Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014138.1 Kokia drynarioides strain JFW-HI SEQ_129171, 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: 75948
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:619 original size:207 final size:207
Alignment explanation
Indices: 151--1012 Score: 1209
Period size: 207 Copynumber: 4.2 Consensus size: 207
141 TCTGGTTTCA
* * * ** * * *
151 TTGACTTGGCCTTCTTCACAGTATCTCATTGGGAAGATGACTGTGTAGTTTGTTTCAAT-TCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCT-GCT
* * *
215 TCTCTGTATCTCATCAGGAAGACGAATTTTGATCAACTTCTCCGTATCTCATCAGGAAGCTAACT
65 TCTCTGTATCTCATCAGGAAGACGAATTTGGTTC-ACTTCTCCGTATCTCATCAGGAAGCTAACC
* ** * * * * * * *
280 GTTTTATTATTTCGCCCTACTTCTCAATATCTTATCATGAAGC-TGGGGTTTGAAGGTTTAT--T
129 G-TCTATTGCTTCGACCTACTTCTCGATGTCTCATCAGGAAGCTTGGGGTTCGAAGATTT-TGCT
* *
342 C--ATCGTGCATGGGT
192 CGTTTCGAGCATGGGT
* * * * * *
356 TTGGTTCGGCCTTCTTCTCAGTATCTCATCGGGAAGATGACCGCATCGCTTGTTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
421 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGT
* *
486 CTATTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTTGGGGTTCGAAGATTTTGCTCGTT
131 CTATTGCTTCGACCTACTTCTCGATGTCTCATCAGGAAGCTTGGGGTTCGAAGATTTTGCTCGTT
*
551 TCGAGCGTGGGT
196 TCGAGCATGGGT
*
563 TTGATTTGGTCTTCTTTTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
*
628 CTCTGTATCTCATCAGGAAGATGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGT
* * *
693 CTATTGCTTCGACCTGCTTCTCGATGTCTCATCAAGAAGCTTGGGGTTTGAAGATTTTGCTCGTT
131 CTATTGCTTCGACCTACTTCTCGATGTCTCATCAGGAAGCTTGGGGTTCGAAGATTTTGCTCGTT
758 TCGAGCATGGGT
196 TCGAGCATGGGT
*
770 TTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
* *
835 CTCTTTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCCTTATCTCATCAGGAAGCTAACCGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGT
*
900 CTATTGCTTCGACCTACTTCTCGGTGTCTCATCAGGAAGCTTGGGGTTCGAAGATTTTGCTCGTT
131 CTATTGCTTCGACCTACTTCTCGATGTCTCATCAGGAAGCTTGGGGTTCGAAGATTTTGCTCGTT
* *
965 TTGAGCGT-GGT
196 TCGAGCATGGGT
* *
976 CTTGGTTTGGTCTTCTTC-CTAGTATCTCATCAAGAAG
1 -TTGATTTGGTCTTCTTCTC-AGTATCTCATCAGGAAG
1013 GCAACCGCAT
Statistics
Matches: 595, Mismatches: 54, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
203 32 0.05
204 44 0.07
205 86 0.14
206 5 0.01
207 428 0.72
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.37
Consensus pattern (207 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGT
CTATTGCTTCGACCTACTTCTCGATGTCTCATCAGGAAGCTTGGGGTTCGAAGATTTTGCTCGTT
TCGAGCATGGGT
Found at i:30286 original size:59 final size:59
Alignment explanation
Indices: 30195--30448 Score: 304
Period size: 59 Copynumber: 4.3 Consensus size: 59
30185 GCACGGGGGC
*
30195 AAAATGGT-AGTTTTGGAAGGTTCGTA-GTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCG-AGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
30253 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGTAGTTTGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
