Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011082.1 Kokia drynarioides strain JFW-HI SEQ_126055, 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: 55282
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:24 original size:17 final size:17
Alignment explanation
Indices: 2--62 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
1 C
2 AAATTTAAATTTAAAAT
1 AAATTTAAATTTAAAAT
*
19 AAATTTAAATTCAAAAT
1 AAATTTAAATTTAAAAT
*
36 CAATTT-AATCTTAAAAT
1 AAATTTAAAT-TTAAAAT
53 AAATCTTAAA
1 AAAT-TTAAA
63 ATGGGTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 3 0.08
17 30 0.81
18 2 0.05
19 2 0.05
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTTAAAAT
Found at i:914 original size:168 final size:169
Alignment explanation
Indices: 634--952 Score: 523
Period size: 168 Copynumber: 1.9 Consensus size: 169
624 GACCGCCTCA
* *
634 CTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTGCACTTCTTAGTATCTC
1 CTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTC
* ** *
699 ATCAGGAAGCTAACCTTTTATTGCTTCGTCCTACTTCTCAATATCTCATCAGGAAGCT-GGGGTC
66 ATCAGGAAGCTAACCTTTTATTACTTCACCCTACTTCTCAATATCTCATCAGGAAGCTAGGAGTC
* *
763 GAAGATTTGCTCGCATTGAGCCTCGAGTTGGTATTCTTG
131 GAAGATTTGCTCACATCGAGCCTCGAGTTGGTATTCTTG
*
802 CTTGTTTCAATCCGCTTCTCTGTATCTCTTCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTC
1 CTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTC
* * *
867 ATCAGGAAGCTAACCTTTTATTACTTCACCCTGCTTCTCAGTATCTCATCAGGAAGCTAGGATTC
66 ATCAGGAAGCTAACCTTTTATTACTTCACCCTACTTCTCAATATCTCATCAGGAAGCTAGGAGTC
932 GAAGATTTGCTCACATCGAGC
131 GAAGATTTGCTCACATCGAGC
953 GTGGGTTTGA
Statistics
Matches: 138, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
168 115 0.83
169 23 0.17
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (169 bp):
CTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTC
ATCAGGAAGCTAACCTTTTATTACTTCACCCTACTTCTCAATATCTCATCAGGAAGCTAGGAGTC
GAAGATTTGCTCACATCGAGCCTCGAGTTGGTATTCTTG
Found at i:1119 original size:373 final size:361
Alignment explanation
Indices: 441--1132 Score: 911
Period size: 373 Copynumber: 1.9 Consensus size: 361
431 GACCGCATCA
** * * * *
441 CTTGTTTTGATCCACTTCTCTGTGTTTCCTCAGGAAGACGGATTTGGTTCACTTCTTCGTATCTC
1 CTTGTTTCAATCCACTTCTCTGTATCTCCTCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTC
* * * * *
506 ATCAGGAAGCTAAGCTTTTTATTGCTTCGCCCTGTTTCTCAGTATCTCATCAGGAAGCTGGGGTC
66 ATCAGGAAGCTAAGCCTTTTATTACTTCACCCTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTC
* ** * *
571 AAAGATTTGTTTGCATTGAGTTGGTATACTTCTTTATATCTCATCAGGAAGATGACCGCCTCACT
131 AAAGATTTGCTCACATCGAGTGGGTATACTTCTTTATATCTCATCAGGAAGATGACCGCCTCACT
* * * * *
636 TGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTGCACTTCTTAGTATCTCAT
196 TGTTTCAATCCGCTTCTCTGTACCTCATCAAGAAGACGAATTTGGTCCACTTCTCAATATCTCAT
* *
701 CAGGAAGCTAACCTTTTATTGCTTCGTCCTACTTCTCAATATCTCATCAGGAAGCTGGGGTCGAA
261 CAAGAAGCTAACCTTTTATTGCTTCGCCCTACTTCTCAATATCTCATCAGGAAGCTGGGGTCGAA
766 GATTTGCTCGCATTGAGCCTCGAGTTGGTATTCTTG
326 GATTTGCTCGCATTGAGCCTCGAGTTGGTATTCTTG
* *
802 CTTGTTTCAATCCGCTTCTCTGTATCTCTTCAGGAAGACGAATTTGGTCCACTTC-TCAGTATCT
1 CTTGTTTCAATCCACTTCTCTGTATCTCCTCAGGAAGACGAATTTGGTCCACTTCTTC-GTATCT
*
866 CATCAGGAAGCTAA-CCTTTTATTACTTCACCCTGCTTCTCAGTATCTCATCAGGAAGCTAGGAT
65 CATCAGGAAGCTAAGCCTTTTATTACTTCACCCTGCTTCTCAGTATCTCATCAGGAAGCT-GGAG
* *
930 TCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG
129 TCAAAGATTTGCTCACATCGA--GTGGG--T-A--T--ACTTCTT-T-A-TATCTCATCAGGAAG
* ** **
995 ATGACTGTGTCGTTTGTTTCAATCCGCTTCTCTGTACCTCATCAAGAAGACGAATTTGGTCCACT
