Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1412
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: 79320
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4854 original size:26 final size:25
Alignment explanation
Indices: 4768--4870 Score: 126
Period size: 26 Copynumber: 4.2 Consensus size: 25
4758 ATGGTACAAT
4768 TGATAATGGGTTA-GTAAATGTTCC-
1 TGATAAT-GGTTAGGTAAATGTTCCA
*
4792 --ATAATGGATTAGGTAAATATTCCA
1 TGATAATGG-TTAGGTAAATGTTCCA
4816 T-ATAATAGGTTAGGTAAATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTTCCA
4841 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGG-TTAGGTAAATGTTCCA
4867 TGAT
1 TGAT
4871 GGGCATTTCA
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
21 2 0.03
22 8 0.11
23 10 0.14
25 23 0.33
26 27 0.39
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTCCA
Found at i:4856 original size:51 final size:47
Alignment explanation
Indices: 4770--4867 Score: 133
Period size: 51 Copynumber: 2.0 Consensus size: 47
4760 GGTACAATTG
*
4770 ATAATGGGTTAGTAAATGTTCCATAATGGATTAGGTAAATATTCCAT
1 ATAATAGGTTAGTAAATGTTCCATAATGGATTAGGTAAATATTCCAT
* *
4817 ATAATAGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCAT
1 ATAATAGGTTA-GTAAATGTTCC---ATAATGGATTAGGTAAATATTCCAT
4868 GATGGGCATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
47 10 0.23
48 11 0.25
51 23 0.52
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (47 bp):
ATAATAGGTTAGTAAATGTTCCATAATGGATTAGGTAAATATTCCAT
Found at i:6514 original size:41 final size:43
Alignment explanation
Indices: 6457--6544 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
6447 GTCCTGGTGG
6457 CTATGCCACAATTATCTGA-TCT-GTCGCTCTGCCACATATAT
1 CTATGCCACAATTATCTGATTCTGGTCGCTCTGCCACATATAT
* *
6498 CTATGCCACAATTATCTGATTTTGGTGGCTCTGCCACATATAT
1 CTATGCCACAATTATCTGATTCTGGTCGCTCTGCCACATATAT
6541 CTAT
1 CTAT
6545 TCTGGGGCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 19 0.44
42 2 0.05
43 22 0.51
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (43 bp):
CTATGCCACAATTATCTGATTCTGGTCGCTCTGCCACATATAT
Found at i:6560 original size:26 final size:27
Alignment explanation
Indices: 6501--6568 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
6491 CATATATCTA
*
6501 TGCCACAATTATCTGATTTTGGTGGCTC
1 TGCCACAA-TATCTGATTCTGGTGGCTC
*
6529 TGCCACATATATCT-ATTCTGG-GGCTT
1 TGCCACA-ATATCTGATTCTGGTGGCTC
6555 TGCCACAATATCTG
1 TGCCACAATATCTG
6569 TATCTGTGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 6 0.17
26 11 0.31
27 6 0.17
28 12 0.33
29 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.37
Consensus pattern (27 bp):
TGCCACAATATCTGATTCTGGTGGCTC
Found at i:6574 original size:26 final size:26
Alignment explanation
Indices: 6501--6595 Score: 77
Period size: 26 Copynumber: 3.5 Consensus size: 26
6491 CATATATCTA
* *
6501 TGCCACAATTATCTG-ATTTTGGTGGCTC
1 TGCCACAA-TATCTGTA-TCTGG-GGCTT
*
6529 TGCCACATATATCTAT-TCTGGGGCTT
1 TGCCACA-ATATCTGTATCTGGGGCTT
* *
6555 TGCCACAATATCTGTATCTGTGACTT
1 TGCCACAATATCTGTATCTGGGGCTT
*
6581 TGTCAACAATATCTG
1 TG-CCACAATATCTG
6596 GCAGCCTCGC
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
25 7 0.12
26 21 0.38
27 15 0.27
28 12 0.21
29 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (26 bp):
TGCCACAATATCTGTATCTGGGGCTT
