Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005323.1 Kokia drynarioides strain JFW-HI SEQ_119261, 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: 72430
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1384 original size:29 final size:30
Alignment explanation
Indices: 1349--1434 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 30
1339 TTTAAATCTC
*
1349 TTAAAAGTTGATAAAAAAAAATTTAGT-TA
1 TTAAAAGTTGATAAAAAAAAATTTAGTCCA
* * * *
1378 TTAAAAGCT-AAAAAAATAAAATTTGGGGTCCC
1 TTAAAAGTTGATAAAAA-AAAATTT--AGTCCA
*
1410 TTAATAGTTGATAAAAAAAAATTTA
1 TTAAAAGTTGATAAAAAAAAATTTA
1435 ACCTTCAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
28 6 0.14
29 15 0.35
31 2 0.05
32 14 0.33
33 6 0.14
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (30 bp):
TTAAAAGTTGATAAAAAAAAATTTAGTCCA
Found at i:1469 original size:25 final size:24
Alignment explanation
Indices: 1423--1483 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
1413 ATAGTTGATA
* *
1423 AAAAAAAATTTAACCTTCAAAAGTT
1 AAAAAAAA-TAAACCTTCAAAAATT
*
1448 AAAAAAAATAAACCTATTAAAAATT
1 AAAAAAAATAAACCT-TCAAAAATT
1473 AAAAAACAATA
1 AAAAAA-AATA
1484 TTTTAAATCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 21 0.68
26 4 0.13
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAAAAAATAAACCTTCAAAAATT
Found at i:6195 original size:199 final size:198
Alignment explanation
Indices: 5939--6737 Score: 1131
Period size: 199 Copynumber: 4.0 Consensus size: 198
5929 AGAAAAATAA
* * * * *
5939 GTATTAATACTTATATAAGTATAGATACCAAATTGGCATTCTATTGATTTTAAAATACTGTTCAT
1 GTATTGATACTTATAT-GGTATCGATATCAAATTGGCATTCTATTGATTTAAAAATACTGTTCAT
* * * * * * *
6004 TTGGAGAAATATCGATACTTCAACTTATAGTATCGATACATTTTGCCGGAAAATTAAAAATTTCA
65 TTGGAAAAATATCGATACTTCAACCTATAGTATTGATACTTTTTGCCAGAAAGTTAAAAATCTCA
* ** ** *
6069 TATTCAGTAGGATTTCTCATGCTCAAACCAAAACCAACTCAAAAGGAACCTTAAGTACACATATA
130 TGTTTGGTATCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGTACACATATA
*
6134 GCTT
195 ACTT
* * *
6138 GTATTGATACTTATATGGGTATCGATA-CGAAATTGG-ATTTTTTTTTATTTAAAAATACTGTTC
1 GTATTGATACTTATAT-GGTATCGATATC-AAATTGGCA-TTCTATTGATTTAAAAATACTGTTC
* * *
6201 ATTTGGAAAAATATTGATACTTCAACCTATAGTATTGATACTTTTTGCTAGAAATTTAAAAATCT
63 ATTTGGAAAAATATCGATACTTCAACCTATAGTATTGATACTTTTTGCCAGAAAGTTAAAAATCT
* * * *
6266 CATTTTTGGTATGATTTCTCATGCTCAAACCAAAACCAACTAAAAAAGAAACTTAAGTACACATA
128 CATGTTTGGTATCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGTACACATA
6331 TAACTT
193 TAACTT
* * * * *
6337 GTATTGATACTTATATGTTATCGATATCAAATTGGCATTTTCTTGATTTAAAAATATTGTTCTTT
1 GTATTGATACTTATATGGTATCGATATCAAATTGGCATTCTATTGATTTAAAAATACTGTTCATT
*
6402 TGGAAAAATATCGATACTTTAACCTATAGTATTGATACTTTTTGCCAGAAAGTTAAAAAAATCTC
66 TGGAAAAATATCGATACTTCAACCTATAGTATTGATACTTTTTGCCAGAAAGTT--AAAAATCTC
