43 0.31
30 43 0.31
32 7 0.05
33 17 0.12
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTT
Found at i:6238 original size:30 final size:30
Alignment explanation
Indices: 6113--6303 Score: 191
Period size: 30 Copynumber: 6.4 Consensus size: 30
6103 ACAGGATCGA
*
6113 AAAATG-AAGTTTTGGAGAA-TTTA-GGGTT
1 AAAATGTAA-TTTTGGAAAAGTTTAGGGGTT
* ** * *
6141 AAAATGTAATTTTTGAAAAAAAAATTAAGAGTT
1 AAAATGTAA-TTTTG--GAAAAGTTTAGGGGTT
*
6174 AAAATGTAATTTTAGG-AAA-TTT-TGGGTT
1 AAAATGTAATTTT-GGAAAAGTTTAGGGGTT
* *
6202 AAAATGTGATTTTGGAAAAGTTT-GAGGGTG
1 AAAATGTAATTTTGGAAAAGTTTAG-GGGTT
6232 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
6262 AAAATGTAATTTT-GAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
6291 AAAATGTAATTTT
1 AAAATGTAATTTT
6304 TGAATAAAGT
Statistics
Matches: 139, Mismatches: 14, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.01
28 25 0.18
29 41 0.29
30 46 0.33
31 4 0.03
32 7 0.05
33 14 0.10
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGGTT
Found at i:10450 original size:52 final size:52
Alignment explanation
Indices: 10284--10485 Score: 264
Period size: 52 Copynumber: 3.9 Consensus size: 52
10274 ATTTCACTTC
* * *
10284 ATTCATATACTCACGATGACACATAG-CTACCGGACCT-TATAATCCACAAGGG
1 ATTCATATACTCACGATGACACATAGTC-ATCGGACCTCT-TAATCCATAAAGG
* * * *
10336 ATTCATATACTCACGATGACACAGAGTCATCAGACCCTCGTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGA-CCTCTTAATCCATAAAGG
* * *
10389 ATTCATATACTCATGATGTCACTTAGTCATCGGACCTCTTAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCCATAAAGG
*
10441 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCC
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCC
10486 GTTTATGGCT
Statistics
Matches: 131, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
52 88 0.67
53 43 0.33
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.27
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCCATAAAGG
Found at i:10469 original size:105 final size:104
Alignment explanation
Indices: 10284--10487 Score: 277
Period size: 105 Copynumber: 2.0 Consensus size: 104
10274 ATTTCACTTC
*
10284 ATTCATATACTCACGATGACACATAGCTACCGGACCTTATAATCCACAAGGGATTCATATACTCA
1 ATTCATATACTCACGATGACACATAGCTACCGGACCTTATAATCCACAAAGGATTCATATACTCA
10349 CGATGACACAGAGTCATCAGACCCTCGTAATCCGTAAAGG
66 CGATGACACAGAGTCATCAGA-CCTCGTAATCCGTAAAGG
* * * * *
10389 ATTCATATACTCATGATGTCACTTAG-TCATCGGACCTCT-TAATCCATAAAGGATTCATATACT
1 ATTCATATACTCACGATGACACATAGCT-ACCGGACCT-TATAATCCACAAAGGATTCATATACT
** * *
10452 CACGATGACACTTAGTCATCGGACCTCTTAATCCGT
64 CACGATGACACAGAGTCATCAGACCTCGTAATCCGT
10488 TTATGGCTCA
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
104 13 0.15
105 73 0.84
106 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (104 bp):
ATTCATATACTCACGATGACACATAGCTACCGGACCTTATAATCCACAAAGGATTCATATACTCA
CGATGACACAGAGTCATCAGACCTCGTAATCCGTAAAGG
Found at i:11366 original size:20 final size:20
Alignment explanation
Indices: 11337--11377 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
11327 GCTTTTATAA
11337 TTAACCTAATTAATC-CACT
1 TTAACCTAATTAATCTCACT
11356 TTAACCCTAATTAATCTCACT
1 TTAA-CCTAATTAATCTCACT
11377 T
1 T
11378 ATAAGCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 11 0.55
21 5 0.25
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAACCTAATTAATCTCACT
Found at i:14072 original size:30 final size:30