Found at i:18351 original size:28 final size:28
Alignment explanation
Indices: 18288--18438 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
18278 ATATTAAGTC
*
18288 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
18315 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
18343 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
18371 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
18399 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
18428 CGCACACTTAG
1 CGCACACTTAG
18439 CGCCAATCTC
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 22 0.19
28 77 0.67
29 16 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:21196 original size:75 final size:75
Alignment explanation
Indices: 21044--21207 Score: 195
Period size: 75 Copynumber: 2.2 Consensus size: 75
21034 TTTTAAGCCT
* * * *
21044 AGCGCTAATCGGGTTAGCCAATGATATTAAATGTGAGCCCAGCTCTAGTCTGATAAACCAACAAT
1 AGCGCTAGTCGGGTTAGCCAACGATATTAAATGTAAGCCCAACTCTAGTCTGATAAACCAACAAT
21109 GTTTGCACCC
66 GTTTGCACCC
* * * * *
21119 AGCGCTAGTCGTGTTAGCCTACGATATTGAATGTAAGCCTAACTCTAGT-TGGATAAACCAACAG
1 AGCGCTAGTCGGGTTAGCCAACGATATTAAATGTAAGCCCAACTCTAGTCT-GATAAACCAACAA
***
21183 TGTTTGTGTCC
65 TGTTTGCACCC
*
21194 AGCGCTAGTTGGGT
1 AGCGCTAGTCGGGT
21208 ATTCTAACGA
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
74 1 0.01
75 73 0.99
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (75 bp):
AGCGCTAGTCGGGTTAGCCAACGATATTAAATGTAAGCCCAACTCTAGTCTGATAAACCAACAAT
GTTTGCACCC
Found at i:22669 original size:20 final size:20
Alignment explanation
Indices: 22641--22684 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
22631 TACCAACTTG
*
22641 CAACTTACCATAATCTTTCA
1 CAACATACCATAATCTTTCA
*
22661 CAACATACCATAGTCTTTCA
1 CAACATACCATAATCTTTCA
22681 CAAC
1 CAAC
22685 TTAAACATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (20 bp):
CAACATACCATAATCTTTCA
Found at i:22848 original size:43 final size:42
Alignment explanation
Indices: 22762--22876 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 42
22752 CCACATAGTA
* * *
22762 CATACCAATGCCATATCCCAGATATGGTCTTACATGGGATCT
1 CATATCAATGCCATATCCCAGATATGGTCTTACACGAGATCT
* *
22804 CATATCAATGCCAATAGCCCAGCTATGGTCTTACACGA-AGTCT
1 CATATCAATGCC-ATATCCCAGATATGGTCTTACACGAGA-TCT
**
22847 CATATTGATGCCATATCCCAGATATGGTCT
1 CATATCAATGCCATATCCCAGATATGGTCT
22877 CTCACGTAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 28 0.45
43 34 0.55
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (42 bp):
CATATCAATGCCATATCCCAGATATGGTCTTACACGAGATCT
Found at i:37231 original size:20 final size:22
Alignment explanation
Indices: 37206--37251 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
37196 TTCATAATTT
37206 TATTAATAGAA-TAAAT-TTAA
1 TATTAATAGAACTAAATGTTAA
* *
37226 TATTAATTGAACTAATTGTTAA
1 TATTAATAGAACTAAATGTTAA
37248 TATT
1 TATT
37252 GTTAGTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 4 0.18
22 8 0.36
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (22 bp):
TATTAATAGAACTAAATGTTAA
Found at i:37598 original size:3 final size:3
Alignment explanation
Indices: 37584--37719 Score: 78
Period size: 3 Copynumber: 48.3 Consensus size: 3
37574 AAAGATGAAC
* **
37584 TAT TAT TGT TAT TAT TAT TAT T-T TGC TAT TAT T-T T-T TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* ** *