6467 ATGTTTGGT-TCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGTACACATAT
129 ATGTTTGGTATCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGTACACATAT
6531 AACTT
194 AACTT
* * *
6536 GTATTGATACTTA-ATCGATAAT-GATATCAAATTGACATTCTATTGATTTAAAAATAATGTTCA
1 GTATTGATACTTATAT-GGT-ATCGATATCAAATTGGCATTCTATTGATTTAAAAATACTGTTCA
*
6599 TTTGGAAAAATATCGATACTTCAACCTATAGTATTGATACTTTTTGCTAGAAAGTTAAAAATCTC
64 TTTGGAAAAATATCGATACTTCAACCTATAGTATTGATACTTTTTGCCAGAAAGTTAAAAATCTC
*
6664 ATGTTTGGTATCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGTACACCTAT
129 ATGTTTGGTATCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGTACACATAT
6729 AACTT
194 AACTT
6734 GTAT
1 GTAT
6738 AAAACACCAT
Statistics
Matches: 544, Mismatches: 47, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
197 18 0.03
198 157 0.29
199 350 0.64
200 19 0.03
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (198 bp):
GTATTGATACTTATATGGTATCGATATCAAATTGGCATTCTATTGATTTAAAAATACTGTTCATT
TGGAAAAATATCGATACTTCAACCTATAGTATTGATACTTTTTGCCAGAAAGTTAAAAATCTCAT
GTTTGGTATCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGTACACATATAA
CTT
Found at i:6682 original size:397 final size:397
Alignment explanation
Indices: 5939--6737 Score: 1160
Period size: 397 Copynumber: 2.0 Consensus size: 397
5929 AGAAAAATAA
*
5939 GTATTAATACTTATATAAGTATAGATACCAAATTGGCATTCTATTGATTTTAAAATACTGTTCAT
1 GTATTAATACTTATAT-AGTATAGATACCAAATTGGCATTCTATTGATTTAAAAATACTGTTCAT
* * * *
6004 TTGGAGAAATATCGATACTTCAACTTATAGTATCGATACATTTTGCCGGAAAATTAAAAATTTCA
65 TTGGAAAAATATCGATACTTCAACCTATAGTATCGATACATTTTGCCAGAAAATTAAAAATCTCA
* *
6069 TATTCAGTAGGATTTCTCATGCTCAAACCAAAACCAACTCAAAAGGAACCTTAAGTACACATATA
130 TATTCAGTAGCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGTACACATATA
* * * * * * * *
6134 GCTTGTATTGATACTTATATGGGTATCGATACGAAATTGGATTTTTTTTTATTTAAAAATACTGT
195 ACTTGTATTGATACTTATATCGATATCGATACGAAATTGGAATTCTATTGATTTAAAAATAATGT
* *
6199 TCATTTGGAAAAATATTGATACTTCAACCTATAGTATTGATACTTTTTGCTAGAAATTTAAAAAT
260 TCATTTGGAAAAATATCGATACTTCAACCTATAGTATTGATACTTTTTGCTAGAAAGTTAAAAAT
* *
6264 CTCATTTTTGGTATGATTTCTCATGCTCAAACCAAAACCAACTAAAAAAGAAACTTAAGTACACA
325 CTCATGTTTGGTATCATTTCTCATGCTCAAACCAAAACCAACTAAAAAAGAAACTTAAGTACACA
6329 TATAACTT
390 TATAACTT
* * * * * * *
6337 GTATTGATACTTATAT-GTTATCGATATCAAATTGGCATTTTCTTGATTTAAAAATATTGTTCTT
1 GTATTAATACTTATATAG-TATAGATACCAAATTGGCATTCTATTGATTTAAAAATACTGTTCAT
* * * *
6401 TTGGAAAAATATCGATACTTTAACCTATAGTATTGATACTTTTTGCCAGAAAGTTAAAAAAATCT
65 TTGGAAAAATATCGATACTTCAACCTATAGTATCGATACATTTTGCCAGAAAATT--AAAAATCT
* ** *
6466 CATGTTTGGT-TCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGTACACATA
128 CATATTCAGTAGCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGTACACATA
