Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2830
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: 64456
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:16123 original size:11 final size:11
Alignment explanation
Indices: 16109--16160 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
16099 TCTTTCAATA
16109 TTCTCTCAAAT
1 TTCTCTCAAAT
16120 TTCTCTCAAA-
1 TTCTCTCAAAT
*
16130 -TCACTCAAAT
1 TTCTCTCAAAT
*
16140 TTCTCTTAAAT
1 TTCTCTCAAAT
*
16151 TCCTCTCAAA
1 TTCTCTCAAA
16161 ACTCTCGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 8 0.24
11 26 0.76
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:16138 original size:20 final size:20
Alignment explanation
Indices: 16113--16150 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16103 TCAATATTCT
16113 CTCAAATTTCTCTCAAATCA
1 CTCAAATTTCTCTCAAATCA
*
16133 CTCAAATTTCTCTTAAAT
1 CTCAAATTTCTCTCAAAT
16151 TCCTCTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.39
Consensus pattern (20 bp):
CTCAAATTTCTCTCAAATCA
Found at i:16216 original size:16 final size:15
Alignment explanation
Indices: 16187--16217 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16177 TAAAAAAAAC
*
16187 TCTAATTTTATTTTT
1 TCTAAATTTATTTTT
16202 TCTAAATTTATTTTT
1 TCTAAATTTATTTTT
16217 T
1 T
16218 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTAAATTTATTTTT
Found at i:17884 original size:30 final size:30
Alignment explanation
Indices: 17834--17897 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
17824 ACGACGCAGA
*
17834 CCCATCAACAGCACCCACACAATCACCCGG
1 CCCAGCAACAGCACCCACACAATCACCCGG
* * * *
17864 CCCAGCAACAGGACCTACACAGTCACCGGG
1 CCCAGCAACAGCACCCACACAATCACCCGG
17894 CCCA
1 CCCA
17898 ACAGTTCAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (30 bp):
CCCAGCAACAGCACCCACACAATCACCCGG
Found at i:17974 original size:18 final size:18
Alignment explanation
Indices: 17951--17993 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
17941 TGCCAAGTAC
*
17951 GTATCCTAGCCCTTTTAT
1 GTATCCTAGCCCTTATAT
17969 GTATCCTAGCCCTTATAT
1 GTATCCTAGCCCTTATAT
*
17987 GTTTCCT
1 GTATCCT
17994 TTTTCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.44
Consensus pattern (18 bp):
GTATCCTAGCCCTTATAT
Found at i:18582 original size:116 final size:116
Alignment explanation
Indices: 18378--18859 Score: 865
Period size: 116 Copynumber: 4.2 Consensus size: 116
18368 TATTTGTACA
* * *
18378 AACATTTTGAATCTTTTTATATTATTTCATGTAATTAGATAAGATGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
18443 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
18494 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
* *
18559 TATAATTTACTTTTATATTTTTAATAAAATAGAAATTATTTTAAATAAGGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
*
18610 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTATTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
*
18675 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAAGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
* * * *
18726 AACATTTTAAATATTTTTTTATTATTTTATGTAATTAGATAAAAGGTTGTTTTAAATAAAATAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
18791 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
18842 AACATTTTGAATATTTTT
1 AACATTTTGAATATTTTT
18860 GTCGAAACCA
Statistics
Matches: 350, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 350 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.48
Consensus pattern (116 bp):
AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
Found at i:18720 original size:54 final size:54
Alignment explanation
Indices: 18656--18838 Score: 190
Period size: 54 Copynumber: 3.2 Consensus size: 54