30312 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * * * **
30371 AAAATGGTAATTTTTAGAA-GTTCGGGGT--AAAATGGTAATTTTGGATAGTTTAAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGA-AGTTCGAGGGT
*
30428 AAAAAATGG-GATTTTTGGAAG
1 --AAAATGGTAATTTTTGGAAG
30449 TTTGGGGGTA
Statistics
Matches: 175, Mismatches: 15, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
56 15 0.09
57 8 0.05
58 27 0.15
59 125 0.71
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:30366 original size:29 final size:27
Alignment explanation
Indices: 30225--30523 Score: 238
Period size: 29 Copynumber: 10.3 Consensus size: 27
30215 TTCGTAGTCA
30225 AAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGGATTTTTGGAAGTTCG-GGGT
* *
30253 AAAATGGTAATTTTTGGAAGGTTCGAGGT
1 AAAATGG-GATTTTTGGAA-GTTCGGGGT
* *
30282 CAAAAATGGGATTTTTGGTAGTTTGGGGGT
1 --AAAATGGGATTTTTGGAAG-TTCGGGGT
* *
30312 AAAATGGTAATTTTTAGAAGGTTCGGGGT
1 AAAATGG-GATTTTTGGAA-GTTCGGGGT
30341 CAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 --AAAATGGGATTTTTGGAAGTTC-GGGGT
* *
30371 AAAATGGTAATTTTTAGAAGTTCGGGGT
1 AAAATGG-GATTTTTGGAAGTTCGGGGT
* * **
30399 AAAATGGTAATTTTGGATAGTTTAAGGGT
1 AAAATGGGATTTTTGGA-AG-TTCGGGGT
*
30428 AAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 --AAAATGGGATTTTTGGAAG-TTCGGGGT
* * * *
30458 AAAGTGGTAGTTTTTAGAAGGTTCGTGGTT
1 AAAATGGGA-TTTTTGGAA-GTTCG-GGGT
*
30488 AAAAATGGGATTTTTGGAAGTTTAGGGGT
1 -AAAATGGGATTTTTGGAAG-TTCGGGGT
30517 AAAATGG
1 AAAATGG
30524 TAATTTTCGG
Statistics
Matches: 218, Mismatches: 33, Indels: 40
0.75 0.11 0.14
Matches are distributed among these distances:
27 7 0.03
28 49 0.22
29 67 0.31
30 59 0.27
31 36 0.17
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (27 bp):
AAAATGGGATTTTTGGAAGTTCGGGGT
Found at i:30433 original size:146 final size:147
Alignment explanation
Indices: 30225--30530 Score: 458
Period size: 146 Copynumber: 2.1 Consensus size: 147
30215 TTCGTAGTCA
* * * *
30225 AAAATGG-GATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAAT
1 AAAATGGTAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTAGAGGTAAAAAAT
*
30289 GGGATTTTTGGTAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATT
66 GGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATT
*
30354 TTTGGAAGTTCGGGGGT
131 TTTGGAAGTTCAGGGGT
*
30371 AAAATGGTAATTTTTAGAAGTTCG-GGGTAAAATGGTAA-TTTTGGATAGTTTA-AGGGTAAAAA
1 AAAATGGTAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGA-AGGTTAGA-GGTAAAAA
* * * *
30433 ATGGGATTTTTGGAAGTTTGGGGGTAAAGTGGTAGTTTTTAGAAGGTTCGTGGTTAAAAATGGGA
64 ATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGA
*
30498 TTTTTGGAAGTTTAGGGGT
129 TTTTTGGAAGTTCAGGGGT
30517 AAAATGGTAATTTT
1 AAAATGGTAATTTT
30531 CGGACAGTTT
Statistics
Matches: 145, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
145 8 0.06
146 123 0.85
147 14 0.10
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (147 bp):
AAAATGGTAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTAGAGGTAAAAAAT
GGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATT
TTTGGAAGTTCAGGGGT
Found at i:30459 original size:59 final size:59
Alignment explanation
Indices: 30371--30541 Score: 186
Period size: 59 Copynumber: 2.9 Consensus size: 59
30361 GTTCGGGGGT
* * *
30371 AAAATGGTAATTTTTAGAAG-TTCGGGGTAAAATGGTAATTTTGGATAGTTTAAG-GGTAA
1 AAAATGG-GATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTGGA-AGTTTAAGTGGTAA
* * * * * * *
30430 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAGTGGTAGTTTTTAGAAGGTT-CGTGGTTA
1 AAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTA-ATTTTGGAAGTTTAAGTGGTAA
30489 AAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTCGGACAGTTTA
1 AAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTT-GGA-AGTTTA
30542 GGGACCTCCG
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
58 15 0.16
59 67 0.73
60 10 0.11
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.36
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTGGAAGTTTAAGTGGTAA
Found at i:30529 original size:29 final size:29
Alignment explanation
Indices: 30190--30540 Score: 263
Period size: 30 Copynumber: 12.0 Consensus size: 29
30180 CGGATGCACG
* * *
30190 GGGGCAAAATGGT-AGTTTTGGAAGGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGTTTC
** *
30218 GTAGTCAAAAATGG-GATTTTTGGAAG-TTC
1 GGGGT--AAAATGGTAATTTTTGGAAGTTTC
*
30247 GAGGGTAAAATGGTAATTTTTGGAAGGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGTTTC
* * * *
30277 GAGGTCAAAAATGG-GATTTTTGGTAGTTTG
1 GGGGT--AAAATGGTAATTTTTGGAAGTTTC
* *
30307 GGGGTAAAATGGTAATTTTTAGAAGGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGTTTC
*
30336 GGGGTCAAAAATGG-GATTTTTGGAAG-TTC
1 GGGGT--AAAATGGTAATTTTTGGAAGTTTC
*
30365 GGGGGTAAAATGGTAATTTTTAGAAG-TTC
1 -GGGGTAAAATGGTAATTTTTGGAAGTTTC
*
30394 GGGGTAAAATGGTAA-TTTTGGATAGTTTA
1 GGGGTAAAATGGTAATTTTTGGA-AGTTTC
* * *
30423 AGGGTAAAAAATGG-GATTTTTGGAAGTTTG
1 GGGGT--AAAATGGTAATTTTTGGAAGTTTC
* * * *
30453 GGGGTAAAGTGGTAGTTTTTAGAAGGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGTTTC
* * *
30482 GTGGTTAAAAATGG-GATTTTTGGAAGTTTA
1 G-GGGT-AAAATGGTAATTTTTGGAAGTTTC
*
30512 GGGGTAAAATGGTAATTTTCGGACAGTTT
1 GGGGTAAAATGGTAATTTTTGGA-AGTTT
30541 AGGGACCTCC
Statistics
Matches: 256, Mismatches: 44, Indels: 44
0.74 0.13 0.13
Matches are distributed among these distances:
27 6 0.02
28 53 0.21
29 79 0.31
30 84 0.33
31 34 0.13
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAGTTTC
Found at i:32003 original size:17 final size:17
Alignment explanation
Indices: 31975--32037 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
31965 GGGTTTTATT
*
31975 TTAAATTTTAAACTTAAA
1 TTAAA-TTTAAATTTAAA
31993 TTAAATTTAAATTTTAAA
1 TTAAATTTAAA-TTTAAA
* *
32011 -CAAATTTAATTTTAAA
1 TTAAATTTAAATTTAAA
*
32027 ATAAATTTAAA
1 TTAAATTTAAA
32038 GGGAGTATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