6530 TAACTTGTATTGATACTTA-ATCGATAAT-GATATC-AAATT-GACATTCTATTGATTTAAAAAT
193 TAACTTGTATTGATACTTATATCGAT-ATCGATA-CGAAATTGGA-ATTCTATTGATTTAAAAAT
6591 AATGTTCATTTGGAAAAATATCGATACTTCAACCTATAGTATTGATACTTTTTGCTAGAAAGTTA
255 AATGTTCATTTGGAAAAATATCGATACTTCAACCTATAGTATTGATACTTTTTGCTAGAAAGTTA
* *
6656 AAAATCTCATGTTTGGTATCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGT
320 AAAATCTCATGTTTGGTATCATTTCTCATGCTCAAACCAAAACCAACTAAAAAAGAAACTTAAGT
*
6721 ACACCTATAACTT
385 ACACATATAACTT
6734 GTAT
1 GTAT
6738 AAAACACCAT
Statistics
Matches: 358, Mismatches: 37, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
396 3 0.01
397 254 0.71
398 87 0.24
399 14 0.04
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (397 bp):
GTATTAATACTTATATAGTATAGATACCAAATTGGCATTCTATTGATTTAAAAATACTGTTCATT
TGGAAAAATATCGATACTTCAACCTATAGTATCGATACATTTTGCCAGAAAATTAAAAATCTCAT
ATTCAGTAGCATTTCTCATGCTCAAACCAAAACCAACTCAAAAAGAACCTTAAGTACACATATAA
CTTGTATTGATACTTATATCGATATCGATACGAAATTGGAATTCTATTGATTTAAAAATAATGTT
CATTTGGAAAAATATCGATACTTCAACCTATAGTATTGATACTTTTTGCTAGAAAGTTAAAAATC
TCATGTTTGGTATCATTTCTCATGCTCAAACCAAAACCAACTAAAAAAGAAACTTAAGTACACAT
ATAACTT
Found at i:7545 original size:24 final size:24
Alignment explanation
Indices: 7515--7563 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
7505 TTCATTTACA
7515 TCATAATTATATCATATAAACATT
1 TCATAATTATATCATATAAACATT
7539 TCATAATTATATCATATAAACATT
1 TCATAATTATATCATATAAACATT
7563 T
1 T
7564 TTAAAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (24 bp):
TCATAATTATATCATATAAACATT
Found at i:9368 original size:11 final size:11
Alignment explanation
Indices: 9352--9376 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9342 TTTTTGTTTG
9352 TTTATTTTTAT
1 TTTATTTTTAT
9363 TTTATTTTTAT
1 TTTATTTTTAT
9374 TTT
1 TTT
9377 TTTCCAAGTC
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:13095 original size:22 final size:22
Alignment explanation
Indices: 13067--13120 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
13057 ACAGAACTGA
*
13067 TGTCACGACACACTAGAGCCTG
1 TGTCACGACACACTAAAGCCTG
13089 TGTCACGACACACTAAAGCCTG
1 TGTCACGACACACTAAAGCCTG
13111 TGTCACGACA
1 TGTCACGACA
13121 TCAAAGATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (22 bp):
TGTCACGACACACTAAAGCCTG
Found at i:14632 original size:2 final size:2
Alignment explanation
Indices: 14627--14677 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
14617 TGTATATATA
* * *
14627 TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG CG TG TG TT TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
14669 TT TG TG TG T
1 TG TG TG TG T
14678 TTAATTTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.04, G:0.45, T:0.51
Consensus pattern (2 bp):
TG
Found at i:20607 original size:21 final size:21
Alignment explanation