37628 TAC TAT TAT T-T TGC TAT TA- TAT TAC TAT TAT T-T TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
37673 T-T GAAA TAT TA- TAT AAT TAT TAT T-T TAT TAT TAAT T-T TGT TAT
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
37716 TAT T
1 TAT T
37720 TTAAGTGTAT
Statistics
Matches: 102, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
2 21 0.21
3 78 0.76
4 3 0.03
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:37664 original size:14 final size:14
Alignment explanation
Indices: 37584--37719 Score: 85
Period size: 14 Copynumber: 10.3 Consensus size: 14
37574 AAAGATGAAC
37584 TATTATTGTTATTAT
1 TATTATT-TTATTAT
**
37599 TATTATTTTGCTAT
1 TATTATTTTATTAT
37613 TATT-TTTTATTA-
1 TATTATTTTATTAT
*
37625 TATTACTATTATT-T
1 TATTA-TTTTATTAT
** * *
37639 TGCTATTATATTAC
1 TATTATTTTATTAT
37653 TATTATTTTATTAT
1 TATTATTTTATTAT
*
37667 TATTATTTGA--A-
1 TATTATTTTATTAT
* *
37678 -A-TATTATATAAT
1 TATTATTTTATTAT
37690 TATTATTTTATTAT
1 TATTATTTTATTAT
*
37704 TA--ATTTTGTTAT
1 TATTATTTTATTAT
37716 TATT
1 TATT
37720 TTAAGTGTAT
Statistics
Matches: 90, Mismatches: 20, Indels: 23
0.68 0.15 0.17
Matches are distributed among these distances:
9 5 0.06
10 1 0.01
11 1 0.01
12 16 0.18
13 12 0.13
14 48 0.53
15 7 0.08
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:37720 original size:11 final size:11
Alignment explanation
Indices: 37584--37722 Score: 100
Period size: 11 Copynumber: 12.2 Consensus size: 11
37574 AAAGATGAAC
*
37584 TATTATTGTTAT
1 TATTATTATT-T
37596 TATTATTATTT
1 TATTATTATTT
**
37607 TGCTATTATTT
1 TATTATTATTT
*
37618 T-TTATTATAT
1 TATTATTATTT
*
37628 TACTATTATTT
1 TATTATTATTT
** *
37639 TGCTATTATAT
1 TATTATTATTT
*
37650 TACTATTATTT
1 TATTATTATTT
37661 TATTATTATTATT
1 TATTATTA-T-TT
* *
37674 TGAAATATTATAT
1 T--ATTATTATTT
*
37687 AATTATTATTT
1 TATTATTATTT
37698 TATTATTAATTT
1 TATTATT-ATTT
*
37710 TGTTATTATTT
1 TATTATTATTT
37721 TA
1 TA
37723 AGTGTATTTG
Statistics
Matches: 101, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
10 8 0.08
11 62 0.61
12 20 0.20
13 4 0.04
14 1 0.01
15 6 0.06
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (11 bp):
TATTATTATTT
Found at i:37801 original size:25 final size:26
Alignment explanation
Indices: 37773--37823 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
37763 TGTAGGAAAT
*
37773 ATTTATTTTGTAT-T-ATATTTTTTAA
1 ATTTATTTT-TATATAAAATTTTTTAA
37798 ATTTATTTTTATATAAAATTTTTTAA
1 ATTTATTTTTATATAAAATTTTTTAA
37824 TACGAGTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 3 0.13
25 10 0.43
26 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
ATTTATTTTTATATAAAATTTTTTAA
Found at i:48709 original size:9 final size:9
Alignment explanation
Indices: 48695--48763 Score: 84
Period size: 9 Copynumber: 7.7 Consensus size: 9
48685 TTTTACAGTC
*
48695 TCTTGTTCT
1 TCTTCTTCT
*
48704 TCTTGTTCT
1 TCTTCTTCT
* *
48713 TGTTCTTGT
1 TCTTCTTCT
*
48722 TCTTGTTCT
1 TCTTCTTCT
48731 TCTTCTTCT
1 TCTTCTTCT
48740 TCTTCTTCT
1 TCTTCTTCT
48749 TCTTCTTCT
1 TCTTCTTCT
*
48758 TTTTCT
1 TCTTCT
48764 CTGTTATTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 52 1.00
ACGTcount: A:0.00, C:0.25, G:0.07, T:0.68
Consensus pattern (9 bp):
TCTTCTTCT
Found at i:48712 original size:6 final size:6
Alignment explanation
