Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2245
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: 31058
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Found at i:2796 original size:20 final size:20
Alignment explanation
Indices: 2767--2805 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2757 CAACCTAATA
* *
2767 TAGTGTATGTATCGATATAT
1 TAGTGAATGTATCAATATAT
2787 TAGTGAATGTATCAATATA
1 TAGTGAATGTATCAATATA
2806 ATTTGGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
TAGTGAATGTATCAATATAT
Found at i:7170 original size:1 final size:1
Alignment explanation
Indices: 7164--7190 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
7154 AAAGTGTTTG
7164 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
7191 TAATTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7223 original size:21 final size:21
Alignment explanation
Indices: 7199--7255 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
7189 AATAATTTTA
7199 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
7220 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
7241 AATGTATCGATACAT
1 AATGTATCGATACAT
7256 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:7335 original size:19 final size:19
Alignment explanation
Indices: 7311--7378 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
7301 AATTCAACAA
7311 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
7330 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
7345 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
7362 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
7379 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:7350 original size:13 final size:13
Alignment explanation
Indices: 7332--7356 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7322 ACATAAGTTT
7332 TGTATCGATACAA
1 TGTATCGATACAA
7345 TGTATCGATACA
1 TGTATCGATACA
7357 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:7354 original size:32 final size:32
Alignment explanation
Indices: 7313--7375 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
7303 TTCAACAATT
*
7313 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
7345 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
7376 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:7436 original size:13 final size:13
Alignment explanation
Indices: 7418--7443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7408 CATTTTTCTG
7418 TGTATCGATACAT
1 TGTATCGATACAT
7431 TGTATCGATACAT
1 TGTATCGATACAT
7444 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7440 original size:33 final size:33
Alignment explanation
Indices: 7398--7464 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
7388 GCCAAGGAAA
***
7398 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
7431 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
7464 T
1 T
7465 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:10061 original size:102 final size:102
Alignment explanation
Indices: 9801--10082 Score: 365
Period size: 102 Copynumber: 2.8 Consensus size: 102
9791 CAAGTTTTCT
* * * * *
9801 CAATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATTAATTTTCCACAAT
1 CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCTATAAT
* * *
9866 CGGGGACACTCCAACTCCGATTTTATTCTCAGAACAC
66 CGGGGATACTCCAACTCCGATTGTATTCTCAAAACAC
**
9903 CAATTTTCCA-CAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACCAATTTTCTATA
1 CAATTTTCCATC-ATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACATTAATTTTCTATA
*
9966 ATCGGGGATACTCCAACTCCGATTGTATT-TCCAAAATAC
64 ATCGGGGATACTCCAACTCCGATTGTATTCT-CAAAACAC
* * * *
10005 TAATTTTTCATCATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAATATTAA-TTTCTCATAA
1 CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCT-ATAA
10069 TCGGGGATACTCCA
65 TCGGGGATACTCCA
10083 TCCCCGTTAT
Statistics
Matches: 157, Mismatches: 17, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
101 7 0.04
102 148 0.94
103 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (102 bp):
CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCTATAAT
CGGGGATACTCCAACTCCGATTGTATTCTCAAAACAC
Found at i:10079 original size:153 final size:153
Alignment explanation
Indices: 9801--10088 Score: 359
Period size: 153 Copynumber: 1.9 Consensus size: 153
9791 CAAGTTTTCT
* * * *
9801 CAATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATTAATTTTCCACAAT
1 CAATTTTGCATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCACAAT
* *
9866 CGGGGACACTCCAACTCCGATTTTATTCTCAGAACACCAATTTTCCACAATCGGGGATACTCCAA
66 CGGGGACACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTCCACAATCGGGGATACTCCAA
9931 CCCCGGTTTTATTTTCAAAACAC
131 CCCCGGTTTTATTTTCAAAACAC
* * * *
9954 CAATTTT-CTATAATCGGGGATACTCCAACTCCGATTGTATTTCCAAAATACTAATTTTTCATC-
1 CAATTTTGC-ATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCA-CA
* * * ** *
10017 ATCGGGGATACTCCAACCCCGTTTTTATT-TCTAAAATATTAA-TTTCTCATAATCGGGGATACT
64 ATCGGGGACACTCCAACCCCGATTTTATTCTC-AAAACACCAATTTTC-CACAATCGGGGATACT
*
10080 CCATCCCCG
127 CCAACCCCG
10089 TTATTTTCGA
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
152 7 0.06
153 106 0.93
154 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (153 bp):
CAATTTTGCATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCACAAT
CGGGGACACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTCCACAATCGGGGATACTCCAA
CCCCGGTTTTATTTTCAAAACAC
Found at i:10090 original size:51 final size:50
Alignment explanation
Indices: 9802--10088 Score: 308
Period size: 51 Copynumber: 5.6 Consensus size: 50
9792 AAGTTTTCTC
* * *
9802 AATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATT
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
* * * * *
9853 AATTTTCCACAATCGGGGACACTCCAACTCCGATTTTA-TTCTCAGAACACC
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACT
* * *
9904 AATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACC
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACT
* * * *
9955 AATTTTCTATAATCGGGGATACTCCAACTCCGATTGTATTTCCAAAATACT
1 AATTTTC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
* * * *
10006 AATTTTTCATCATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAATATT
1 AA-TTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
*
10057 AATTTCTCATAATCGGGGATACTCCATCCCCG
1 AATTT-TCATAATCGGGGATACTCCAACCCCG
10089 TTATTTTCGA
Statistics
Matches: 203, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
50 8 0.04
51 188 0.93
52 7 0.03
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
AATTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
Found at i:22667 original size:11 final size:11
Alignment explanation
Indices: 22651--22687 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
22641 TCTCTTCAAA
*
22651 AAAAAAAAAAG
1 AAAAAAAAAAC
22662 AAAAAAAAAAC
1 AAAAAAAAAAC
22673 AAAAAAAAAAC
1 AAAAAAAAAAC
22684 AAAA
1 AAAA
22688 CAAAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.92, C:0.05, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:22668 original size:15 final size:15