Indices: 20565--20608 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20555 ATAATGCAGA
*
20565 CTTCTACCGATACAAGAGACT
1 CTTCTACCGATACAAGAAACT
20586 CTTCTACCGATACTAA-AAACT
1 CTTCTACCGATAC-AAGAAACT
20607 CT
1 CT
20609 AGAGAGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.34, C:0.30, G:0.09, T:0.27
Consensus pattern (21 bp):
CTTCTACCGATACAAGAAACT
Found at i:21020 original size:30 final size:30
Alignment explanation
Indices: 20985--21045 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
20975 AAATTCAAAT
*
20985 AATTCATACAATAAGTAGAAAGACAACTTC
1 AATTCATACAAGAAGTAGAAAGACAACTTC
*
21015 AATTCATACAAGAAGTAGAAAGACTACTTC
1 AATTCATACAAGAAGTAGAAAGACAACTTC
21045 A
1 A
21046 TACTAGTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.23
Consensus pattern (30 bp):
AATTCATACAAGAAGTAGAAAGACAACTTC
Found at i:27718 original size:21 final size:20
Alignment explanation
Indices: 27669--27719 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
27659 AGAATAGTGC
*
27669 AGACTTT-TACCGATACAAG
1 AGACTTTCTACCGATACAAA
* *
27688 TGACAGTTCTACCGATACAAA
1 AGAC-TTTCTACCGATACAAA
27709 AGACTCTTCTA
1 AGACT-TTCTA
27720 TAGAAACAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 19 0.79
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (20 bp):
AGACTTTCTACCGATACAAA
Found at i:31729 original size:21 final size:20
Alignment explanation
Indices: 31690--31729 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31680 CCTGTGACAT
*
31690 GGGCATGTGGAGGGCCACAA
1 GGGCATGTGGAGAGCCACAA
*
31710 GGGCGTGTGGAAGAGCCACA
1 GGGCATGTGG-AGAGCCACA
31730 CAGTCGTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.25, C:0.20, G:0.45, T:0.10
Consensus pattern (20 bp):
GGGCATGTGGAGAGCCACAA
Found at i:35172 original size:69 final size:69
Alignment explanation
Indices: 35081--35723 Score: 378
Period size: 69 Copynumber: 9.3 Consensus size: 69
35071 CTGTGAGTTA
* * * * * *
35081 TTTTGGAAGATGCGATCTTAAACTAGCAAGCCTTTATAATATCAATTGGGAATATAGGTTCGCTA
1 TTTTGGAGGTTGCGATCATAAACTAGCAAGCCTTTAAAATATCAATTGGGAACATAGGTCCGCTA
35146 GCTG
66 GCTG
* * * * * * * **
35150 TTTTGGAGGTTGTGATCATAAACT-GACAAAACTTTTAGAATATTAATTAGGAACGTAGGTCTAC
1 TTTTGGAGGTTGCGATCATAAACTAG-C-AAGCCTTTAAAATATCAATTGGGAACATAGGTCCGC
*
35214 TAACTG
64 TAGCTG
* * * ** * * * *
35220 TTTTGGAGGCTGCAATCATAAAC-CG-ATGAGCCTTTAAAATATCAGCTGGTAGCGTAGGTCTGC
1 TTTTGGAGGTTGCGATCATAAACTAGCA--AGCCTTTAAAATATCAATTGGGAACATAGGTCCGC
*
35283 TAACTG
64 TAGCTG
* * * ** * * *
35289 CTTTGGAGGTTACAATCATAAA-TCAGTGAGCC-TTAATAATATCAGTTGGG-ACGTAAGTCCGC
1 TTTTGGAGGTTGCGATCATAAACT-AGCAAGCCTTTAA-AATATCAATTGGGAACATAGGTCCGC
*
35351 TAGTTG
64 TAGCTG
* ** * * * *
35357 TTTTGGTGGTTGCGGCCATAAATTGATG-AA-TCTTTAAAATATCAATTGGGAACATAGTTCTGC
1 TTTTGGAGGTTGCGATCATAAACT-A-GCAAGCCTTTAAAATATCAATTGGGAACATAGGTCCGC