Alignment explanation
Indices: 13998--14137 Score: 160
Period size: 30 Copynumber: 4.6 Consensus size: 30
13988 TAAAGAATTT
*
13998 AGGGTTAAAATGTATTTTTTTAGGAAAA-TTTA
1 AGGGTTAAAATGTA--ATTTT-GGAAAAGTTTA
* *
14030 GGGGTTAAAATGTGATTTTGGAAAAGTTTA
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTA
* *
14060 AGGGTGAAAATGTAATTTTAGAAAAGTTTA
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTA
* *
14090 A-GGTTAAAATGCAATTTTGGAAAAG-TTC
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTA
14118 AGAGGTTAAAATGTAATTTT
1 AG-GGTTAAAATGTAATTTT
14138 TGAATAAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.03
29 27 0.29
30 51 0.55
32 12 0.13
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (30 bp):
AGGGTTAAAATGTAATTTTGGAAAAGTTTA
Found at i:14098 original size:59 final size:60
Alignment explanation
Indices: 14015--14137 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 60
14005 AAATGTATTT
* **
14015 TTTTAGGAAAATTTAGGGGTTAAAATGTGATTTTGGAAAAGTTTAAG-GGTGAAAATGTAA
1 TTTTAGGAAAATTTAGAGGTTAAAATGCAATTTTGGAAAAG-TTAAGAGGTGAAAATGTAA
* *
14075 TTTTA-GAAAAGTTTA-AGGTTAAAATGCAATTTTGGAAAAGTTCAGAGGTTAAAATGTAA
1 TTTTAGGAAAA-TTTAGAGGTTAAAATGCAATTTTGGAAAAGTTAAGAGGTGAAAATGTAA
14134 TTTT
1 TTTT
14138 TGAATAAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
58 4 0.07
59 43 0.77
60 9 0.16
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.37
Consensus pattern (60 bp):
TTTTAGGAAAATTTAGAGGTTAAAATGCAATTTTGGAAAAGTTAAGAGGTGAAAATGTAA
Found at i:14542 original size:29 final size:29
Alignment explanation
Indices: 14487--14542 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
14477 CAGAAANAAA
*
14487 AAAAAAAAAACTTCATTTCTCTTTTTTTC
1 AAAAAAAAAACTTCATTTCTCTCTTTTTC
** * *
14516 AAAAAAAAAGTTTCTTTTTTCTCTTTT
1 AAAAAAAAAACTTCATTTCTCTCTTTT
14543 CTCTCAATTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (29 bp):
AAAAAAAAAACTTCATTTCTCTCTTTTTC
Found at i:19284 original size:22 final size:22
Alignment explanation
Indices: 19256--19297 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
19246 ATTTTAATTA
19256 TTGTGTTT-ATGATGTCCTAATG
1 TTGTGTTTAATG-TGTCCTAATG
19278 TTGTGTTTAATGTGTCCTAA
1 TTGTGTTTAATGTGTCCTAA
19298 AAACACTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.19, C:0.10, G:0.21, T:0.50
Consensus pattern (22 bp):
TTGTGTTTAATGTGTCCTAATG
Found at i:25822 original size:2 final size:2
Alignment explanation
Indices: 25815--25844 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25805 CATACATGTA
25815 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
25845 GTATGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29330 original size:21 final size:21
Alignment explanation
Indices: 29298--29348 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
29288 TACATTTTAA
29298 AATAAAATCATTAATTAAAAAT
1 AATAAAATCATTAATT-AAAAT
**
29320 AATAAAA-CATTTCTTAAAAT
1 AATAAAATCATTAATTAAAAT
29340 AATACAAAT
1 AATA-AAAT
29349 GTGTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 9 0.36
21 9 0.36
22 7 0.28
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (21 bp):
AATAAAATCATTAATTAAAAT
Found at i:33048 original size:2 final size:2
Alignment explanation
Indices: 33041--33070 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33031 TTTTTGTGCC
33041 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