Indices: 48695--48763 Score: 84
Period size: 6 Copynumber: 11.5 Consensus size: 6
48685 TTTTACAGTC
* * * * *
48695 TCTTGT TCTTCT TGTTCT TGTTCT TGTTCT TGTTCT TCTTCT TCTTCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
*
48743 TCTTCT TCTTCT TCTTTT TCT
1 TCTTCT TCTTCT TCTTCT TCT
48764 CTGTTATTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.00, C:0.25, G:0.07, T:0.68
Consensus pattern (6 bp):
TCTTCT
Found at i:48864 original size:21 final size:21
Alignment explanation
Indices: 48838--48877 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
48828 AACGTGACAA
48838 GTTAACTTGCCACATCAGCTT
1 GTTAACTTGCCACATCAGCTT
48859 GTTAACTTGCCACATCAGC
1 GTTAACTTGCCACATCAGC
48878 GGTCCCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (21 bp):
GTTAACTTGCCACATCAGCTT
Found at i:48965 original size:30 final size:31
Alignment explanation
Indices: 48913--48980 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
48903 CTGTTAACCG
*
48913 GTGACTGTTTTGTCACTTTTTTATAACGTT-A
1 GTGACTGTTTTGTCACTTTTTTA-AAAGTTGA
*
48944 GTGACTGTTTTGTTA-TTTTTTAAAAGTTGA
1 GTGACTGTTTTGTCACTTTTTTAAAAGTTGA
48974 GTGACTG
1 GTGACTG
48981 ATATGAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 5 0.15
30 15 0.44
31 14 0.41
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.50
Consensus pattern (31 bp):
GTGACTGTTTTGTCACTTTTTTAAAAGTTGA
Found at i:52504 original size:3 final size:3
Alignment explanation
Indices: 52483--52529 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
52473 CTATCTCAAT
52483 TAA TAGA TAA -AA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52527 TAA
1 TAA
52530 GTAAATATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:57174 original size:26 final size:26
Alignment explanation
Indices: 57091--57224 Score: 172
Period size: 25 Copynumber: 5.3 Consensus size: 26
57081 CTAGAGGCCT
*
57091 AGCCTCTTTT-AAT-AACTGGGG-AAA
1 AGCC-CTTTTCAATAAACTGGGGCATA
* *
57115 AACCCTTTT-GATAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
57139 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
57165 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
* *
57191 AGCCC-TTTCAATAAATTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
57216 AGCCCTTTT
1 AGCCCTTTT
57225 GCACTTCCTC
Statistics
Matches: 99, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
23 7 0.07
24 20 0.20
25 37 0.37
26 35 0.35
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:57183 original size:51 final size:51
Alignment explanation
Indices: 57091--57224 Score: 170
Period size: 51 Copynumber: 2.7 Consensus size: 51
57081 CTAGAGGCCT
* * *
57091 AGCCTCTTTT-AAT-AACTGGGG-AAAAACCCTTTTGATAAACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATAAGCCCTTTTAATAAACTGGGGCATA
57139 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT-AATAAACTGGGGCATA
* *
57191 AGCCC-TTTCAATAAATTAGGGCATAAGCCCTTTT
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
57225 GCACTTCCTC
Statistics
Matches: 76, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
47 5 0.07
48 7 0.09
49 8 0.11
50 10 0.13
51 40 0.53
52 6 0.08
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (51 bp):
AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTAATAAACTGGGGCATA
Found at i:57299 original size:20 final size:20