16 6 0.16
17 22 0.58
18 10 0.26
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:32028 original size:24 final size:23
Alignment explanation
Indices: 31972--32026 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
31962 TTTGGGTTTT
31972 ATTTTAAATTTTAAACTTAAATTA
1 ATTTTAAATTTTAAAC-TAAATTA
*
31996 AATTTAAATTTTAAAC-AAATTTA
1 ATTTTAAATTTTAAACTAAA-TTA
32019 ATTTTAAA
1 ATTTTAAA
32027 ATAAATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 10 0.36
24 15 0.54
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTTAAATTTTAAACTAAATTA
Found at i:35949 original size:17 final size:17
Alignment explanation
Indices: 35927--35963 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
35917 TATTAAATTA
35927 ATTTTTTATAA-ATGTTT
1 ATTTTTTA-AATATGTTT
35944 ATTTTTTAAATATGTTT
1 ATTTTTTAAATATGTTT
35961 ATT
1 ATT
35964 ATATTATGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (17 bp):
ATTTTTTAAATATGTTT
Found at i:36240 original size:28 final size:31
Alignment explanation
Indices: 36198--36275 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 31
36188 TAACGGGAGA
* *
36198 ATAGTTTAGGTACCACTTTTGA-TAAAA-AA-
1 ATAGTTTAAGTACCA-TTTTGAGAAAAATAAT
*
36227 A-AGTTTAAGTACCAATTTGAGAAAAATAAT
1 ATAGTTTAAGTACCATTTTGAGAAAAATAAT
36257 ATAGTTTAAGTACCATTTT
1 ATAGTTTAAGTACCATTTT
36276 ATTGCTTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.12
28 16 0.39
29 3 0.07
30 1 0.02
31 16 0.39
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (31 bp):
ATAGTTTAAGTACCATTTTGAGAAAAATAAT
Found at i:39862 original size:3 final size:3
Alignment explanation
Indices: 39842--39905 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
39832 CTCAAGAACA
* *
39842 ACT ACT ATT ACT ATT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
39890 ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT A
39906 TTATTATTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (3 bp):
ACT
Found at i:41151 original size:18 final size:19
Alignment explanation
Indices: 41086--41152 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 19
41076 CTCACTTATA
*
41086 TATTTTATTTAATTTG-TAT
1 TATTTTATTT-ATTTGTTAC
* *
41105 TATTTTAATTATTTTTTATC
1 TATTTTATTTATTTGTTA-C
41125 TA--TTATTTATTTGTTAC
1 TATTTTATTTATTTGTTAC
41142 TATTTT-TTTAT
1 TATTTTATTTAT
41153 ATTATTTACA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
17 3 0.08
18 21 0.54
19 13 0.33
20 2 0.05
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (19 bp):
TATTTTATTTATTTGTTAC
Found at i:41190 original size:14 final size:14
Alignment explanation
Indices: 41171--41204 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
41161 CATTTATGCC
*
41171 TTATTTAGTTTTAT
1 TTATTTAATTTTAT
41185 TTATTTAATTTTAT
1 TTATTTAATTTTAT
41199 TTATTT
1 TTATTT
41205 TTTTATGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
TTATTTAATTTTAT
Found at i:48832 original size:21 final size:21
Alignment explanation