33071 AGGGTATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:33221 original size:4 final size:4
Alignment explanation
Indices: 33191--33259 Score: 84
Period size: 4 Copynumber: 16.5 Consensus size: 4
33181 ACGGTAGAAC
* * *
33191 AAAG AAAA AAAG AAAAA AAAG AGAG AAAG AAAGG AAAG AAAGG AAAG AAAG
1 AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAA-G AAAG AAA-G AAAG AAAG
33242 AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AA
33260 GGAAGAAGGA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
4 45 0.80
5 11 0.20
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:33322 original size:12 final size:13
Alignment explanation
Indices: 33305--33333 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
33295 AAGATAGTGT
33305 ATTTATTTTTA-A
1 ATTTATTTTTATA
33317 ATTTATTTTTATA
1 ATTTATTTTTATA
33330 ATTT
1 ATTT
33334 TTTAATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTATTTTTATA
Found at i:34016 original size:16 final size:16
Alignment explanation
Indices: 33971--34018 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
33961 AAATACTCTA
*
33971 AATTAATTACCAAAAT
1 AATTAATTATCAAAAT
*
33987 -A-TAA-TATAAAAAT
1 AATTAATTATCAAAAT
34000 AATTAATTATCAAAAT
1 AATTAATTATCAAAAT
34016 AAT
1 AAT
34019 ATCCTCATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
13 7 0.27
14 4 0.15
15 4 0.15
16 11 0.42
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAATTATCAAAAT
Found at i:35565 original size:97 final size:97
Alignment explanation
Indices: 35380--35572 Score: 223
Period size: 97 Copynumber: 2.0 Consensus size: 97
35370 CACTTTTGAA
* * * *
35380 AAGGATGTTCGATTATCACGATTTAAAGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTC
1 AAGGATATTCGATTATCACGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAAGCACAAATTTTC
* *
35445 AGAATCAGAGATAAGAAACATTGCCTCGATTC
66 AAAATCAGAGATAACAAACATTGCCTCGATTC
* ***
35477 AAGGATATTCGATTATTC-CGATTTGAAGAAAAA-TCGTGTCTAGTAAGTTAAAGCACAAATTTT
1 AAGGATATTCGATTA-TCACGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAAGCACAAATTTT
*
35540 CAAAATTC-GA-ATTAACAGAATATTGCCTCGATT
65 CAAAA-TCAGAGA-TAACA-AACATTGCCTCGATT
35573 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 1 0.01
96 34 0.42
97 44 0.54
98 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (97 bp):
AAGGATATTCGATTATCACGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAAGCACAAATTTTC
AAAATCAGAGATAACAAACATTGCCTCGATTC
Found at i:36039 original size:30 final size:30
Alignment explanation
Indices: 35942--36035 Score: 111
Period size: 30 Copynumber: 3.1 Consensus size: 30
35932 AAAATGATAA
35942 TTTTAGAAAAACTCGAGGTCAAAAATGGAAT
1 TTTTAGAAAAA-TCGAGGTCAAAAATGGAAT
* ** *
35973 TTTAAG-AAGTTCGAGGGT-AAAAATGTAAT
1 TTTTAGAAAAATCGA-GGTCAAAAATGGAAT
*
36002 TTTTGGAAAAATCGAGGTCAAAAATGGAAT
1 TTTTAGAAAAATCGAGGTCAAAAATGGAAT
36032 TTTT
1 TTTT
36036 GGAAGTTTAG
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
29 21 0.41
30 25 0.49
31 5 0.10
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.31
Consensus pattern (30 bp):
TTTTAGAAAAATCGAGGTCAAAAATGGAAT
Found at i:36083 original size:58 final size:59
Alignment explanation
Indices: 35901--36126 Score: 275
Period size: 59 Copynumber: 3.8 Consensus size: 59
35891 AAAAAAAAGA
* * *
35901 TCAAAAATGGAATTTTTGGAAGTTTTGTGGT-AAAATGATAA-TTTTAGAAAAACTCGAGG