18646 AGATAAAAGG
18656 TTATTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAA
1 TTATTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAA
* * * * * *
18710 TTATTTTAAATAAAGCAACATTTTAAATATT-TTTTTATTATTTTATGTAATTAGAT-AAAA
1 TTATTTTAAATAAAG-TA-ATTGT-AAT-TTACTTTTA-TA-TTT-T-TAATAAAATGGAAA
* *
18770 GGTTGTTTTAAATAAAATAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAA
1 --TTATTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAA
18826 TTATTTTAAATAA
1 TTATTTTAAATAA
18839 GGCAACATTT
Statistics
Matches: 102, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
54 27 0.26
55 8 0.08
56 8 0.08
57 11 0.11
58 8 0.08
59 11 0.11
60 8 0.08
61 8 0.08
62 13 0.13
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (54 bp):
TTATTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAA
Found at i:20359 original size:3 final size:3
Alignment explanation
Indices: 20351--20389 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
20341 CATATATGTG
20351 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20390 CGCGCAGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25334 original size:126 final size:126
Alignment explanation
Indices: 25104--25642 Score: 837
Period size: 126 Copynumber: 4.3 Consensus size: 126
25094 GCCCAAGTTA
* * * * *
25104 TTTCAGAAACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTAAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTAATTTTGCTGAAAA
* **
25169 TGCAGCCTGCTTGAAGCGTTTTTGACACTATTTATGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * *
25230 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTAATTTTGCTGAAAA
* *
25295 TGCATCATGCTTGAAGCGTTTTT-ACCATTATTTGCGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGA-CACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * *
25356 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTAATTTTGCTGAAAA
* * * *
25421 TGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCACAGACACGTCTTTTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * *
25482 TTTCAGATACTACTGTAGCAAAAAAGCGTCCACGTGGGAGCTTCTTTCAGTAATTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTAATTTTGCTGAAAA
*
25547 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAATTTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
*
25608 TTTTAGAGACTACTGTAGCAAAAGAGCGTCCACGT
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
25643 AGAAGGTTTT
Statistics
Matches: 377, Mismatches: 34, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
125 1 0.00
126 375 0.99
127 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (126 bp):
TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTAATTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
Found at i:25853 original size:95 final size:96
Alignment explanation
Indices: 25752--25924 Score: 251
Period size: 96 Copynumber: 1.8 Consensus size: 96
25742 CCTAAAATCC
* * * * ** *
25752 TAATCTATTTTTTTAAATTTA-TAATTAATTTACTCAAGTAACCCTAAATCC-TAATTTATTTAA
1 TAATCTAATTTTTTAAAATTAGCAATTAATTTAATCAACAAACACTAAA-CCTTAATTTATTTAA
25815 TTTTTTCCTTAAAAACCATAAGCACTAAACCA
65 TTTTTTCCTTAAAAACCATAAGCACTAAACCA
*
25847 TAATCTAATTTTTTAAAATTAGCAATTAATTTAATTAACAAACACTAAACCTTAATTTATTTAAT
1 TAATCTAATTTTTTAAAATTAGCAATTAATTTAATCAACAAACACTAAACCTTAATTTATTTAAT
25912 TTTTTCCTTAAAA
66 TTTTTCCTTAAAA
25925 CCCTAAAATT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
95 21 0.31
96 47 0.69
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.43
Consensus pattern (96 bp):
TAATCTAATTTTTTAAAATTAGCAATTAATTTAATCAACAAACACTAAACCTTAATTTATTTAAT
TTTTTCCTTAAAAACCATAAGCACTAAACCA
Found at i:25942 original size:16 final size:17