35420 T-GACTG
64 TAG-CTG
* * * * * * * *
35426 TTCTGAAGGTTGCGATCCTAAAC-CGACGAGCCTTTAAAATATCAACTGGGAGCATAGGTCCACT
1 TTTTGGAGGTTGCGATCATAAACTAG-CAAGCCTTTAAAATATCAATTGGGAACATAGGTCCGCT
*
35490 AGCTA
65 AGCTG
* * * ** *
35495 CTTTGGAGGCTGCGATCATAAA-TCGACAAGCC-TTAATAATATCAATTGGGAATGTAGGTCCAC
1 TTTTGGAGGTTGCGATCATAAACTAG-CAAGCCTTTAA-AATATCAATTGGGAACATAGGTCCGC
*
35558 TAGCTA
64 TAGCTG
** * * * * * *
35564 TTTTATAGGTTGCGATCATAAACCAACAAACCTTTAGAATATCAACTAGGAACATAGGTCCGCTA
1 TTTTGGAGGTTGCGATCATAAACTAGCAAGCCTTTAAAATATCAATTGGGAACATAGGTCCGCTA
35629 GCTG
66 GCTG
* * * * * * *
35633 TTTTGGAGGCTGCGATCATAAA-TCGACGAGCCTTTAAAATATCAGTTAGGAGCGTAGGTCCGCT
1 TTTTGGAGGTTGCGATCATAAACTAG-CAAGCCTTTAAAATATCAATTGGGAACATAGGTCCGCT
*
35697 AGCTAC
65 AGCT-G
* *
35703 TTTT-GAGGCTGTGATCATAAA
1 TTTTGGAGGTTGCGATCATAAA
35724 TCGATGAGCC
Statistics
Matches: 439, Mismatches: 111, Indels: 48
0.73 0.19 0.08
Matches are distributed among these distances:
66 1 0.00
67 1 0.00
68 53 0.12
69 322 0.73
70 62 0.14
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (69 bp):
TTTTGGAGGTTGCGATCATAAACTAGCAAGCCTTTAAAATATCAATTGGGAACATAGGTCCGCTA
GCTG
Found at i:35675 original size:207 final size:208
Alignment explanation
Indices: 34953--35727 Score: 722
Period size: 207 Copynumber: 3.7 Consensus size: 208
34943 ATATGGAGGC
* * * * * * * * * * *
34953 TGCGATCTTAAACTGACGAGCCTTAATAATATCAACTGGGAGCATAGGT-TCGCAACCTATTTTG
1 TGCGATCATAAACTGACAAACCTTTAGAATATCAATTAGGAACATAGGTCT-GCTAGCTGTTTTG
* * ** ** * * * *
35017 GAGGTTGCGATCTTAAACCGATAAAG-CTTTAAAATATCAGCTAAGAGTGTAAGTCTG-TGAGTT
65 GAGGCTGCGATCATAAACCGA-CGAGCCTTTAAAATATCAGCTGGGAGCGTAGGTCCGCT-AGCT
* * * * * * * *
35080 ATTTTGGAAGATGCGATCTTAAA-CTAGCAAGCCTTTATAATATCAATTGGGAATATAGGTTCGC
128 ACTTTGGAGGCTGCGATCATAAATCGAGCAAGCCTTAATAATATCAATTGGGAATGTAGGTCCGC
*
35144 TAGCTGTTTTGGAGGT
193 TAGCTGTTTTGTAGGT
* * * * * *
35160 TGTGATCATAAACTGACAAAACTTTTAGAATATTAATTAGGAACGTAGGTCTACTAACTGTTTTG
1 TGCGATCATAAACTGAC-AAACCTTTAGAATATCAATTAGGAACATAGGTCTGCTAGCTGTTTTG
* * * * * *
35225 GAGGCTGCAATCATAAACCGATGAGCCTTTAAAATATCAGCTGGTAGCGTAGGTCTGCTAACTGC
65 GAGGCTGCGATCATAAACCGACGAGCCTTTAAAATATCAGCTGGGAGCGTAGGTCCGCTAGCTAC
* * * ** * * *
35290 TTTGGAGGTTACAATCATAAATC-AGTGAGCCTTAATAATATCAGTTGGG-ACGTAAGTCCGCTA
130 TTTGGAGGCTGCGATCATAAATCGAGCAAGCCTTAATAATATCAATTGGGAATGTAGGTCCGCTA
*
35353 GTTGTTTTGGT-GGT
195 GCTGTTTT-GTAGGT
** * ** * * * * *
35367 TGCGGCCATAAATTGATGAATCTTTAAAATATCAATTGGGAACATAGTTCTGCT-GACTGTTCTG
1 TGCGATCATAAACTGACAAACCTTTAGAATATCAATTAGGAACATAGGTCTGCTAG-CTGTTTTG
* * * * * *
35431 AAGGTTGCGATCCTAAACCGACGAGCCTTTAAAATATCAACTGGGAGCATAGGTCCACTAGCTAC
65 GAGGCTGCGATCATAAACCGACGAGCCTTTAAAATATCAGCTGGGAGCGTAGGTCCGCTAGCTAC
*
35496 TTTGGAGGCTGCGATCATAAATCGA-CAAGCCTTAATAATATCAATTGGGAATGTAGGTCCACTA
