Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2942
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: 45771
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2394 original size:7 final size:7
Alignment explanation
Indices: 2382--2411 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2372 TTTTCTAAGA
2382 AAAATTC
1 AAAATTC
2389 AAAATTC
1 AAAATTC
2396 AAAATTC
1 AAAATTC
2403 AAAATTC
1 AAAATTC
2410 AA
1 AA
2412 GCCGATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTC
Found at i:2910 original size:25 final size:24
Alignment explanation
Indices: 2854--2904 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
2844 ATTAATAACT
2854 AGTTAAGTT-AATTAAATTATGATTA
1 AGTTAA-TTAAATTAAATTA-GATTA
2879 AGTTAATTAAATTAAATTA-ATTA
1 AGTTAATTAAATTAAATTAGATTA
2902 AGT
1 AGT
2905 CTTAATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 7 0.28
24 2 0.08
25 16 0.64
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (24 bp):
AGTTAATTAAATTAAATTAGATTA
Found at i:7273 original size:43 final size:43
Alignment explanation
Indices: 7199--7566 Score: 459
Period size: 43 Copynumber: 8.6 Consensus size: 43
7189 AATATTTTGC
* * * * *
7199 ACGCCGCTATAGAACATGACCTTTAGTGGCACTTTTACAACAA
1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA
* * * * *
7242 ACGCTGCTAAAGAACATGGCATTTAGCGGCACTTTTTCCACAA
1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA
* * * * *
7285 ACGCCGTTAAAGAAAATAACCTTTAGTGGCGCTTTTCCCAAAA
1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA
*
7328 ACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA
1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA
* * *
7371 ATGCCACTAAAGAACATGACCTTTAGCGGCGTTTTTCCCACAA
1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA
* *
7414 ACGCCGCTATAGAACATGACCTTTAGCGGCGTTTTTCCCACAA
1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA
* *
7457 ACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCACGA
1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA
* * * *
7500 ACACCGCTATAGAACA-GACCTTTACCGACGCTTTTCCCACAA
1 ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA
* * *
7542 ACGCCGATAAAGAATATGACTTTTA
1 ACGCCGCTAAAGAACATGACCTTTA
7567 AAAAATATTT
Statistics
Matches: 283, Mismatches: 41, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
42 35 0.12
43 248 0.88
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
ACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAA
Found at i:7875 original size:17 final size:18
Alignment explanation
Indices: 7839--7876 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
7829 ATTTAGAATC
7839 AAAACTAAAATAAATAAT
1 AAAACTAAAATAAATAAT
* *
7857 AAAATTAAATTAAAT-AT
1 AAAACTAAAATAAATAAT
7874 AAA
1 AAA
7877 GATATCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAACTAAAATAAATAAT
Found at i:9432 original size:48 final size:47
Alignment explanation
Indices: 9331--9742 Score: 218
Period size: 48 Copynumber: 8.7 Consensus size: 47
9321 TCATTTGTGC
*
9331 GCTAGTATAAGA-CATGTCTGGGACAT-GCATCAGCCACATT---ATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-G---CATTGAGATGAGA
* *
9377 GCCAGTGTAAGACCATGTTTGGGACATGGCATCTGCATTGAGATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GCATTGAGATGAGA
* * *
9425 GCTAGTGTAAGA-CGTGTCTGGGACAT-GCATCGGCCTCGAGATGTA-A
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GCATTGAGATG-AGA
* * * * *
9471 GCCAGTGTAAGA-CATGTATGGGATAT-GCATCG-AGT-ACGAT-ATGT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCATTGA-GATGA-GA
* * *
9515 G-TCAGTGAAAGACCATGTCTGGGACATGGCAACAGCACGTAT-AGA-G-GT
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATC-GCA--T-TGAGATGAGA
* * * *
9563 GTTAGTGTAAGACCATGTCTAGGACATGGCATCAGCATGGATATGTGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GCATTGAGA--TGAGA