1 TCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATG-TAATTTTTGGAAAAA-TCGAGG
** *
35960 TCAAAAATGGAATTTTAAGAAG-TTCGAGGGTAAAAATGTAATTTTTGGAAAAATCGAGG
1 TCAAAAATGGAATTTTTGGAAGTTTAG-GGGTAAAAATGTAATTTTTGGAAAAATCGAGG
* * *
36019 TCAAAAATGGAATTTTTGGAAGTTTAGGGGT-AAAATGTTAATTTTGGGAAAATTAG-GG
1 TCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATG-TAATTTTTGGAAAAATCGAGG
*
36077 TTAAAAATGGAATTTTAT-GAAGTTTAGGGGTAAAAATGTAATTTTTGGAA
1 TCAAAAATGGAATTTT-TGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAA
36127 GTTTAGGGGT
Statistics
Matches: 147, Mismatches: 13, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
58 50 0.34
59 78 0.53
60 19 0.13
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (59 bp):
TCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAAATCGAGG
Found at i:36200 original size:29 final size:28
Alignment explanation
Indices: 35962--36209 Score: 135
Period size: 29 Copynumber: 8.5 Consensus size: 28
35952 ACTCGAGGTC
* * **
35962 AAAAATGGAATTTTAAGAAGTTCGAGGGT
1 AAAAATGTAATTTT-GGAAGTTTAAGGGT
*** *
35991 AAAAATGTAATTTTTGGAAAAAT-CGAGGT
1 AAAAATGTAA-TTTTGGAAGTTTAAG-GGT
* *
36020 CAAAAATGGAATTTTTGGAAGTTTAGGGGT
1 -AAAAATGTAA-TTTTGGAAGTTTAAGGGT
**
36050 -AAAATGTTAATTTTGGGAAAATT-AGGGTT
1 AAAAATG-TAATTTT-GGAAGTTTAAGGG-T
* * *
36079 AAAAATGGAATTTTATGAAGTTTAGGGGT
1 AAAAATGTAATTTT-GGAAGTTTAAGGGT
*
36108 AAAAATGTAATTTTTGGAAGTTTAGGGGT
1 AAAAATGTAA-TTTTGGAAGTTTAAGGGT
* * ** *
36137 ACAAATGTAATTCTTGAAAAAATCAA-GGT
1 AAAAATGTAATT-TTG-GAAGTTTAAGGGT
*
36166 CAAAAATGGAATTTTGGAAAGTTTAAGGGT
1 -AAAAATGTAATTTTGG-AAGTTTAAGGGT
*
36196 GAAAATGTAATTTT
1 AAAAATGTAATTTT
36210 CAAAAAGTTT
Statistics
Matches: 166, Mismatches: 38, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
28 16 0.10
29 93 0.56
30 56 0.34
31 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (28 bp):
AAAAATGTAATTTTGGAAGTTTAAGGGT
Found at i:36201 original size:88 final size:87
Alignment explanation
Indices: 36021--36209 Score: 256
Period size: 88 Copynumber: 2.2 Consensus size: 87
36011 AATCGAGGTC
* ** * * *
36021 AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGTTAATTTTGGGAAAATTAGGGTTAAAAATG
1 AAAAATGTAATTTTTGGAAGTTTAGGGGTAAAATGTTAATTTTGAAAAAATCAAGGTCAAAAATG
* *
36086 GAATTTTATGAAGTTTAGGGGT
66 GAATTTTAGGAAGTTTAAGGGT
36108 AAAAATGTAATTTTTGGAAGTTTAGGGGTACAAATG-TAATTCTTGAAAAAATCAAGGTCAAAAA
1 AAAAATGTAATTTTTGGAAGTTTAGGGGTA-AAATGTTAATT-TTGAAAAAATCAAGGTCAAAAA
36172 TGGAATTTT-GGAAAGTTTAAGGGT
64 TGGAATTTTAGG-AAGTTTAAGGGT
*
36196 GAAAATGTAATTTT
1 AAAAATGTAATTTT
36210 CAAAAAGTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
87 35 0.39
88 55 0.61
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.34
Consensus pattern (87 bp):
AAAAATGTAATTTTTGGAAGTTTAGGGGTAAAATGTTAATTTTGAAAAAATCAAGGTCAAAAATG
GAATTTTAGGAAGTTTAAGGGT
Found at i:36248 original size:30 final size:29
Alignment explanation
Indices: 36032--36280 Score: 100
Period size: 29 Copynumber: 8.5 Consensus size: 29
36022 AAAATGGAAT
* *
36032 TTTTGG-AAGTTTAGGGGT-AAAATGTTAA
1 TTTTGGAAAGTTTAAGGGTAAAAAT-ATAA
* **
36060 TTTTGGGAAA-ATT-AGGGTTAAAAATGGAA
1 TTTT-GGAAAGTTTAAGGG-TAAAAATATAA
* * *
36089 TTTTATG-AAGTTTAGGGGTAAAAATGTAA
1 TTTT-GGAAAGTTTAAGGGTAAAAATATAA
* * *
36118 TTTTTGG-AAGTTTAGGGGTACAAATGTAA
1 -TTTTGGAAAGTTTAAGGGTAAAAATATAA
* ** * **
36147 TTCTTGAAAAAATCAA-GGTCAAAAATGGAA