130 TTTGGAGGCTGCGATCATAAATCGAGCAAGCCTTAATAATATCAATTGGGAATGTAGGTCCGCTA
* *
35560 GCTATTTTATAGGT
195 GCTGTTTTGTAGGT
** * *
35574 TGCGATCATAAACCAACAAACCTTTAGAATATCAACTAGGAACATAGGTCCGCTAGCTGTTTTGG
1 TGCGATCATAAACTGACAAACCTTTAGAATATCAATTAGGAACATAGGTCTGCTAGCTGTTTTGG
* * *
35639 AGGCTGCGATCATAAATCGACGAGCCTTTAAAATATCAGTTAGGAGCGTAGGTCCGCTAGCTACT
66 AGGCTGCGATCATAAACCGACGAGCCTTTAAAATATCAGCTGGGAGCGTAGGTCCGCTAGCTACT
* *
35704 TTTGAGGCTGTGATCATAAATCGA
131 TTGGAGGCTGCGATCATAAATCGA
35728 TGAGCCTTTA
Statistics
Matches: 447, Mismatches: 110, Indels: 22
0.77 0.19 0.04
Matches are distributed among these distances:
206 130 0.29
207 197 0.44
208 117 0.26
209 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (208 bp):
TGCGATCATAAACTGACAAACCTTTAGAATATCAATTAGGAACATAGGTCTGCTAGCTGTTTTGG
AGGCTGCGATCATAAACCGACGAGCCTTTAAAATATCAGCTGGGAGCGTAGGTCCGCTAGCTACT
TTGGAGGCTGCGATCATAAATCGAGCAAGCCTTAATAATATCAATTGGGAATGTAGGTCCGCTAG
CTGTTTTGTAGGT
Found at i:36928 original size:22 final size:21
Alignment explanation
Indices: 36888--36928 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
36878 ATAGGTTTTG
*
36888 GAAACAACTGAACAAAGATTA
1 GAAACAACTAAACAAAGATTA
*
36909 GAAACAAGCTAAACAGAGAT
1 GAAACAA-CTAAACAAAGAT
36929 ACATTCAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (21 bp):
GAAACAACTAAACAAAGATTA
Found at i:37918 original size:28 final size:28
Alignment explanation
Indices: 37859--37919 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
37849 TTCAATTTCT
* * ** * *
37859 TCGCAGTTTCACTGTGATAGTTCGCACT
1 TCGCAGTTTCAATGTGACAACTCACACC
37887 TCGCAGTTTCAATGTGACAACTCACACC
1 TCGCAGTTTCAATGTGACAACTCACACC
37915 TCGCA
1 TCGCA
37920 ACTCGCCAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.30
Consensus pattern (28 bp):
TCGCAGTTTCAATGTGACAACTCACACC
Found at i:45621 original size:120 final size:120
Alignment explanation
Indices: 45403--45635 Score: 351
Period size: 120 Copynumber: 1.9 Consensus size: 120
45393 ACAGATACCA
* * *
45403 TATCGATGACTAAGGTATTGCATCTGTTGTGAGTCCTCAATAGCTTGTGTGAGCAGCATCGTATA
1 TATCGATGACTAAGGTACTGCATATGTTGCGAGTCCTCAATAGCTTGTGTGAGCAGCATCGTATA
* * *
45468 CTGGTAACAGAGTTGATACAGACATGAGAATGAAATTTTGGATTATAGCATATCG
66 CTGATAACAGAGTTGATACAGACATGAGAATGAAATTCTAGATTATAGCATATCG
** *
45523 TATCGATGACTGGGGTACTGCATATGTTGCGAGTCCTCGATAGCTTGTGTGAGCAGCATCGTATA
1 TATCGATGACTAAGGTACTGCATATGTTGCGAGTCCTCAATAGCTTGTGTGAGCAGCATCGTATA
* *
45588 CTGATAACAGAGTTGATGC-GAACATGAGGATGAAATTCTAGATTATAG
66 CTGATAACAGAGTTGATACAG-ACATGAGAATGAAATTCTAGATTATAG
45636 TTTGTGGAAG
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
119 1 0.01
120 100 0.99
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (120 bp):
TATCGATGACTAAGGTACTGCATATGTTGCGAGTCCTCAATAGCTTGTGTGAGCAGCATCGTATA