* * * * ** *
9613 GCTAATGTAAGACCATGTCTGGGACATGGCATTGGCCTCGATTTCGATA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCA-TCGCATTGAGAT-GAGA
* *
9662 G-TCAGTGTACGACCATGTATGGGACATGGCATCG-ACTT--GATGGATGA
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGCA-TTGAGAT-GA-GA
*
9709 GCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCG
9743 GTATTACACC
Statistics
Matches: 285, Mismatches: 51, Indels: 59
0.72 0.13 0.15
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 12 0.04
45 17 0.06
46 62 0.22
47 58 0.20
48 63 0.22
49 31 0.11
50 37 0.13
51 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25
Consensus pattern (47 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCATTGAGATGAGA
Found at i:13572 original size:46 final size:46
Alignment explanation
Indices: 13522--13694 Score: 185
Period size: 46 Copynumber: 3.7 Consensus size: 46
13512 TTGAGCATCT
13522 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
* * *
13568 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCC
* *
13615 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGACG-CC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
* * *
13660 CAAGCTGGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
13695 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 7 0.07
46 55 0.52
47 29 0.27
48 3 0.03
50 4 0.04
51 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
Found at i:13675 original size:93 final size:93
Alignment explanation
Indices: 13516--13687 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
13506 GGATGGTTGA
* * *
13516 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT
13581 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
13609 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGACG-CCCAAGCTGGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTGAG
13673 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
13688 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 4 0.05
93 69 0.95
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:21233 original size:114 final size:108
Alignment explanation
Indices: 21033--21328 Score: 281
Period size: 114 Copynumber: 2.7 Consensus size: 108
21023 AGATAAAATG
* * * * * * * * *
21033 TTTTTTGTGGCGTTTTTGATAAAGTGCCACTAA-AGCTCGATCTATAGCTGCGTTTTTCAAAAAG
1 TTTTTTGCGGAGTTTTTCAAAAAGCGCCGCTAATA-CTCGATCTATAGCGGCATTTTTAAAAAAG
* * * *
21097 CGCCGCTAGTGACACTAAAGCTCAACATAAAACGATGTGGTTTTG-TTTAA
65 CGCCGCTAATGACACTAAAGCT---CA-AAAACG--G-CGTTGTGCTTAAA
* *
21147 TTTTTTGCGGTGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGCGGCATTTTTTAAAAAGC
1 TTTTTTGCGGAGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGCGGCATTTTTAAAAAAGC
* * *
21212 GCTGCTAATGCCACTAAAGCTCAAACACGGCGTTGTGCTTAAA
66 GCCGCTAATGACACTAAAGCTCAAAAACGGCGTTGTGCTTAAA
** ** * * *
21255 TTTTTTGCGGAGTTTTTTGAAAAGCGCCGCTAATGGTCGACCTATAGTGGCACTTTTAAAAAAGC
1 TTTTTTGCGGAGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGCGGCATTTTTAAAAAAGC
21320 GCCGCTAAT
66 GCCGCTAAT
21329 ACTAGATCTA
Statistics
Matches: 154, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
107 5 0.03
108 69 0.45
110 5 0.03
111 2 0.01
114 72 0.47
115 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (108 bp):
TTTTTTGCGGAGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGCGGCATTTTTAAAAAAGC
GCCGCTAATGACACTAAAGCTCAAAAACGGCGTTGTGCTTAAA
Found at i:21340 original size:40 final size:40
Alignment explanation
Indices: 21274--21351 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
21264 GAGTTTTTTG
** *
21274 AAAAGCGCCGCTAATGGTCGACCTATAGTGGCACTTTTAA
1 AAAAGCGCCGCTAATACTAGACCTATAGTGGCACTTTTAA
* *
21314 AAAAGCGCCGCTAATACTAGATCTATAGTGGCATTTTT
1 AAAAGCGCCGCTAATACTAGACCTATAGTGGCACTTTT
21352 TATAGCGACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (40 bp):