1 TT-TTGGAAAGTTTAAGGGT-AAAAATATAA
* *
36177 TTTTGGAAAGTTTAAGGGTGAAAATGTAA
1 TTTTGGAAAGTTTAAGGGTAAAAATATAA
** *
36206 TTTTCAAAAAGTTT-TGGGTAAAAAATATAA
1 TTTT-GGAAAGTTTAAGGGT-AAAAATATAA
** * *
36236 TTTTGGAGAAGTTTGGGGGTCAAAATAAAA
1 TTTTGGA-AAGTTTAAGGGTAAAAATATAA
*
36266 TTTTTGGATAGTTTA
1 -TTTTGGAAAGTTTA
36281 GGGACCTTTA
Statistics
Matches: 169, Mismatches: 36, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
28 11 0.07
29 78 0.46
30 69 0.41
31 11 0.07
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (29 bp):
TTTTGGAAAGTTTAAGGGTAAAAATATAA
Found at i:36250 original size:29 final size:27
Alignment explanation
Indices: 36175--36279 Score: 66
Period size: 30 Copynumber: 3.6 Consensus size: 27
36165 TCAAAAATGG
* *
36175 AATTTTGGAAAGTTTAAGGGTGAAAATGT
1 AATTTTGGAAAGTTT--GGGTAAAAATAT
**
36204 AATTTTCAAAAAGTTTTGGGTAAAAAATAT
1 AATTTT-GGAAAG-TTTGGGT-AAAAATAT
* *
36234 AATTTTGGAGAAGTTTGGGGGTCAAAATAA
1 AATTTTGGA-AAGTTT--GGGTAAAAATAT
*
36264 AATTTTTGGATAGTTT
1 AA-TTTTGGAAAGTTT
36280 AGGGACCTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
29 14 0.23
30 32 0.53
31 14 0.23
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (27 bp):
AATTTTGGAAAGTTTGGGTAAAAATAT
Found at i:36676 original size:11 final size:11
Alignment explanation
Indices: 36660--36690 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
36650 CTAGGTTAGG
36660 TCGGGTCGAAT
1 TCGGGTCGAAT
36671 TCGGGTCGAAT
1 TCGGGTCGAAT
36682 TCGGGTCGA
1 TCGGGTCGA
36691 TTCATGGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.39, T:0.26
Consensus pattern (11 bp):
TCGGGTCGAAT
Found at i:37404 original size:21 final size:21
Alignment explanation
Indices: 37378--37422 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
37368 CTTTTTTTTG
37378 TTATTAATA-TATTAATATTTA
1 TTATTAATATTATT-ATATTTA
*
37399 TTATTATTATTATTATATTTA
1 TTATTAATATTATTATATTTA
37420 TTA
1 TTA
37423 CTTCGTCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTAATATTATTATATTTA
Found at i:37472 original size:72 final size:71
Alignment explanation
Indices: 37356--37496 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 71
37346 AGGGTCCTTT
37356 GTCCCTTAGTTTCTTTTTTTTGTTATTAATATATTAATATTTATTATTATTATTATTATATTTAT
1 GTCCCTTAGTTTCTTTTTTTTGTTATTAATATATTAATATTTATTATTATTATTATTATATTTAT
37421 TACTTC
66 TACTTC
37427 GTCCCTTAGTTTCTTTTTTTTTGTTATTAATATATTAATATTTATTATTATTATTATTATATTTA
1 GTCCCTTAGTTTC-TTTTTTTTGTTATTAATATATTAATATTTATTATTATTATTATTATATTTA
37492 TTACT
65 TTACT
37497 ACTACTACTA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 13 0.19
72 56 0.81
ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62
Consensus pattern (71 bp):
GTCCCTTAGTTTCTTTTTTTTGTTATTAATATATTAATATTTATTATTATTATTATTATATTTAT
TACTTC
Found at i:37476 original size:3 final size:3
Alignment explanation
Indices: 37450--37566 Score: 112
Period size: 3 Copynumber: 39.0 Consensus size: 3
37440 TTTTTTTTTG
* *
37450 TTA TTA ATA -TA TTA ATA TTTA TTA TTA TTA TTA TTA -TA TTTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* * * * * * *
37495 CTA CTA CTA CTA CTA CTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
37543 TTA TTA TTA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
37567 ATGTTATTTA
Statistics
Matches: 103, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
2 4 0.04
3 95 0.92
4 4 0.04