CTGATAACAGAGTTGATACAGACATGAGAATGAAATTCTAGATTATAGCATATCG
Found at i:57112 original size:29 final size:29
Alignment explanation
Indices: 57070--57158 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
57060 TAAACATTTC
57070 AAATTTAAGCAATTTAAACAATACCTTTA
1 AAATTTAAGCAATTTAAACAATACCTTTA
* *
57099 AAATTTAAGCAATTCAATA-AA-AGCAATTT-
1 AAATTTAAGCAATTTAA-ACAATA-C-CTTTA
* *
57128 AAATTTAAACAATTTAAGCAATACCTTTA
1 AAATTTAAGCAATTTAAACAATACCTTTA
57157 AA
1 AA
57159 CAAGTTTCCA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
28 4 0.08
29 39 0.81
30 5 0.10
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (29 bp):
AAATTTAAGCAATTTAAACAATACCTTTA
Found at i:57713 original size:22 final size:22
Alignment explanation
Indices: 57686--57765 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 22
57676 ATGATTATTG
57686 TTATTAAATTTTAATAAAATTA
1 TTATTAAATTTTAATAAAATTA
57708 TTATTAAATATAATTTAATAAATAATT-
1 TTATT-AA-AT--TTTAAT-AA-AATTA
* * * *
57735 TAATTATATTTTAACATAATTA
1 TTATTAAATTTTAATAAAATTA
57757 TTATTAAAT
1 TTATTAAAT
57766 ACAATTTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
21 4 0.09
22 13 0.29
23 7 0.16
24 2 0.04
25 2 0.04
26 7 0.16
27 6 0.13
28 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATTAAATTTTAATAAAATTA
Found at i:57765 original size:49 final size:50
Alignment explanation
Indices: 57688--57783 Score: 149
Period size: 49 Copynumber: 1.9 Consensus size: 50
57678 GATTATTGTT
* *
57688 ATTAAATTTTAATAAAATTATTATTAAATATAATTTAAT-AAATAATTTA
1 ATTAAATTTTAACAAAATTATTATTAAATACAATTTAATAAAATAATTTA
* *
57737 ATTATATTTTAACATAATTATTATTAAATACAATTTAATAAAATAAT
1 ATTAAATTTTAACAAAATTATTATTAAATACAATTTAATAAAATAAT
57784 ATATAATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 35 0.83
50 7 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (50 bp):
ATTAAATTTTAACAAAATTATTATTAAATACAATTTAATAAAATAATTTA
Found at i:57799 original size:49 final size:48
Alignment explanation
Indices: 57703--57800 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 48
57693 ATTTTAATAA
* *
57703 AATTATTATTAAATATAATTTAATAAATAATTTAATTATATTTTAACAT
1 AATTATTATTAAATACAATTTAATAAATAATTTAATTATA-TATAACAT
57752 AATTATTATTAAATACAATTTAATAAAATAATATATAATT-TA-ATAACAT
1 AATTATTATTAAATACAATTTAAT-AAATAAT-T-TAATTATATATAACAT
57801 TTTTAATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
49 29 0.66
50 7 0.16
51 3 0.07
52 5 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (48 bp):
AATTATTATTAAATACAATTTAATAAATAATTTAATTATATATAACAT
Found at i:69910 original size:6 final size:6
Alignment explanation
Indices: 69885--69929 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
69875 ACAATTCATA
* * *
69885 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
69930 ATTTTGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Done.