Alignment explanation
Indices: 25921--25962 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
25911 TTTTTTCCTT
25921 AAAACCCTAAAATTT-A
1 AAAACCCTAAAATTTCA
*
25937 AAAA-CCTAAAATTTCC
1 AAAACCCTAAAATTTCA
25953 AAAACCCTAA
1 AAAACCCTAA
25963 CCCTAATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 10 0.43
16 8 0.35
17 5 0.22
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAACCCTAAAATTTCA
Found at i:27940 original size:3 final size:3
Alignment explanation
Indices: 27932--27966 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
27922 ATATTGAAAT
27932 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
27967 GCAACACATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27941 original size:199 final size:201
Alignment explanation
Indices: 27678--28096 Score: 547
Period size: 217 Copynumber: 2.0 Consensus size: 201
27668 TTTTCATTAT
*
27678 ATATAAATATATATTAAAAATATATAATAAAAAATGACACCGTAAAATTTG-A-AAT-TAATAAT
1 ATATAAATATATATTAAAAATATATAATAAAAAATGACACCATAAAATTTGAATAATATAATAAT
* * *
27740 AATAATAATAGCAACACTTTAATAAGGTTTAAAAATATTTTAAGATTATTTTAATAATTTAATTA
66 AATAATAATAGCAACACATCAATAAAGTTTAAAAATATTTTAAGATTATTTTAATAATTTAATTA
* *
27805 ATTAAGTTAGTGTTAAATTCACTCGTAACACAAATTTAATCATGCACTTAAATAATAATAATAAC
131 ACTAAGTTAGTGTT-AATTCACTCGTAACACAAATTTAATCATGCAATTAAATAATAATAATAAC
27870 AATAACA
195 AATAACA
* * *
27877 ATATAAATATATATTAGAAATATATAATAAACAATGACACCATAAATATTGAAATTAATAATAAT
1 ATATAAATATATATTAAAAATATATAATAAAAAATGACACC----ATA---AAA-T--T--T--G
27942 AATAATAATAATAATAATAATAATAGCAACACATCAATAAAGTTTAAAAATATTTTAAGATTATT
52 AATAAT-ATAATAATAATAATAATAGCAACACATCAATAAAGTTTAAAAATATTTTAAGATTATT
* * *
28007 TTAATAATTTAATTAACTAAGTTGGTGTTGATTTACTCGTAACACAAATTTAATCATGCAATTAA
116 TTAATAATTTAATTAACTAAGTTAGTGTTAATTCACTCGTAACACAAATTTAATCATGCAATTAA
* *
28072 ATAATAATAATAATAATAATA
181 ATAATAATAATAACAATAACA
28093 ATAT
1 ATAT
28097 TATGGATACT
Statistics
Matches: 188, Mismatches: 14, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
199 39 0.21
203 2 0.01
206 3 0.02
207 1 0.01
209 1 0.01
211 1 0.01
214 1 0.01
215 3 0.02
216 56 0.30
217 81 0.43
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.35
Consensus pattern (201 bp):
ATATAAATATATATTAAAAATATATAATAAAAAATGACACCATAAAATTTGAATAATATAATAAT
AATAATAATAGCAACACATCAATAAAGTTTAAAAATATTTTAAGATTATTTTAATAATTTAATTA
ACTAAGTTAGTGTTAATTCACTCGTAACACAAATTTAATCATGCAATTAAATAATAATAATAACA
ATAACA
Found at i:28079 original size:3 final size:3
Alignment explanation
Indices: 28071--28095 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28061 CATGCAATTA
28071 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
28096 TTATGGATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28579 original size:16 final size:16
Alignment explanation
Indices: 28558--28590 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28548 GATTAATTTA
28558 TTTAAAACAAATAGAT
1 TTTAAAACAAATAGAT
*
28574 TTTAAAATAAATAGAT
1 TTTAAAACAAATAGAT
28590 T
1 T
28591 AATTTACATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (16 bp):
TTTAAAACAAATAGAT
Found at i:30270 original size:384 final size:386
Alignment explanation
Indices: 29258--30354 Score: 1571
Period size: 384 Copynumber: 2.8 Consensus size: 386
29248 GACACCGAGC
29258 GGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
1 GGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
*
29323 GGGTTCAAAATCCTGAAACAATCGGATCCTTCTTTTTTTTGTTTTGCCATCTTCGGATATGGCCG
66 GGGTTCAAAATCCTGAAACAGTCGGA----TC---TTTTT-TTTT-CCATCTTCGGATATGGCCG
* *
29388 ATCTCGGCTAAACTCGACCCGAGTCGTTCCTGAAAGAATAAGGGAATCCTTGCCTGCCGACCGTT
122 ATCT-GGCTAAACTCGACCCGAGTCGTTCCTGAAAGAATAAGGGAATCCCTGCCTGCCGTCCGTT