Alignment explanation
Indices: 57274--57347 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
57264 TTATGAATAC
*
57274 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
57294 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
57314 TTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
57334 GTCATGTGCATATC
1 ATCATGTGCATATC
57348 GTATCAACCA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:57305 original size:11 final size:11
Alignment explanation
Indices: 57274--57347 Score: 52
Period size: 11 Copynumber: 7.3 Consensus size: 11
57264 TTATGAATAC
57274 ATCATGTGCAT
1 ATCATGTGCAT
* *
57285 TTCA--TACAT
1 ATCATGTGCAT
57294 ATCATGTGCAT
1 ATCATGTGCAT
*
57305 ATCA--TACAT
1 ATCATGTGCAT
*
57314 TTCATGTGCAT
1 ATCATGTGCAT
*
57325 ATCA--TACAT
1 ATCATGTGCAT
*
57334 GTCATGTGCAT
1 ATCATGTGCAT
57345 ATC
1 ATC
57348 GTATCAACCA
Statistics
Matches: 45, Mismatches: 12, Indels: 12
0.65 0.17 0.17
Matches are distributed among these distances:
9 21 0.47
11 24 0.53
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:57360 original size:40 final size:40
Alignment explanation
Indices: 57276--57368 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
57266 ATGAATACAT
* **
57276 CATGTGCATTTCATACATATCATGTGCATATCATACATTT
1 CATGTGCATATCATACATATCATGTGCATATCATACATAC
* *
57316 CATGTGCATATCATACATGTCATGTGCATATCGTATCA-AC
1 CATGTGCATATCATACATATCATGTGCATATCATA-CATAC
57356 CATGT--ATATCATA
1 CATGTGCATATCATA
57369 TCCCACGTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 8 0.17
40 37 0.79
41 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (40 bp):
CATGTGCATATCATACATATCATGTGCATATCATACATAC
Found at i:60276 original size:28 final size:28
Alignment explanation
Indices: 60244--60298 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
60234 CAAGGCTGAC
60244 TTTT-ATCT-CTTGATTTCAATTTCAATCT
1 TTTTAATCTACTTG-TTT-AATTTCAATCT
*
60272 TTTTAATTTACTTGTTTAATTTCAATC
1 TTTTAATCTACTTGTTTAATTTCAATC
60299 ATTTACTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 14 0.58
29 6 0.25
30 4 0.17
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.58
Consensus pattern (28 bp):
TTTTAATCTACTTGTTTAATTTCAATCT
Found at i:70206 original size:52 final size:52
Alignment explanation
Indices: 70144--70247 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
70134 GTCATAGGAT
70144 AGATTGAGTATGAGTTACTTCGGCTATATGTTGATGAGCGCTCAGTGCATTC
1 AGATTGAGTATGAGTTACTTCGGCTATATGTTGATGAGCGCTCAGTGCATTC
70196 AGATTGAGTATGAGTTACTTCGGCTATATGTTGATGAGCGCTCAGTGCATTC
1 AGATTGAGTATGAGTTACTTCGGCTATATGTTGATGAGCGCTCAGTGCATTC
70248 TCCTTCAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (52 bp):
AGATTGAGTATGAGTTACTTCGGCTATATGTTGATGAGCGCTCAGTGCATTC
Found at i:75028 original size:39 final size:40
Alignment explanation
Indices: 74951--75030 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
74941 TGTACAACGG
74951 TTGCAAGCAAGCCAAGCCAGTGAGACCAGAGAGACTAGCT
1 TTGCAAGCAAGCCAAGCCAGTGAGACCAGAGAGACTAGCT
74991 TTGCAAGCAAGCCAAGCCAGTG-GACCAGAGAGACTAGCT
1 TTGCAAGCAAGCCAAGCCAGTGAGACCAGAGAGACTAGCT
75030 T
1 T
75031 GGCGGTTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 18 0.45
40 22 0.55
ACGTcount: A:0.34, C:0.25, G:0.28, T:0.14
Consensus pattern (40 bp):
TTGCAAGCAAGCCAAGCCAGTGAGACCAGAGAGACTAGCT
Done.