Alignment explanation
Indices: 22648--22713 Score: 71
Period size: 15 Copynumber: 4.3 Consensus size: 15
22638 CCTTCTCTTC
22648 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
22663 AAAAAAAAACAAAA-A
1 AAAAAAAAA-AAAAGA
*
22678 AAAAACAAAACAAAGA
1 AAAAA-AAAAAAAAGA
* * *
22694 AAAAGAGAGAAAAGA
1 AAAAAAAAAAAAAGA
22709 AAAAA
1 AAAAA
22714 CCTACTTAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
15 29 0.69
16 13 0.31
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:22669 original size:16 final size:16
Alignment explanation
Indices: 22648--22697 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
22638 CCTTCTCTTC
22648 AAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAGAA
*
22664 AAAAAAAACAAAA-AA
1 AAAAAAAAAAAAAGAA
* *
22679 AAAACAAAACAAAGAA
1 AAAAAAAAAAAAAGAA
22695 AAA
1 AAA
22698 GAGAGAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.90, C:0.06, G:0.04, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAGAA
Found at i:22713 original size:1 final size:1
Alignment explanation
Indices: 22648--22697 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
22638 CCTTCTCTTC
* * * * *
22648 AAAAAAAAAAAAAGAAAAAAAAAACAAAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22698 GAGAGAAAAG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.90, C:0.06, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:23763 original size:55 final size:55
Alignment explanation
Indices: 23678--24900 Score: 1809
Period size: 55 Copynumber: 22.3 Consensus size: 55
23668 TCCGCTTTTT
* * *
23678 AGTCCTCAAAGAGCAGGACACGTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
23733 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
23788 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
23843 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
23898 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA--TTGTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-T-C
*
23953 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
24008 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
24063 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
24118 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA--TTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
24172 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
24227 AGTCC-CAAAGAGCAGGACACC-TTTAAAGCCCACACAAGTTGGTGG-ACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* **
24279 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCGTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTT--T-C
*
24337 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
24392 AGTCCTCAAAGAGCAGGACACC-TTTCAAGCCCACACAAGTTGGTGGCA--TTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
24444 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCA-ACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
24498 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
24553 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
24608 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* * *
24663 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
24718 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
24773 ATTCCCCAAAGAGCAGGACA-CTTTTCAAAGCCCACACAAGTGGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * *
24828 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
24883 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
24901 TACAATTTAT
Statistics