182 ATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATCAAGAAGACGAATTTGGTCCACT
* * * *
1060 TCTCAATATCTCATCAAGAAGCTAACCTTTTGTTGCTTCGCCCTGCTTCTTAGTATCTCATCAGG
247 TCTCAATATCTCATCAAGAAGCTAACCTTTTATTGCTTCGCCCTACTTCTCAATATCTCATCAGG
1125 AAGCTGGG
312 AAGCTGGG
1133 ATTCAGAGAT
Statistics
Matches: 280, Mismatches: 37, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
360 43 0.15
361 85 0.30
363 4 0.01
365 1 0.00
366 1 0.00
368 1 0.00
370 6 0.02
371 1 0.00
372 1 0.00
373 137 0.49
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (361 bp):
CTTGTTTCAATCCACTTCTCTGTATCTCCTCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTC
ATCAGGAAGCTAAGCCTTTTATTACTTCACCCTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTC
AAAGATTTGCTCACATCGAGTGGGTATACTTCTTTATATCTCATCAGGAAGATGACCGCCTCACT
TGTTTCAATCCGCTTCTCTGTACCTCATCAAGAAGACGAATTTGGTCCACTTCTCAATATCTCAT
CAAGAAGCTAACCTTTTATTGCTTCGCCCTACTTCTCAATATCTCATCAGGAAGCTGGGGTCGAA
GATTTGCTCGCATTGAGCCTCGAGTTGGTATTCTTG
Found at i:1273 original size:115 final size:114
Alignment explanation
Indices: 1057--1263 Score: 274
Period size: 115 Copynumber: 1.8 Consensus size: 114
1047 AATTTGGTCC
* * * *
1057 ACTTCTCAATATCTCATCAAGAAGCTAACCTTTTGTTGCTTCGCCCTGCTTCTTAGTATCTCATC
1 ACTTCTCAATATCTCATCAAGAAGCTAACCTTTTATTACTTCGACCTACTTCTTAGTATCTCATC
* *
1122 AGGAAGCTGGGATTCAGAGATTTTCTCACATCGAGCCCTGAGTTGGTAT
66 AGGAAGCTGGGATTCAGAAATTTGCTCACATCGAGCCCTGAGTTGGTAT
** * * *
1171 ACTTCTCTGTATCTCTTCAAGGAGTTAACCATTTTATTACTTCGACCTACTTCTTAGTATCTCAT
1 ACTTCTCAATATCTCATCAAGAAGCTAACC-TTTTATTACTTCGACCTACTTCTTAGTATCTCAT
1236 CAGGAAGCT-GGAGTTC-GAAAATTTGCTC
65 CAGGAAGCTGGGA-TTCAG-AAATTTGCTC
1264 GCTTTGAGCC
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
114 29 0.37
115 50 0.63
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.36
Consensus pattern (114 bp):
ACTTCTCAATATCTCATCAAGAAGCTAACCTTTTATTACTTCGACCTACTTCTTAGTATCTCATC
AGGAAGCTGGGATTCAGAAATTTGCTCACATCGAGCCCTGAGTTGGTAT
Found at i:13095 original size:28 final size:28
Alignment explanation
Indices: 13060--13121 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
13050 AAACGGGACT
*
13060 TTTTGGATACCCGAG-GGCAAAATGGTAA
1 TTTTGGAT-CCCGAGTGGCAAAATGATAA
* * *
13088 TTTTGGATTCTGGGTGGCAAAATGATAA
1 TTTTGGATCCCGAGTGGCAAAATGATAA
13116 TTTTGG
1 TTTTGG
13122 GAAAATTGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 3 0.10
28 26 0.90
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (28 bp):
TTTTGGATCCCGAGTGGCAAAATGATAA
Found at i:13333 original size:29 final size:29
Alignment explanation
Indices: 13232--13517 Score: 289
Period size: 29 Copynumber: 9.8 Consensus size: 29
13222 ATCCGGGGAC
* **
13232 AAAATGGTAATTTTTGAAAGTTTCAAGGTCA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGT-A
* * *
13263 AAAATGGAAATTTTGG-AGGTTCAGGGG-C
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
*
13291 AAAATGGAATTTTTGGAAGTTTCGGGGTT
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* *
13320 AAAATGAAAATTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
* *
13349 AAAATGAAATTTTTTGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
13378 AAAATGG-ATTTTTGGAAGTTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
*
13407 AAAATGGAATTCTTGGAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
* *
13436 AAAATGGAATTTTTGGAAGTTTTGGGGTCG
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
13466 AAAATGGAATTTTTGGAAGTTT-GGAGGTA
1 AAAATGGAATTTTTGGAAGTTTCGG-GGTA
* *
13495 AAAATGTAATTTTCGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