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:37526 original size:72 final size:72
Alignment explanation
Indices: 37378--37566 Score: 208
Period size: 72 Copynumber: 2.6 Consensus size: 72
37368 CTTTTTTTTG
* * * * *
37378 TTATTAATATATTAATATTTATTATTATTATTATTATATTTATTACTTCGTCCCTTAGTTTCTTT
1 TTATTAATATATTAATATTTATTATTATTATTATTATATTTATTACTACGTCACTTAGCTACTCT
* * *
37443 TTTTTTG
66 ATTATTA
37450 TTATTAATATATTAATATTTATTATTATTATTATTATATTTATTACTAC-T-ACTACTA-CTACT
1 TTATTAATATATTAATATTTATTATTATTATTATTATATTTATTACTACGTCACT--TAGCTACT
37512 ACTATTATTA
64 -CTATTATTA
* *
37522 TTATTATTATTATTATTA-TTATTATTATTATTATTAT-TGTTATTA
1 TTATTAATA-TATTAATATTTATTATTATTATTATTATAT-TTATTA
37567 ATGTTATTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
70 2 0.02
71 5 0.05
72 88 0.86
73 7 0.07
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (72 bp):
TTATTAATATATTAATATTTATTATTATTATTATTATATTTATTACTACGTCACTTAGCTACTCT
ATTATTA
Found at i:38180 original size:17 final size:17
Alignment explanation
Indices: 38147--38232 Score: 84
Period size: 17 Copynumber: 4.9 Consensus size: 17
38137 AATTTAATTT
*
38147 TAAAGTTTAAGTTTAAAA
1 TAAA-TTTAAATTTAAAA
* *
38165 T-TATTTCAAATTTAAAC
1 TAAATTT-AAATTTAAAA
38182 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
38199 CAAATTTAAACTTAAAAA
1 TAAATTTAAA-TTTAAAA
*
38217 TGAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
38233 TTTAAGGTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
16 3 0.05
17 33 0.60
18 19 0.35
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:38193 original size:6 final size:6
Alignment explanation
Indices: 38137--38237 Score: 66
Period size: 6 Copynumber: 17.2 Consensus size: 6
38127 ATGGACTTTG
* * * *
38137 AATTTA ATTTTA AAGTTTA AGTTTA AAATT- -ATTTCA AATTTA AA-CTA
1 AATTTA AATTTA AA-TTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
** * ** *
38184 AATTTA AATTTA AA-ACA AATTTA AACTTA AAAATG AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
38231 AATTTA A
1 AATTTA A
38238 GGTAAATTAA
Statistics
Matches: 70, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
4 3 0.04
5 7 0.10
6 51 0.73
7 9 0.13
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:38806 original size:43 final size:43
Alignment explanation
Indices: 38724--38808 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
38714 ATTAACATGT
* *
38724 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
38767 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
38809 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:39668 original size:21 final size:22
Alignment explanation
Indices: 39642--39687 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
39632 TCCATACTTA
*
39642 TAAACCCTAAATTATAAACC-T
1 TAAACCCTAAATTAAAAACCAT
*
39663 TAAACCCTGAATTAAAAACCAT
1 TAAACCCTAAATTAAAAACCAT
39685 TAA
1 TAA
39688 CCTCAATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.26
Consensus pattern (22 bp):
TAAACCCTAAATTAAAAACCAT
Found at i:42181 original size:24 final size:24
Alignment explanation
Indices: 42149--42194 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
42139 ACCATACACA
42149 GAGTTGGATCTTCATTTTCTACTG
1 GAGTTGGATCTTCATTTTCTACTG
42173 GAGTTGGATCTTCATTTTCTAC
1 GAGTTGGATCTTCATTTTCTAC
42195 AAGTTCCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (24 bp):
GAGTTGGATCTTCATTTTCTACTG
Done.