Matches: 1095, Mismatches: 51, Indels: 44
0.92 0.04 0.04
Matches are distributed among these distances:
52 51 0.05
53 50 0.05
54 164 0.15
55 762 0.70
56 15 0.01
57 3 0.00
58 50 0.05
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:24303 original size:26 final size:25
Alignment explanation
Indices: 24219--24305 Score: 70
Period size: 26 Copynumber: 3.4 Consensus size: 25
24209 AAGTTGGTGG
24219 CACCTTTCAGTCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCAAAGAGCAGGA
* ** *
24244 CACCTTTAAAG-CCCACACA-AGTTGGTG
1 CACCTTT-CAGTCCCA-A-AGAGCAGG-A
*
24271 GACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCC-CAAAGAGCAGGA
24297 CACCTTTCA
1 CACCTTTCA
24306 AAGCCCACAC
Statistics
Matches: 45, Mismatches: 10, Indels: 13
0.66 0.15 0.19
Matches are distributed among these distances:
25 11 0.24
26 18 0.40
27 14 0.31
28 2 0.04
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (25 bp):
CACCTTTCAGTCCCAAAGAGCAGGA
Found at i:24828 original size:29 final size:29
Alignment explanation
Indices: 24681--24828 Score: 71
Period size: 29 Copynumber: 5.3 Consensus size: 29
24671 AAGAACAGGA
*
24681 CACCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
* * * * * * *
24710 CA-TTTTC-CAGTCCTCA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
24736 CACCTCTT-AAAGCCCACACAAGTTGGTGG
1 CACCT-TTCAAAGCCCACACAAGTGGGTGG
** * * *
24765 CACCTTTC-ATTCCC-CA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
24791 CACTTTTCAAAGCCCACACAAGTGGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
24820 CACCTTTCA
1 CACCTTTCA
24829 GTCCTCAAAG
Statistics
Matches: 78, Mismatches: 29, Indels: 24
0.60 0.22 0.18
Matches are distributed among these distances:
26 17 0.22
27 15 0.19
28 22 0.28
29 24 0.31
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (29 bp):
CACCTTTCAAAGCCCACACAAGTGGGTGG
Found at i:25501 original size:1 final size:1
Alignment explanation
Indices: 25495--25525 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
25485 AAAGTGTTTG
25495 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25526 TTTTAAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25555 original size:21 final size:21
Alignment explanation
Indices: 25531--25587 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
25521 AAAAATTTTA
25531 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
25552 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
25573 AATGTATCGATACAT
1 AATGTATCGATACAT
25588 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:25667 original size:19 final size:19
Alignment explanation
Indices: 25643--25710 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
25633 AATTCAACAA
25643 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
25662 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
25677 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
25694 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
25711 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:25682 original size:13 final size:13
Alignment explanation
Indices: 25664--25688 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25654 ACATAAGTTT
25664 TGTATCGATACAA
1 TGTATCGATACAA
25677 TGTATCGATACA
1 TGTATCGATACA
25689 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:25686 original size:32 final size:32
Alignment explanation
Indices: 25645--25707 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
25635 TTCAACAATT
*
25645 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