13518 AGGGACCTTC
Statistics
Matches: 221, Mismatches: 23, Indels: 23
0.83 0.09 0.09
Matches are distributed among these distances:
28 33 0.15
29 129 0.58
30 52 0.24
31 7 0.03
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:14587 original size:3 final size:3
Alignment explanation
Indices: 14579--14618 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
14569 TCTTTTTTAT
* *
14579 TTA TTA TTA GTA TTAA TTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
14619 ATGATATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:14627 original size:15 final size:15
Alignment explanation
Indices: 14579--14620 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
14569 TCTTTTTTAT
*
14579 TTATTATTAGTATTAA
1 TTATTATTAATATT-A
14595 TTATTATTAATATTA
1 TTATTATTAATATTA
14610 TTATTATTAAT
1 TTATTATTAAT
14621 GATATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TTATTATTAATATTA
Found at i:15332 original size:6 final size:6
Alignment explanation
Indices: 15321--15398 Score: 72
Period size: 6 Copynumber: 13.3 Consensus size: 6
15311 TATAATAAGT
* *
15321 TTTAAA TTTAAA TATAAA TCTAAA TTTAAA -TTAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
** * *
15369 -ACAAA TTAAAA TTTAAA -ATAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
15399 CAAAATCAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
5 12 0.21
6 40 0.69
7 6 0.10
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:15360 original size:35 final size:34
Alignment explanation
Indices: 15321--15431 Score: 111
Period size: 35 Copynumber: 3.2 Consensus size: 34
15311 TATAATAAGT
* *
15321 TTTAAATTTAAATATAAATCT-AAATTTAAATTAAA
1 TTTAAATTTAAA-ACAAAT-TAAAATTTAAAATAAA
15356 TTTAAATTTTAAAACAAATTAAAATTTAAAATAAA
1 TTTAAA-TTTAAAACAAATTAAAATTTAAAATAAA
* *
15391 TTTAAATTCAAAATC-AATT-TAATCTTAAAATAAA
1 TTTAAATTTAAAA-CAAATTAAAAT-TTAAAATAAA
15425 TCTTAAA
1 T-TTAAA
15432 ATGGGTTTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
33 3 0.04
34 22 0.33
35 36 0.54
36 6 0.09
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (34 bp):
TTTAAATTTAAAACAAATTAAAATTTAAAATAAA
Found at i:15361 original size:17 final size:17
Alignment explanation
Indices: 15321--15431 Score: 125
Period size: 17 Copynumber: 6.4 Consensus size: 17
15311 TATAATAAGT
15321 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* *
15339 TCTAAATTTAAATTAAA
1 TTTAAATTTAAAATAAA
*
15356 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
*
15374 TTAAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
15391 TTTAAATTCAAAATCAA
1 TTTAAATTTAAAATAAA
15408 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
15425 TCTTAAA
1 T-TTAAA
15432 ATGGGTTTAA
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
16 3 0.04
17 45 0.58
18 27 0.35
19 2 0.03
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:15374 original size:29 final size:29
Alignment explanation
Indices: 15322--15381 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
15312 ATAATAAGTT
* *
15322 TTAAATTTAAATATAAATCTAAATTTAAA
1 TTAAATTTAAATATAAAACTAAATTAAAA
*
15351 TTAAATTTAAATTTTAAAAC-AAATTAAAA
1 TTAAATTTAAA-TATAAAACTAAATTAAAA
15380 TT
1 TT
15382 TAAAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (29 bp):
TTAAATTTAAATATAAAACTAAATTAAAA
Found at i:15643 original size:17 final size:17
Alignment explanation
Indices: 15621--15670 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
15611 ATAAATTTCG
15621 AAAATTCAAAATATTAT-
1 AAAATT-AAAATATTATA
* *
15638 AAAATTGAAAGTTTTATA
1 AAAATT-AAAATATTATA