AAAAGCGCCGCTAATACTAGACCTATAGTGGCACTTTTAA
Found at i:31719 original size:22 final size:21
Alignment explanation
Indices: 31689--31754 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
31679 TACAAATTAA
31689 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
31711 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
31732 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
31751 ATCT
1 ATCT
31755 AAGATTGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:31741 original size:19 final size:19
Alignment explanation
Indices: 31706--31803 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
31696 AGATTACAAG
31706 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
31727 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
31746 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
31763 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
31782 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
31801 ATC
1 ATC
31804 CTTAAAGATT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
20 1 0.01
21 8 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:31770 original size:36 final size:37
Alignment explanation
Indices: 31706--31803 Score: 153
Period size: 36 Copynumber: 2.6 Consensus size: 37
31696 AGATTACAAG
31706 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATTGCAT
31746 ATCATATCTAAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
31782 ATCATATCTAAGATTGCATATC
1 ATCATATCTAAGATTG-ATATC
31804 CTTAAAGATT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
36 36 0.64
38 11 0.20
39 1 0.02
40 8 0.14
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
Found at i:33246 original size:26 final size:26
Alignment explanation
Indices: 33210--33264 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
33200 TTATACATGA
33210 CATATCATCATATATGACCAAGTATC
1 CATATCATCATATATGACCAAGTATC
33236 CATATCATCATATATGACCAAGTATC
1 CATATCATCATATATGACCAAGTATC
33262 CAT
1 CAT
33265 GCTTAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (26 bp):
CATATCATCATATATGACCAAGTATC
Found at i:34015 original size:17 final size:19
Alignment explanation
Indices: 33993--34031 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
33983 TGTACAAAAC
*
33993 TATAAT-TC-GTCAATTTA
1 TATAATATCTGTCAATTCA
34010 TATAATATCTGTCAATTCA
1 TATAATATCTGTCAATTCA
34029 TAT
1 TAT
34032 TCCAGAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 11 0.58
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (19 bp):
TATAATATCTGTCAATTCA
Found at i:34149 original size:24 final size:24
Alignment explanation
Indices: 34074--34150 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
34064 AGCACTTTCA
* *
34074 AGCCATAAT-AGGAAGCTTATGTG
1 AGCCATAATCGGGAAGCTCATGTG
* ***
34097 AGTCATGTAA-CGGGAAGCTCATAAA
1 AGCCA--TAATCGGGAAGCTCATGTG
34122 AGCCATAATCGGGAAGCTCATGTG
1 AGCCATAATCGGGAAGCTCATGTG
34146 AGCCA
1 AGCCA
34151 ATATCGTGTA
Statistics
Matches: 40, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
23 7 0.17
24 17 0.43
25 16 0.40
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (24 bp):
AGCCATAATCGGGAAGCTCATGTG
Found at i:34323 original size:25 final size:26
Alignment explanation
Indices: 34210--34349 Score: 64
Period size: 25 Copynumber: 5.6 Consensus size: 26
34200 CTTTTATCGT
* *
34210 GAAGCTCTTGAGAGC-C-AATTATCAG
1 GAAGCTCATGAGAGCTCAAATAAT-AG
* *
34235 GAAGCTCAT-ACGAGCT-ATA-AATCAA
1 GAAGCTCATGA-GAGCTCAAATAAT-AG
* *
34260 GAAGCTCAAGAGAG-TCATATAATAG
1 GAAGCTCATGAGAGCTCAAATAATAG
* * * *
34285 GATGCTTATAAGAGCT-AAATAATGG
1 GAAGCTCATGAGAGCTCAAATAATAG
*
34310 GAAGCTCATGAGAGC-CAAGT-ATCAG
1 GAAGCTCATGAGAGCTCAAATAAT-AG
* *
34335 GACGCTCATAAGAGC
1 GAAGCTCATGAGAGC
34350 AGTGGTGTGT
Statistics
Matches: 87, Mismatches: 19, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