Indices: 48793--48832 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
48783 TGTGAAGGTT
* *
48793 TTGAGAAAATTGTTCTTGAGA
1 TTGAGAAAATTCTACTTGAGA
*
48814 TTGAGAAAATTCTAGTTGA
1 TTGAGAAAATTCTACTTGA
48833 AGTTAAACCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (21 bp):
TTGAGAAAATTCTACTTGAGA
Found at i:52463 original size:49 final size:48
Alignment explanation
Indices: 52349--53055 Score: 408
Period size: 49 Copynumber: 14.4 Consensus size: 48
52339 ATCCTAAAGT
* * * *
52349 TGAAGAGGGACAAATTAAAGCCGCAACGACGAATCTTACA-CCTAAAA
1 TGAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACACCCTAAAA
* *
52396 TCGAAGAGGGACAAATTAAAGTCGTAATGATGAATCTTACACCCTAAAA
1 T-GAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACACCCTAAAA
* *
52445 CTGAAGAGGGGCAGATTAAAGTCGTAACGATGAGTCTTACACCCTAAAA
1 -TGAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACACCCTAAAA
* * *
52494 CCGAAGAGGGATAGATTAAAG-C-TACAACGATGAATCTTACACCCCAAAA
1 -TGAAGAGGGACAGATTAAAGTCGT--AACGATGAATCTTACACCCTAAAA
* * * * * * *
52543 TAAAATAGAGACATATTAAAG-C-TACAACGGTGAATCTTATATCCTAAAA
1 T-GAAGAGGGACAGATTAAAGTCGT--AACGATGAATCTTACACCCTAAAA
** * * * *** * * * *
52592 CCATAAAGGGCCAGATAAAAGTTACAATGGTGAAACTTACACCCCAAAAA
1 TGA-AGAGGGACAGATTAAAGTCGTAACGATGAATCTTACA-CCCTAAAA
** * **
52642 TTGAAGAGGGACAGATTAAAGTTATAACGAAGAATCTTACATAGC-AAAA
1 -TGAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACA-CCCTAAAA
* * * * *
52691 TCGAAGAGTGACAAATTAAAGTCGCAACAATGAATCTTACACCCAAAAA
1 T-GAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACACCCTAAAA
* * * * * * *
52740 CT-AAAAGGGGATAGATTAAAATTGTAACGGTAAATCTTACACCCCAAAA
1 -TGAAGA-GGGACAGATTAAAGTCGTAACGATGAATCTTACACCCTAAAA
* * * * * *
52789 TCGAAGATGGATAGATTAAAG-CGGCAACGGTGAATCTTACATCGTAAAAA
1 T-GAAGAGGGACAGATTAAAGTC-GTAACGATGAATCTTACACCCT-AAAA
* * * * * *
52839 TGAAAAGGGACAGATTAAAGCCGCAATGGTGAATCTTACACCGCAAAAA
1 TGAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACACC-CTAAAA
* * * * * *
52888 TAAAGAGGAATAAATTAAAG-CTGTAATGATGAATCTTACATCCTAAAA
1 TGAAGAGGGACAGATTAAAGTC-GTAACGATGAATCTTACACCCTAAAA
* * * * * *
52936 TCGAATAGGGACATATTAAAGTCATAA-TAGTGAATCTAACACCTTAAAA
1 T-GAAGAGGGACAGATTAAAGTCGTAACGA-TGAATCTTACACCCTAAAA
* ** ** * *
52985 TCGAAGAGGGATAGATTAAAGTCACAATAACGAATCTTACATGCCTAAAA
1 T-GAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACA-CCCTAAAA
*
53035 TTGAAGAGGAACAGATTAAAG
1 -TGAAGAGGGACAGATTAAAG
53056 CTGCAAAGGC
Statistics
Matches: 516, Mismatches: 116, Indels: 53
0.75 0.17 0.08
Matches are distributed among these distances:
47 2 0.00
48 51 0.10
49 389 0.75
50 72 0.14
51 2 0.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.21
Consensus pattern (48 bp):
TGAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACACCCTAAAA
Found at i:52533 original size:98 final size:96
Alignment explanation
Indices: 52349--53055 Score: 469
Period size: 98 Copynumber: 7.2 Consensus size: 96
52339 ATCCTAAAGT
* * * * * *