15656 AAAATTAAAA-ATTAT
1 AAAATTAAAATATTAT
15671 TTAAATTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (17 bp):
AAAATTAAAATATTATA
Found at i:15703 original size:24 final size:25
Alignment explanation
Indices: 15649--15710 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 25
15639 AAATTGAAAG
*
15649 TTTTATAAAAATTAAAAATTATTTAAA
1 TTTTA-AAAAATTAAAAA-TACTTAAA
*
15676 TTTTAGAAAATTAAAAA-ACTTAAA
1 TTTTAAAAAATTAAAAATACTTAAA
15700 TTTTAAAAAAT
1 TTTTAAAAAAT
15711 ATATATTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.50
26 11 0.34
27 5 0.16
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
TTTTAAAAAATTAAAAATACTTAAA
Found at i:15843 original size:18 final size:19
Alignment explanation
Indices: 15817--15853 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
15807 ATATTCTAGC
15817 ATTTGAAAAAAAAATGAAA
1 ATTTGAAAAAAAAATGAAA
*
15836 ATTT-AAAAACAAATGAAA
1 ATTTGAAAAAAAAATGAAA
15854 GTATATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.22
Consensus pattern (19 bp):
ATTTGAAAAAAAAATGAAA
Found at i:19555 original size:17 final size:17
Alignment explanation
Indices: 19533--19567 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19523 ATTATAAAAT
*
19533 CAAATCTTATCAGATTA
1 CAAATCTTATAAGATTA
*
19550 CAAATCTTGTAAGATTA
1 CAAATCTTATAAGATTA
19567 C
1 C
19568 TTTCCTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (17 bp):
CAAATCTTATAAGATTA
Found at i:20618 original size:17 final size:17
Alignment explanation
Indices: 20582--20620 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
20572 CTCCACCTTG
*
20582 ACAAGAACTCTCTACGA
1 ACAAGAACTCTCTACAA
20599 ACAAGAACTCT-TAACAA
1 ACAAGAACTCTCT-ACAA
20616 ACAAG
1 ACAAG
20621 TTCTGCACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCTACAA
Found at i:27685 original size:45 final size:45
Alignment explanation
Indices: 27621--27709 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
27611 TATATCAAGT
* *
27621 TGGCTGGTGTTAGTGAGGAAGTCTTAAACAAAATTGTTAGCAACC
1 TGGCTAGTGTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAACC
*
27666 TGGCTAGTTTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAAC
1 TGGCTAGTGTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAAC
27710 ATTGGTATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (45 bp):
TGGCTAGTGTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAACC
Found at i:29467 original size:29 final size:29
Alignment explanation
Indices: 29434--29801 Score: 114
Period size: 30 Copynumber: 12.5 Consensus size: 29
29424 TGCACGGGGG
* *
29434 CAAAATGGTAGTTTTGGAGGGTTCG-GAGT
1 CAAAATGGTAATTTTGGA-AGTTCGAGAGT
* * *
29463 CAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
** *
29493 -AAAATGGTAATTTTTAAAAGGTTCG-GGGT
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * *
29522 CAAAAATAGG-ATTTTTGGATGTTCGGGGGT
1 C-AAAAT-GGTAATTTTGGAAGTTCGAGAGT
* * *
29552 -AAAATGGTAATTTTCGAAAGGTTTG-GGGT
1 CAAAATGGTAATTTT-GGAA-GTTCGAGAGT
* * * * * *
29581 CAAAAATGGGATTTTTGAAAGTTTGGGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
* *
29611 -AAAATGGTAATTTTTAGAAGGTTCGGGA-T
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * *
29640 CAAAAATGGGATTTTTGAAAGTTCGAGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
* * *
29670 -AAAATGGTAATTTTTAGAAGGCTCG-GGGT
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * * *
29699 CAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
* *
29729 -AAAATGGTAATTTTTAGAAGGTTCG-GGGT
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * *
29758 CAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
29788 -AAAATGGTAATTTT
1 CAAAATGGTAATTTT
29802 TAGATGGTTT
Statistics
Matches: 261, Mismatches: 49, Indels: 59
0.71 0.13 0.16
Matches are distributed among these distances:
27 2 0.01
28 54 0.21
29 74 0.28
30 87 0.33
31 42 0.16
32 2 0.01
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (29 bp):
CAAAATGGTAATTTTGGAAGTTCGAGAGT
Found at i:29526 original size:59 final size:59
Alignment explanation
Indices: 29428--29865 Score: 646
Period size: 59 Copynumber: 7.4 Consensus size: 59
29418 TTCTGATGCA
* * * * *
29428 CGGGGGCAAAATGGT-AGTTTTGGAGGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * * *
29486 CGAGGGTAAAATGGTAATTTTTAAAAGGTTCGGGGTCAAAAATAGGATTTTTGGATGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
29545 CGGGGGTAAAATGGTAA-TTTTCGAAAGGTTTGGGGTCAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTAG-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
29604 TGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGATCAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* *
29663 CGAGGGTAAAATGGTAATTTTTAGAAGGCTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
*
29722 TGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * * * *
29781 CGGGGGTAAAATGGTAATTTTTAGATGGTTTGTGGCCAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
29840 CGGGGGTAAAATGGTAATTTTTAGAA
1 CGGGGGTAAAATGGTAATTTTTAGAA
29866 AGTTTAGGGA
Statistics
Matches: 342, Mismatches: 35, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
58 17 0.05
59 320 0.94
60 5 0.01
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:38778 original size:45 final size:45
Alignment explanation
Indices: 38714--38802 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
38704 TATATCAAGT
* *
38714 TGGCTGGTGTTAGTGAGGAAGTCTTAAACAAAATTGTTAGCAACC
1 TGGCTAGTGTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAACC
*
38759 TGGCTAGTTTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAAC
1 TGGCTAGTGTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAAC
38803 ATTGGTATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (45 bp):
TGGCTAGTGTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAACC
Found at i:40560 original size:29 final size:29
Alignment explanation
Indices: 40527--40894 Score: 114
Period size: 30 Copynumber: 12.5 Consensus size: 29
40517 TGCACGGGGG
* *
40527 CAAAATGGTAGTTTTGGAGGGTTCG-GAGT
1 CAAAATGGTAATTTTGGA-AGTTCGAGAGT
* * *
40556 CAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
** *
40586 -AAAATGGTAATTTTTAAAAGGTTCG-GGGT
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * *
40615 CAAAAATAGG-ATTTTTGGATGTTCGGGGGT
1 C-AAAAT-GGTAATTTTGGAAGTTCGAGAGT
* * *
40645 -AAAATGGTAATTTTCGAAAGGTTTG-GGGT
1 CAAAATGGTAATTTT-GGAA-GTTCGAGAGT
* * * * * *
40674 CAAAAATGGGATTTTTGAAAGTTTGGGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
* *
40704 -AAAATGGTAATTTTTAGAAGGTTCGGGA-T
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * *
40733 CAAAAATGGGATTTTTGAAAGTTCGAGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
* * *
40763 -AAAATGGTAATTTTTAGAAGGCTCG-GGGT
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * * *
40792 CAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
* *
40822 -AAAATGGTAATTTTTAGAAGGTTCG-GGGT
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * *
40851 CAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
40881 -AAAATGGTAATTTT
1 CAAAATGGTAATTTT
40895 TAGATGGTTT
Statistics
Matches: 261, Mismatches: 49, Indels: 59
0.71 0.13 0.16