* *
29453 GATTAGA----AGT--GG--GTTAAGACTGTGATTCCTGATTTACTGTTGAAGAAGATTAAGAGG
186 GATTAGAGGTGAGTGAGGAAGTTAAGACTGTGATTCCTGATTCACTGTTGAAGAAGAATAAGAGG
*
29510 AATGAAGAATGGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAGAGAGGAAGAAAGTCGAGAA
251 AATGAAGAATGGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAAAGAGGAAGAAAGTCGAGAA
* * * *
29575 CCGCAAGCTCATTTACTGAAGAGCAGTTATACGAAAGAGTCTGAGAGTCAGGTATATTTGAGAGT
316 CCGCAAGCTCA--TACT-AAGAGCAGTTATACAAAAGACTATGAGAGTCAGGTATATGTGAGAGT
*
29640 GAAAGCTAT
378 GAAACCTAT
** *
29649 GGATCCGTGGCGCAATGGTAAAGCGTCTGACTCCAGATCAGACGGTTGCGTGTTCGATTCACGTC
1 GGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
* * * * ** *
29714 GGGTTCAAAATCTTGGAACAGTTGGATC-TCTTTTTGGCATCTTCGTATATGGCCGATCTGGGCT
66 GGGTTCAAAATCCTGAAACAGTCGGATCTTTTTTTTTCCATCTTCGGATATGGCCGATCT-GGCT
* * * *
29778 AAACTCGACCCGAATCGTTCCTGAAAGAGTAAGGGAATCCCTGCCTGCCGTCCGTCGATTAAAGG
130 AAACTCGACCCGAGTCGTTCCTGAAAGAATAAGGGAATCCCTGCCTGCCGTCCGTTGATTAGAGG
*
29843 TGGGTGAGGAAGTTAAGACTGTGATTCCTGATTCACTGTTGAAGAAGAATAAGAGGAATGAAGAA
195 TGAGTGAGGAAGTTAAGACTGTGATTCCTGATTCACTGTTGAAGAAGAATAAGAGGAATGAAGAA
* *
29908 TGGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAAAGAGGAAGAATGTCGAGAAACGCAAGCT
260 TGGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAAAGAGGAAGAAAGTCGAGAACCGCAAGCT
* * *
29973 -A-GCT-A-TGCAG-TATGCAAAAGACTATGAG-GCTCAGGTATATGTGA-AGGTGAAACCTAAT
325 CATACTAAGAGCAGTTATACAAAAGACTATGAGAG-TCAGGTATATGTGAGA-GTGAAACCT-AT
30031 GGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
1 GGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
* *
30096 GGGTTCAAAATCCTGAAACAGTCGGATCTATTTTTTTTCCCTCTTCGGATATGGCTGATCTGAGC
66 GGGTTCAAAATCCTGAAACAGTCGGATCT-TTTTTTTTCCATCTTCGGATATGGCCGATCTG-GC
* *
30161 TAAACTCGACCCGAGTCGTTCCTGAATGAATAAGGAAATCCCTGCCTGCCGTCCGTTGATTAGAG
129 TAAACTCGACCCGAGTCGTTCCTGAAAGAATAAGGGAATCCCTGCCTGCCGTCCGTTGATTAGAG
*
30226 GTGAGTGAGGAAGTTAAGACTGTGATTCCTGATTCACCGTTGAAGAAGAATAAGAGGAATGAAGA
194 GTGAGTGAGGAAGTTAAGACTGTGATTCCTGATTCACTGTTGAAGAAGAATAAGAGGAATGAAGA
*
30291 A-GGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAAAGAGGAAGAAAGTCTAGAACCGCAAGC
259 ATGGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAAAGAGGAAGAAAGTCGAGAACCGCAAGC
30355 CCATTTACTC
Statistics
Matches: 637, Mismatches: 55, Indels: 36
0.88 0.08 0.05
Matches are distributed among these distances:
380 2 0.00
381 117 0.18
382 96 0.15
383 65 0.10
384 150 0.24
385 4 0.01
387 4 0.01
388 1 0.00
389 114 0.18
391 84 0.13
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (386 bp):
GGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGTC
GGGTTCAAAATCCTGAAACAGTCGGATCTTTTTTTTTCCATCTTCGGATATGGCCGATCTGGCTA
AACTCGACCCGAGTCGTTCCTGAAAGAATAAGGGAATCCCTGCCTGCCGTCCGTTGATTAGAGGT
GAGTGAGGAAGTTAAGACTGTGATTCCTGATTCACTGTTGAAGAAGAATAAGAGGAATGAAGAAT
GGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAAAGAGGAAGAAAGTCGAGAACCGCAAGCTC
ATACTAAGAGCAGTTATACAAAAGACTATGAGAGTCAGGTATATGTGAGAGTGAAACCTAT
Found at i:42549 original size:26 final size:26
Alignment explanation
Indices: 42518--42577 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
42508 GTGTTTCTCA
*
42518 ACAAGGGCCTATATGTGGACAACCTC
1 ACAAGGGCCTACATGTGGACAACCTC
*
42544 ACAAGGGGTCTACATGTGGACAACCTC
1 ACAA-GGGCCTACATGTGGACAACCTC
42571 ACAAGGG
1 ACAAGGG
42578 GTGGTTGACC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.32, C:0.25, G:0.27, T:0.17
Consensus pattern (26 bp):
ACAAGGGCCTACATGTGGACAACCTC
Found at i:44572 original size:23 final size:23
Alignment explanation
Indices: 44531--44583 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