52349 TGAAGAGGGACAAATTAAAGCCGCAACGACGAATCTTACA-CCTAAAATCGAAGAGGGACAAATT
1 TGAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACACCCTAAAATCGAAGAGGGATAGATT
52413 AAAGT-CGTAATGATGAATCTTACACCCTAAAA
66 AAAGTAC--AATGATGAATCTTACACCCTAAAA
* * *
52445 CTGAAGAGGGGCAGATTAAAGTCGTAACGATGAGTCTTACACCCTAAAACCGAAGAGGGATAGAT
1 -TGAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACACCCTAAAATCGAAGAGGGATAGAT
* *
52510 TAAAGCTACAACGATGAATCTTACACCCCAAAA
65 TAAAG-TACAATGATGAATCTTACACCCTAAAA
* * * * * * * * * **
52543 TAAAATAGAGACATATTAAAG-C-TACAACGGTGAATCTTATATCCTAAAA-CCATAAAGGGCCA
1 T-GAAGAGGGACAGATTAAAGTCGT--AACGATGAATCTTACACCCTAAAATCGA-AGAGGGATA
* * * *
52605 GATAAAAGTTACAATGGTGAAACTTACACCCCAAAAA
62 GATTAAAG-TACAATGATGAATCTTACA-CCCTAAAA
** * ** * * *
52642 TTGAAGAGGGACAGATTAAAGTTATAACGAAGAATCTTACATAGC-AAAATCGAAGAGTGACAAA
1 -TGAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACA-CCCTAAAATCGAAGAGGGATAGA
* ** *
52706 TTAAAGTCGCAACAATGAATCTTACACCCAAAAA
64 TTAAAGT-ACAATGATGAATCTTACACCCTAAAA
* * * * * * * *
52740 CT-AAAAGGGGATAGATTAAAATTGTAACGGTAAATCTTACACCCCAAAATCGAAGATGGATAGA
1 -TGAAGA-GGGACAGATTAAAGTCGTAACGATGAATCTTACACCCTAAAATCGAAGAGGGATAGA
** * * * *
52804 TTAAAGCGGCAACGGTGAATCTTACATCGTAAAAA
64 TTAAAG-TACAATGATGAATCTTACACCCT-AAAA
* * * * * * * * *
52839 TGAAAAGGGACAGATTAAAGCCGCAATGGTGAATCTTACACCGCAAAAAT-AAAGAGGAATAAAT
1 TGAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACACC-CTAAAATCGAAGAGGGATAGAT
** *
52903 TAAAGCTGTAATGATGAATCTTACATCCTAAAA
65 TAAAG-TACAATGATGAATCTTACACCCTAAAA
* * * * * *
52936 TCGAATAGGGACATATTAAAGTCATAA-TAGTGAATCTAACACCTTAAAATCGAAGAGGGATAGA
1 T-GAAGAGGGACAGATTAAAGTCGTAACGA-TGAATCTTACACCCTAAAATCGAAGAGGGATAGA
* * *
53000 TTAAAGTCACAATAACGAATCTTACATGCCTAAAA
64 TTAAAGT-ACAATGATGAATCTTACA-CCCTAAAA
*
53035 TTGAAGAGGAACAGATTAAAG
1 -TGAAGAGGGACAGATTAAAG
53056 CTGCAAAGGC
Statistics
Matches: 475, Mismatches: 109, Indels: 50
0.75 0.17 0.08
Matches are distributed among these distances:
96 1 0.00
97 53 0.11
98 312 0.66
99 102 0.21
100 6 0.01
101 1 0.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.21
Consensus pattern (96 bp):
TGAAGAGGGACAGATTAAAGTCGTAACGATGAATCTTACACCCTAAAATCGAAGAGGGATAGATT
AAAGTACAATGATGAATCTTACACCCTAAAA
Found at i:52778 original size:197 final size:196
Alignment explanation
Indices: 52421--52778 Score: 416
Period size: 197 Copynumber: 1.8 Consensus size: 196
52411 TTAAAGTCGT
* * * * * *
52421 AATGATGAATCTTACACCCTAAAACTGAAGAGGGGCAGATTAAAGTCGTAACGATGAGTCTTACA
1 AATGATGAAACTTACACCCAAAAACTGAAGAGGGACAGATTAAAGTCATAACGAAGAATCTTACA
* * * * *
52486 CCCTAAAACCGAAGAGGGATAGATTAAAGCTACAACGATGAATCTTACACCCCAAAATAAAATAG
66 ACCTAAAACCGAAGAGGGACAAATTAAAGCTACAACAATGAATCTTACACCCAAAAATAAAATAG
* * *
52551 AGACATATTAAAGCTACAACGGTGAATCTTATATCCTAAAACCATAAAGGGCCAGATAAAAGTTA
131 AGACAGATTAAAACTACAACGGTAAATCTTATATCCTAAAACCATAAAGGGCCAGATAAAAGTTA
52616 C
196 C
* * *
52617 AATGGTGAAACTTACACCCCAAAAATTGAAGAGGGACAGATTAAAGTTATAACGAAGAATCTTAC