Matches are distributed among these distances:
27 2 0.01
28 54 0.21
29 74 0.28
30 87 0.33
31 42 0.16
32 2 0.01
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (29 bp):
CAAAATGGTAATTTTGGAAGTTCGAGAGT
Found at i:40619 original size:59 final size:59
Alignment explanation
Indices: 40521--40958 Score: 646
Period size: 59 Copynumber: 7.4 Consensus size: 59
40511 TTCTGATGCA
* * * * *
40521 CGGGGGCAAAATGGT-AGTTTTGGAGGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * * *
40579 CGAGGGTAAAATGGTAATTTTTAAAAGGTTCGGGGTCAAAAATAGGATTTTTGGATGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
40638 CGGGGGTAAAATGGTAA-TTTTCGAAAGGTTTGGGGTCAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTAG-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
40697 TGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGATCAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* *
40756 CGAGGGTAAAATGGTAATTTTTAGAAGGCTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
*
40815 TGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * * * *
40874 CGGGGGTAAAATGGTAATTTTTAGATGGTTTGTGGCCAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
40933 CGGGGGTAAAATGGTAATTTTTAGAA
1 CGGGGGTAAAATGGTAATTTTTAGAA
40959 AGTTTAGGGA
Statistics
Matches: 342, Mismatches: 35, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
58 17 0.05
59 320 0.94
60 5 0.01
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:48974 original size:45 final size:45
Alignment explanation
Indices: 48910--48998 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
48900 TATATCAAGT
* *
48910 TGGCTGGTGTTAGTGAGGAAGTCTTAAACAAAATTGTTAGCAACC
1 TGGCTAGTGTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAACC
*
48955 TGGCTAGTTTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAAC
1 TGGCTAGTGTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAAC
48999 ATTGGTATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (45 bp):
TGGCTAGTGTTAGTGAGGAAGTCTTAAACAAAATAGTTAGCAACC
Found at i:50756 original size:29 final size:29
Alignment explanation
Indices: 50723--51090 Score: 114
Period size: 30 Copynumber: 12.5 Consensus size: 29
50713 TGCACGGGGG
* *
50723 CAAAATGGTAGTTTTGGAGGGTTCG-GAGT
1 CAAAATGGTAATTTTGGA-AGTTCGAGAGT
* * *
50752 CAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
** *
50782 -AAAATGGTAATTTTTAAAAGGTTCG-GGGT
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * *
50811 CAAAAATAGG-ATTTTTGGATGTTCGGGGGT
1 C-AAAAT-GGTAATTTTGGAAGTTCGAGAGT
* * *
50841 -AAAATGGTAATTTTCGAAAGGTTTG-GGGT
1 CAAAATGGTAATTTT-GGAA-GTTCGAGAGT
* * * * * *
50870 CAAAAATGGGATTTTTGAAAGTTTGGGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
* *
50900 -AAAATGGTAATTTTTAGAAGGTTCGGGA-T
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * *
50929 CAAAAATGGGATTTTTGAAAGTTCGAGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
* * *
50959 -AAAATGGTAATTTTTAGAAGGCTCG-GGGT
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * * *
50988 CAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
* *
51018 -AAAATGGTAATTTTTAGAAGGTTCG-GGGT
1 CAAAATGGTAA-TTTTGGAA-GTTCGAGAGT
* * * *
51047 CAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 C-AAAATGGTAATTTTGGAAGTTCGAGAGT
51077 -AAAATGGTAATTTT
1 CAAAATGGTAATTTT
51091 TAGATGGTTT
Statistics
Matches: 261, Mismatches: 49, Indels: 59
0.71 0.13 0.16
Matches are distributed among these distances:
27 2 0.01
28 54 0.21
29 74 0.28
30 87 0.33
31 42 0.16
32 2 0.01
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (29 bp):