24 4 0.05
25 77 0.89
26 6 0.07
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.21
Consensus pattern (26 bp):
GAAGCTCATGAGAGCTCAAATAATAG
Found at i:34346 original size:50 final size:49
Alignment explanation
Indices: 34210--34349 Score: 131
Period size: 50 Copynumber: 2.8 Consensus size: 49
34200 CTTTTATCGT
* * *
34210 GAAGCTCTTGAGAGCCAATTATCAGGAAGCTCATACGAGCTATAAATCAA
1 GAAGCTCATGAGAGCCAA-TATCAGGAAGCTCATAAGAGCTAAAAATCAA
* * * * **
34260 GAAGCTCAAGAGAGTCATATAAT-AGGATGCTTATAAGAGCTAAATAAT-GG
1 GAAGCTCATGAGAGCCA-AT-ATCAGGAAGCTCATAAGAGCTAAA-AATCAA
*
34310 GAAGCTCATGAGAGCCAAGTATCAGGACGCTCATAAGAGC
1 GAAGCTCATGAGAGCCAA-TATCAGGAAGCTCATAAGAGC
34350 AGTGGTGTGT
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
49 3 0.04
50 63 0.88
51 6 0.08
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.21
Consensus pattern (49 bp):
GAAGCTCATGAGAGCCAATATCAGGAAGCTCATAAGAGCTAAAAATCAA
Found at i:35411 original size:15 final size:15
Alignment explanation
Indices: 35391--35420 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35381 CATTTTATTT
*
35391 ATATTAGGATAATTA
1 ATATTAAGATAATTA
35406 ATATTAAGATAATTA
1 ATATTAAGATAATTA
35421 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:35448 original size:27 final size:26
Alignment explanation
Indices: 35387--35449 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
35377 ACTCCATTTT
35387 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
* * * *
35414 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
35442 ATTTTATT
1 ATTTTATT
35450 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:35464 original size:10 final size:10
Alignment explanation
Indices: 35445--35476 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
35435 TTTTAGGATT
35445 TTAT-TTTAA
1 TTATCTTTAA
35454 TTATCTTTAA
1 TTATCTTTAA
35464 TTATCTTTAA
1 TTATCTTTAA
35474 TTA
1 TTA
35477 AATGTGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:36844 original size:46 final size:44
Alignment explanation
Indices: 36737--36844 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
36727 TGTCTTTGAC
** * * *
36737 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
* *
36781 ATGGACTTACATTGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
36827 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
36845 TTTCTGTTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 32 0.59
46 22 0.41
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:42056 original size:25 final size:26
Alignment explanation
Indices: 41999--42104 Score: 153
Period size: 26 Copynumber: 4.2 Consensus size: 26
41989 TGAAATGCCC
*
41999 ATCATGGAACATTTAGCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
42025 ATCATGGAACATTTACCT-ACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
42050 ATTATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
42076 ATCATGGAACATTTTCCTAACCC-TT
1 ATCATGGAACATTTACCTAACCCATT
42101 ATCA
1 ATCA
42105 ATTTGTACCA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
25 29 0.41
26 42 0.59
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:42064 original size:51 final size:51
Alignment explanation
Indices: 42002--42102 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
41992 AATGCCCATC
*
42002 ATGGAACATTTAGCTAACCCATTATCATGGAACATTTACCT-ACCCATTATT
1 ATGGAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCC-TTATT
* * *
42053 ATGGAATATTTACCTAATCCATTATCATGGAACATTTTCCTAACCCTTAT
1 ATGGAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCCTTAT
42103 CAATTTGTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 41 0.91
52 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.36
Consensus pattern (51 bp):
ATGGAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCCTTATT
Done.