1 AATGATGAAACTTACA-CCCAAAAACTGAAGAGGGACAGATTAAAGTCATAACGAAGAATCTTAC
* * * *
52682 ATAGC-AAAATCGAAGAGTGACAAATTAAAG-TCGCAACAATGAATCTTACACCCAAAAACTAAA
65 A-ACCTAAAACCGAAGAGGGACAAATTAAAGCT-ACAACAATGAATCTTACACCCAAAAA-TAAA
* * * * **
52745 A-GGGGATAGATTAAAATTGTAACGGTAAATCTTA
127 ATAGAGACAGATTAAAACTACAACGGTAAATCTTA
52779 CACCCCAAAA
Statistics
Matches: 131, Mismatches: 27, Indels: 7
0.79 0.16 0.04
Matches are distributed among these distances:
196 15 0.11
197 110 0.84
198 6 0.05
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.21
Consensus pattern (196 bp):
AATGATGAAACTTACACCCAAAAACTGAAGAGGGACAGATTAAAGTCATAACGAAGAATCTTACA
ACCTAAAACCGAAGAGGGACAAATTAAAGCTACAACAATGAATCTTACACCCAAAAATAAAATAG
AGACAGATTAAAACTACAACGGTAAATCTTATATCCTAAAACCATAAAGGGCCAGATAAAAGTTA
C
Found at i:53082 original size:50 final size:50
Alignment explanation
Indices: 53015--53180 Score: 165
Period size: 50 Copynumber: 3.3 Consensus size: 50
53005 GTCACAATAA
** * * *
53015 CGAATCTTACATGCCTAAAATTGAAGAGGAACAGATTAAAGCTGCAAAGG
1 CGAATCTTACACCCCTAAAACTGAAGAGGAACAGATTGAAGCCGCAAAGG
* ** *
53065 C-ATATCTTACACCCCTAAACCCAAAGA-GAGACAGATTGAAGCCACAAAGG
1 CGA-ATCTTACACCCCTAAAACTGAAGAGGA-ACAGATTGAAGCCGCAAAGG
* * * * *
53115 CGAATCGTACACCCCTAAAACTGTAGAGGGATAGATTGAAGCCGTAAAGG
1 CGAATCTTACACCCCTAAAACTGAAGAGGAACAGATTGAAGCCGCAAAGG
*
53165 CGAATCTTATACCCCT
1 CGAATCTTACACCCCT
53181 GAAGTTGCTG
Statistics
Matches: 92, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
49 3 0.03
50 87 0.95
51 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (50 bp):
CGAATCTTACACCCCTAAAACTGAAGAGGAACAGATTGAAGCCGCAAAGG
Found at i:53601 original size:16 final size:16
Alignment explanation
Indices: 53577--53639 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
53567 AAGCCCAAAC
*
53577 CTAACGAAACCCTAAG
1 CTAATGAAACCCTAAG
53593 CTAATGAAACCCTAA-
1 CTAATGAAACCCTAAG
53608 C--A--AAACCCTAAG
1 CTAATGAAACCCTAAG
53620 CTAATGAAACCCTAAG
1 CTAATGAAACCCTAAG
53636 CTAA
1 CTAA
53640 CTTAAGCCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
11 9 0.22
12 1 0.02
13 1 0.02
14 1 0.02
15 1 0.02
16 28 0.68
ACGTcount: A:0.46, C:0.29, G:0.10, T:0.16
Consensus pattern (16 bp):
CTAATGAAACCCTAAG
Found at i:53613 original size:27 final size:27
Alignment explanation
Indices: 53576--53634 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
53566 AAAGCCCAAA
*
53576 CCTAACGAAACCCTAAGCTAATGAAAC
1 CCTAACAAAACCCTAAGCTAATGAAAC
53603 CCTAACAAAACCCTAAGCTAATGAAAC
1 CCTAACAAAACCCTAAGCTAATGAAAC
53630 CCTAA
1 CCTAA
53635 GCTAACTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (27 bp):
CCTAACAAAACCCTAAGCTAATGAAAC
Found at i:60473 original size:10 final size:10
Alignment explanation
Indices: 60460--60502 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
60450 TATATATATA
60460 TTCTTTCTTT
1 TTCTTTCTTT
60470 TTCTTTC-TT
1 TTCTTTCTTT
*
60479 TT-TTTCAATT
1 TTCTTTC-TTT
60489 TTCTTTCTTT
1 TTCTTTCTTT
60499 TTCT
1 TTCT