CAAAATGGTAATTTTGGAAGTTCGAGAGT
Found at i:50815 original size:59 final size:59
Alignment explanation
Indices: 50717--51154 Score: 646
Period size: 59 Copynumber: 7.4 Consensus size: 59
50707 TTCTGATGCA
* * * * *
50717 CGGGGGCAAAATGGT-AGTTTTGGAGGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * * *
50775 CGAGGGTAAAATGGTAATTTTTAAAAGGTTCGGGGTCAAAAATAGGATTTTTGGATGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
50834 CGGGGGTAAAATGGTAA-TTTTCGAAAGGTTTGGGGTCAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTAG-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
50893 TGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGATCAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* *
50952 CGAGGGTAAAATGGTAATTTTTAGAAGGCTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
*
51011 TGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * * * *
51070 CGGGGGTAAAATGGTAATTTTTAGATGGTTTGTGGCCAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
51129 CGGGGGTAAAATGGTAATTTTTAGAA
1 CGGGGGTAAAATGGTAATTTTTAGAA
51155 AGTTTAGGGA
Statistics
Matches: 342, Mismatches: 35, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
58 17 0.05
59 320 0.94
60 5 0.01
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:53957 original size:210 final size:201
Alignment explanation
Indices: 53360--54012 Score: 1017
Period size: 210 Copynumber: 3.2 Consensus size: 201
53350 TTGACTCGGC
* * * *
53360 CTTCTTCTCGGTATCTCATCAGG-AGAATGACCGCGTCGCTTGTTTCAAATCCGCTTCTCTGTAT
1 CTTCTTCTCGGTGTCTCATCAGGAAG-ATGACCGCATCGTTTGTTTCAACT-CGCTTCTCTGTAT
* * *
53424 CTCATCAGGAAGACGAATTTGGTTAATTTCTCAGTATCTCATCAGGAAGCTAACCA--T-TTGCT
64 ATCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTGCT
53486 TCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTTTGAAGATTTCGCTCGCTTTGAGCCTC
129 TCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTTTGAAGATTTCGCTCGCTTTGAGCCTC
*
53551 GTTTGGTT
194 GTTTGGGT
53559 CTTCTTCTCGGTGTCTCATCAGGAAGATGACCGCATCGTTTGTTTCAACTCGCTTCTCTGTATAT
1 CTTCTTCTCGGTGTCTCATCAGGAAGATGACCGCATCGTTTGTTTCAACTCGCTTCTCTGTATAT
53624 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTC
66 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTC
*
53689 CACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTCTTGAAGATTTCGCTCGCTTTGAGCCTCGT
131 CACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTTTGAAGATTTCGCTCGCTTTGAGCCTCGT
53754 TTGGGT
196 TTGGGT
53760 CTTCTTCTCGGTGTCTCATCAGGAAGATGACCGCATCGTTTGTTTCAACTCGCTTCTCTGTATAT
1 CTTCTTCTCGGTGTCTCATCAGGAAGATGACCGCATCGTTTGTTTCAACTCGCTTCTCTGTATAT
*
53825 CATCANNNNNNNNNNGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
66 CATCA---------GGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
* * * * *
53890 TATTGCTTCCACCTGCTTTTTAATGTCTCATCAGGAAGCTGGGTTTTGAATATTTCGCTCACTTT
122 TATTGCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTTTGAAGATTTCGCTCGCTTT
*
53955 GAGCCTTGTTTGGGT
187 GAGCCTCGTTTGGGT
* *
53970 CTTCTTCTTGGTGTCTCATCAGGAAGATGACCGCGTCGTTTGT
1 CTTCTTCTCGGTGTCTCATCAGGAAGATGACCGCATCGTTTGT
54013 GGGTATCGTA
Statistics
Matches: 422, Mismatches: 19, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
198 66 0.16
199 43 0.10
200 3 0.01
201 146 0.35
210 164 0.39
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.35
Consensus pattern (201 bp):
CTTCTTCTCGGTGTCTCATCAGGAAGATGACCGCATCGTTTGTTTCAACTCGCTTCTCTGTATAT
CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTC
CACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTTTGAAGATTTCGCTCGCTTTGAGCCTCGT
TTGGGT
Done.