25677 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
25708 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:25768 original size:13 final size:13
Alignment explanation
Indices: 25750--25775 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25740 CATTTTTCTG
25750 TGTATCGATACAT
1 TGTATCGATACAT
25763 TGTATCGATACAT
1 TGTATCGATACAT
25776 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:25772 original size:33 final size:33
Alignment explanation
Indices: 25730--25796 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
25720 GCCAAGGAAA
***
25730 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
25763 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
25796 T
1 T
25797 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:28290 original size:52 final size:51
Alignment explanation
Indices: 28121--28402 Score: 259
Period size: 52 Copynumber: 5.5 Consensus size: 51
28111 TCAAGTTTCT
* * * *
28121 CAATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTA-CTTCTAAAACAT
1 CAATTTTTCATAATCGGGGATACTCCAACCTCGGTTTTATTTTC-AAAACAC
* * * * * * * *
28172 TAATTTTCCACAATCGGGGACACTCCAA-CTCCGATTTATTCTCAGAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCTCGGTTTTATTTTCAAAACAC
*
28222 CAATTTTTCCACAATCGGGGATACTCCAACCTCGGTTTTATTTTCAAAACAC
1 CAATTTTT-CATAATCGGGGATACTCCAACCTCGGTTTTATTTTCAAAACAC
* * *
28274 CAATTTTTCTATAATCGGGGATACTCCAA-CTCCGATTTGTATTTCCAAAATAC
1 CAATTTTTC-ATAATCGGGGATACTCCAACCT-CGGTTT-TATTTTCAAAACAC
* * * * * *
28327 TAACTTTTCATCATCGGGGATACTCCAACC-CCGTTTT-TTTTCTAAAATAT
1 CAATTTTTCATAATCGGGGATACTCCAACCTCGGTTTTATTTTC-AAAACAC
* *
28377 TAATTTCTCATAATCGGGGATACTCC
1 CAATTTTTCATAATCGGGGATACTCC
28403 TCCCCGTTAT
Statistics
Matches: 191, Mismatches: 32, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
49 4 0.02
50 48 0.25
51 52 0.27
52 67 0.35
53 20 0.10
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.34
Consensus pattern (51 bp):
CAATTTTTCATAATCGGGGATACTCCAACCTCGGTTTTATTTTCAAAACAC
Found at i:28435 original size:77 final size:76
Alignment explanation
Indices: 28342--28489 Score: 201
Period size: 77 Copynumber: 1.9 Consensus size: 76
28332 TTTCATCATC
* * * * *
28342 GGGGATACTCCAACCCC-GTTTTTTTTCTAAAATATTAATTTCTCATAATCGGGGATACTCC-TC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAA-TTCT--TAATCGGGGATACTCCAAC
28405 CCCGTTATTTTCGG
63 CCCGTTATTTTCGG
*
28419 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTCTTCATCGGGGATACTCCAACCCC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTCTTAATCGGGGATACTCCAACCCC
28484 GTTATT
66 GTTATT
28490 CTCATAATCA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
75 15 0.24
76 10 0.16
77 21 0.33
78 17 0.27
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.34
Consensus pattern (76 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTCTTAATCGGGGATACTCCAACCCC
GTTATTTTCGG
Found at i:30058 original size:30 final size:30
Alignment explanation
Indices: 30019--30195 Score: 148
Period size: 30 Copynumber: 5.9 Consensus size: 30
30009 CAAATCTCTC
* *
30019 TTCTTAAAGTCCACGACTCAGTGGCATCTT
1 TTCTCAAAGTCCACAACTCAGTGGCATCTT
* *
30049 TTCTCAAAGTCCACGACTCAGTGGCATTTTTT
1 TTCTCAAAGTCCACAACTCAGTGGCA--TCTT
30081 TTCTTCAAAGTCCAC-ACTCA-TGGCAATCTT
1 TTC-TCAAAGTCCACAACTCAGTGGC-ATCTT
* * * * *
30111 TTCTCCAAAGCCCACTAGTTAGTGTCCATCTT
1 TTCT-CAAAGTCCACAACTCAGTG-GCATCTT
* *
30143 TT-TC-AAGTCCACAAGTTAGTGGCATCTT
1 TTCTCAAAGTCCACAACTCAGTGGCATCTT
* *
30171 TT-TCAAAGCCCACAAGTCAGTGGCA
1 TTCTCAAAGTCCACAACTCAGTGGCA
30196 ACCTTTAAAA