60503 CTTTCTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 4 0.14
9 4 0.14
10 17 0.59
11 4 0.14
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:62882 original size:23 final size:23
Alignment explanation
Indices: 62854--62955 Score: 100
Period size: 23 Copynumber: 4.4 Consensus size: 23
62844 ACATTAGTGC
*
62854 GCTTACTGTTCAGCACTGTGTGT
1 GCTTACTGTTCTGCACTGTGTGT
* ***
62877 GCTTACTGATTC-GCACTATACAT
1 GCTTACTG-TTCTGCACTGTGTGT
*
62900 GCTTACTGATT-TGCATTGTGTGT
1 GCTTACTG-TTCTGCACTGTGTGT
* *
62923 GCTTACTATTTTGCACTGTGTGT
1 GCTTACTGTTCTGCACTGTGTGT
62946 GCTTACTGTT
1 GCTTACTGTT
62956 TCCCCAGCAC
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
22 2 0.03
23 59 0.92
24 3 0.05
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTTACTGTTCTGCACTGTGTGT
Found at i:63005 original size:21 final size:21
Alignment explanation
Indices: 62966--63005 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
62956 TCCCCAGCAC
* *
62966 TTTTGTGCTCATTGATAGTAT
1 TTTTGTACTCACTGATAGTAT
*
62987 TTTTGTACTCACTGTTAGT
1 TTTTGTACTCACTGATAGT
63006 TCCGTATATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.53
Consensus pattern (21 bp):
TTTTGTACTCACTGATAGTAT
Found at i:68715 original size:12 final size:13
Alignment explanation
Indices: 68698--68729 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
68688 ATTTAATTTG
68698 TATTATTTTTAT-
1 TATTATTTTTATC
68710 TATTA-TTTTATC
1 TATTATTTTTATC
68722 TATTATTT
1 TATTATTT
68730 ATTTGTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 10 0.56
13 2 0.11
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTATTTTTATC
Found at i:73926 original size:61 final size:61
Alignment explanation
Indices: 73831--73954 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
73821 TGGATCTTGG
73831 ACTAGATTAATTTGTCTCAGTAAGGTGGCTGGAAATTAGGTATGCAGTTCCATAACGAGAA
1 ACTAGATTAATTTGTCTCAGTAAGGTGGCTGGAAATTAGGTATGCAGTTCCATAACGAGAA
73892 ACTAGATTAATTTGTCTCAGTAAGGTGGCTGGAAATTAGGTATGCAGTTCCATAACGAGAA
1 ACTAGATTAATTTGTCTCAGTAAGGTGGCTGGAAATTAGGTATGCAGTTCCATAACGAGAA
73953 AC
1 AC
73955 CATTGGCAAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (61 bp):
ACTAGATTAATTTGTCTCAGTAAGGTGGCTGGAAATTAGGTATGCAGTTCCATAACGAGAA
Found at i:73978 original size:61 final size:60
Alignment explanation
Indices: 73847--73978 Score: 151
Period size: 61 Copynumber: 2.2 Consensus size: 60
73837 TTAATTTGTC
* * * ** *
73847 TCAGTAAGGTGGCTGGAAATTAGGTATGCAGTTCCATAACGAGAAACTAGATTAATTTGTC
1 TCAGCAAGGTGGCTGGAAATTAGGTATGCAGTTCCATAACGAGAAAC-ACATTAACTACTA
*
73908 TCAGTAAGGTGGCTGGAAATTAGGTATGCAGTTCCATAACGAGAAAC-CATTGGCAACTACTA
1 TCAGCAAGGTGGCTGGAAATTAGGTATGCAGTTCCATAACGAGAAACACATT---AACTACTA
73970 TC-GCAAGGT
1 TCAGCAAGGT
73979 TGCATGAAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
59 3 0.05
61 53 0.85
62 6 0.10
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (60 bp):
TCAGCAAGGTGGCTGGAAATTAGGTATGCAGTTCCATAACGAGAAACACATTAACTACTA
Done.