44521 TTAACTGACT
* * *
44531 TATTTAAAATATTATAAAATATA
1 TATTTAAAATATGATAAAAAAAA
44554 TATTTAAAATAATGA-AAAAAAAA
1 TATTTAAAAT-ATGATAAAAAAAA
44577 TATTTAA
1 TATTTAA
44584 GTGACTTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TATTTAAAATATGATAAAAAAAA
Found at i:50290 original size:15 final size:13
Alignment explanation
Indices: 50279--50311 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
50269 ATTCTTGCTG
50279 TTTTTTTTCTTG-
1 TTTTTTTTCTTGT
50291 TTTTTTTT-TTGT
1 TTTTTTTTCTTGT
50303 TTTTTTTTC
1 TTTTTTTTC
50312 ACTATTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.16
12 16 0.84
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTGT
Found at i:50309 original size:11 final size:11
Alignment explanation
Indices: 50277--50310 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
50267 CTATTCTTGC
50277 TGTTTTTTTTCT
1 TGTTTTTTTT-T
50289 TGTTTTTTTTT
1 TGTTTTTTTTT
50300 TGTTTTTTTTT
1 TGTTTTTTTTT
50311 CACTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (11 bp):
TGTTTTTTTTT
Found at i:50500 original size:18 final size:18
Alignment explanation
Indices: 50474--50516 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
50464 TTTATTTTTA
*
50474 ATTTATTGATGT-TTTTAGT
1 ATTT-TTGATGTATTATA-T
50493 ATTTTTGATGTATTATAT
1 ATTTTTGATGTATTATAT
50511 ATTTTT
1 ATTTTT
50517 AAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (18 bp):
ATTTTTGATGTATTATAT
Found at i:52283 original size:31 final size:31
Alignment explanation
Indices: 52248--52330 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
52238 CTTCCTGCAT
* * *
52248 TAAAATTCAACCAAATACAACAAATATAATA
1 TAAAATGCAACCAAAAACAACAAATATAACA
* * *
52279 TAAAATGCAGCCAAAAACAGCAAATTTAACA
1 TAAAATGCAACCAAAAACAACAAATATAACA
*
52310 TAAAAAATACAACCAAAAACA
1 T--AAAATGCAACCAAAAACA
52331 TTAATTCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 26 0.62
33 16 0.38
ACGTcount: A:0.61, C:0.18, G:0.04, T:0.17
Consensus pattern (31 bp):
TAAAATGCAACCAAAAACAACAAATATAACA
Found at i:56651 original size:21 final size:23
Alignment explanation
Indices: 56605--56652 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
56595 TGGATGAAAT
56605 ATAATTAAAAATATGATAGTTGAA
1 ATAATTAAAAATATGA-AGTTGAA
*
56629 ATAATTAAAAGTATG-AG-TGAA
1 ATAATTAAAAATATGAAGTTGAA
56650 ATA
1 ATA
56653 TATATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 2 0.09
24 14 0.61
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (23 bp):
ATAATTAAAAATATGAAGTTGAA
Found at i:57299 original size:41 final size:41
Alignment explanation
Indices: 57133--57288 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
57123 TTTATCGTTA
* * * *
57133 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
57174 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
57215 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
57256 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
57289 AAGAGCCGGT
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 102 0.95
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:57559 original size:33 final size:33
Alignment explanation
Indices: 57503--57600 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
57493 ATAGATATGT
*
57503 ATATATATATATGT-TGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
*
57535 ATATATTTATGTGTATGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
* * *
57568 AAATAAGTGTATGTATCTATGCATTCGGCATAG
1 ATAT-A-TATATG--TGTATGCATTCGGCATAG
57601 ATGGGTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 21 0.38
34 1 0.02
35 5 0.09
37 17 0.30
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
ATATATATATGTGTATGCATTCGGCATAGGTGA
Done.