Statistics
Matches: 126, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
28 10 0.08
29 34 0.27
30 41 0.33
31 8 0.06
32 21 0.17
33 12 0.10
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (30 bp):
TTCTCAAAGTCCACAACTCAGTGGCATCTT
Found at i:30146 original size:63 final size:62
Alignment explanation
Indices: 30019--30192 Score: 164
Period size: 63 Copynumber: 2.9 Consensus size: 62
30009 CAAATCTCTC
* * *
30019 TTCTTAAAGTCCACGACTCAGTGGCATCTTTTCTCAAAGTCCACGACTCAGTGGCATTTTTT
1 TTCTTAAAGTCCACGACTCAGTGGCATCTTTTCTCAAAGCCCACGACTCAGTGCCATTCTTT
* * *
30081 TTCTTCAAAGTCCAC-ACTCA-TGGCAATCTTTTCTCCAAAGCCCACTAGTTAGTGTCCA-TCTT
1 TTCTT-AAAGTCCACGACTCAGTGGC-ATCTTTTCT-CAAAGCCCACGACTCAGTG-CCATTCTT
30143 T
62 T
* * * * *
30144 TTC---AAGTCCACAAGTTAGTGGCATCTTTT-TCAAAGCCCACAAGTCAGTG
1 TTCTTAAAGTCCACGACTCAGTGGCATCTTTTCTCAAAGCCCACGACTCAGTG
30193 GCAACCTTTA
Statistics
Matches: 96, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
58 17 0.18
59 9 0.09
60 10 0.10
61 8 0.08
62 19 0.20
63 31 0.32
64 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (62 bp):
TTCTTAAAGTCCACGACTCAGTGGCATCTTTTCTCAAAGCCCACGACTCAGTGCCATTCTTT
Found at i:30193 original size:29 final size:29
Alignment explanation
Indices: 30036--30254 Score: 139
Period size: 29 Copynumber: 7.5 Consensus size: 29
30026 AGTCCACGAC
* * *
30036 TCAGTGGCATCTTTTCTCAAAGTCCACGAC
1 TCAGTGGCATCTTTT-TCAAAGCCCACAAG
* * *
30066 TCAGTGGCATTTTTTTTCTTCAAAGTCCAC-AC
1 TCAGTGGCA---TCTTT-TTCAAAGCCCACAAG
*
30098 TCA-TGGCAATCTTTTCTCCAAAGCCCACTAG
1 TCAGTGGC-ATCTTTT-T-CAAAGCCCACAAG
* * *
30129 TTAGTGTCCATCTTTTTC-AAGTCCACAAG
1 TCAGTG-GCATCTTTTTCAAAGCCCACAAG
*
30158 TTAGTGGCATCTTTTTCAAAGCCCACAAG
1 TCAGTGGCATCTTTTTCAAAGCCCACAAG
* * * *
30187 TCAGTGGCAAC-CTTTAAAAGCACACAAG
1 TCAGTGGCATCTTTTTCAAAGCCCACAAG
* *
30215 TC-GTGGCAAC--CTTCAAAGCCCACAAG
1 TCAGTGGCATCTTTTTCAAAGCCCACAAG
*
30241 TCAATGGCA-CTTTT
1 TCAGTGGCATCTTTT
30255 CCTTTTAAGT
Statistics
Matches: 155, Mismatches: 20, Indels: 30
0.76 0.10 0.15
Matches are distributed among these distances:
26 16 0.10
27 13 0.08
28 28 0.18
29 39 0.25
30 19 0.12
31 8 0.05
32 15 0.10
33 16 0.10
34 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (29 bp):
TCAGTGGCATCTTTTTCAAAGCCCACAAG
Found at i:30248 original size:27 final size:28
Alignment explanation
Indices: 30143--30249 Score: 121
Period size: 28 Copynumber: 3.9 Consensus size: 28
30133 TGTCCATCTT
* * * *
30143 TTTC-AAGTCCACAAGTTAGTGGCATCTT
1 TTTCAAAGCCCACAAGTCAGTGGCAAC-C
30171 TTTCAAAGCCCACAAGTCAGTGGCAACC
1 TTTCAAAGCCCACAAGTCAGTGGCAACC
* *
30199 TTTAAAAGCACACAAGTC-GTGGCAACC
1 TTTCAAAGCCCACAAGTCAGTGGCAACC
*
30226 -TTCAAAGCCCACAAGTCAATGGCA
1 TTTCAAAGCCCACAAGTCAGTGGCA
30250 CTTTTCCTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
26 15 0.22
27 14 0.21
28 20 0.29
29 19 0.28
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCAACC
Found at i:30515 original size:35 final size:34
Alignment explanation
Indices: 30251--30798 Score: 436
Period size: 33 Copynumber: 16.7 Consensus size: 34
30241 TCAATGGCAC
30251 TTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT
* * * *
30285 GTTTCCTATTAAGTCCACAATTCCTGTGGCAC-AT
1 TTTTCCTTTTAAGTCCACAACTCC-GTGGCACTTT
**
30319 TTTT-CTTTTAAGTCCACAACTCCGTGGCACACT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT
* * *
30352 TTTT-CTTTTAAAGCCCACAACTCCATGGC-C-CT
1 TTTTCCTTTT-AAGTCCACAACTCCGTGGCACTTT
30384 TTTT--TTTTAAGTCCACAACT-CGTGGCACATTT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCAC-TTT
* * * *
30416 TCTT--TTTAAAG-CCA-TACTCCGTGGCAC--C
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT
* *
30444 TTTTCTTTTTAAGTCCACGACT-CG-GGCACTTTTTT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCAC---TTT
* **
30479 TTTTCCTTTTAAG-CC-CACCTCCGTGGCATCCCT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCA-CTTT
** *
30512 TTTTCC-TAAAAGTCCCACAACTCTGTGGCA-TTT
1 TTTTCCTTTTAAGT-CCACAACTCCGTGGCACTTT
30545 TTTTCCTTTTAA-TCCACAACTCCGTGGCAC-TT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT
* * **
30577 TGTTCCATTTAAGTCCACAACTCCGTGGCACCCT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT
* * **
30611 TTTTCCTGTTTAAGCCCACACCTCTATGGCATCCTTT
1 TTTTCCT-TTTAAGTCCACAACTCCGTGGCA--CTTT
* *
30648 TTTTCC-TATAAGTCCACAACTCCATGGCA-TTT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT
*
30680 TTTTCCTTTTAAGTCCACAACTCCGTGGCAC-CT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT
* * * * *
30713 TGTTCCATTTAAGTCCATAACTCCGTGGCAATCT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT
*
30747 TTTT-CTTTT-AGTCC-CAACTCCGT-GCA-TCT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT
*
30776 TTTTCTTTTTAAGTCCACAACTC
1 TTTTCCTTTTAAGTCCACAACTC
30799 TATGGCACAA
Statistics
Matches: 418, Mismatches: 61, Indels: 72
0.76 0.11 0.13
Matches are distributed among these distances:
28 3 0.01
29 12 0.03
30 33 0.08
31 33 0.08
32 77 0.18
33 117 0.28
34 62 0.15
35 72 0.17
36 1 0.00
37 8 0.02
ACGTcount: A:0.20, C:0.30, G:0.12, T:0.39
Consensus pattern (34 bp):
TTTTCCTTTTAAGTCCACAACTCCGTGGCACTTT
Found at i:30785 original size:136 final size:136
Alignment explanation
Indices: 30261--30751 Score: 461
Period size: 136 Copynumber: 3.7 Consensus size: 136
30251 TTTTCCTTTT
* * * * * *
30261 AAGT-CCACAACTCCGTGGCACTTTGTTTCCTATTAAGTCCACAATTCCTGTGGCACATT-TTTC
1 AAGTCCCACAACTCCATGGCA-TTTTTTTCCTTTTAA-TCCACAACTCC-GTGGCACCTTGTTCC
* *
30324 TTTTAAGTCCACAACTCCGTGGC-ACACTTTTT-CT-TTTAAAGCCCACAACTCCATGGC--CCT
63 ATTTAAGTCCACAACTCCGTGGCAAC-CTTTTTCCTGTTT-AAGCCCACACCTCCATGGCATCCT
*
30384 TTTTTT--T-T
126 TTTTTTCCTAA
* ** * * * **
30392 AAGT-CCACAACT-CGTGGCA-CATTTTCTTTTTAAAGCCA-TACTCCGTGGCACCTT-TTCTTT
1 AAGTCCCACAACTCCATGGCATTTTTTTCCTTTT-AATCCACAACTCCGTGGCACCTTGTTCCAT
* * *
30452 TTAAGTCCACGACT-CG-GGC-ACTTTTTTTTTTCCT-TTTAAG-CC-CACCTCCGTGGCATCC-
65 TTAAGTCCACAACTCCGTGGCAAC----CTTTTTCCTGTTTAAGCCCACACCTCCATGGCATCCT
*
30510 CTTTTTCCTAA
126 TTTTTTCCTAA
** *
30521 AAGTCCCACAACTCTGTGGCATTTTTTTCCTTTTAATCCACAACTCCGTGGCACTTTGTTCCATT
1 AAGTCCCACAACTCCATGGCATTTTTTTCCTTTTAATCCACAACTCCGTGGCACCTTGTTCCATT
* *
30586 TAAGTCCACAACTCCGTGGCACCCTTTTTCCTGTTTAAGCCCACACCTCTATGGCATCCTTTTTT
66 TAAGTCCACAACTCCGTGGCAACCTTTTTCCTGTTTAAGCCCACACCTCCATGGCATCCTTTTTT
*
30651 TCCTAT
131 TCCTAA
30657 AAGT-CCACAACTCCATGGCATTTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCAT
1 AAGTCCCACAACTCCATGGCATTTTTTTCCTTTTAA-TCCACAACTCCGTGGCACCTTGTTCCAT
* *
30721 TTAAGTCCATAACTCCGTGGCAATCTTTTTC
65 TTAAGTCCACAACTCCGTGGCAACCTTTTTC
30752 TTTTAGTCCC
Statistics
Matches: 297, Mismatches: 40, Indels: 41
0.79 0.11 0.11
Matches are distributed among these distances:
124 5 0.02
125 12 0.04
126 33 0.11
127 14 0.05
128 16 0.05
129 6 0.02
130 15 0.05
131 23 0.08
132 31 0.10
133 23 0.08
134 4 0.01
135 46 0.15
136 69 0.23
ACGTcount: A:0.20, C:0.30, G:0.12, T:0.37
Consensus pattern (136 bp):
AAGTCCCACAACTCCATGGCATTTTTTTCCTTTTAATCCACAACTCCGTGGCACCTTGTTCCATT
TAAGTCCACAACTCCGTGGCAACCTTTTTCCTGTTTAAGCCCACACCTCCATGGCATCCTTTTTT
TCCTAA
Done.