Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold621
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: 42711
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:885 original size:13 final size:13
Alignment explanation
Indices: 875--906 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
865 TGTAAAATCT
875 AAAATTAAAATTA
1 AAAATTAAAATTA
888 AAAATT--AATTA
1 AAAATTAAAATTA
899 AAAATTAA
1 AAAATTAA
907 TAAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTA
Found at i:910 original size:10 final size:11
Alignment explanation
Indices: 883--912 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
873 CTAAAATTAA
883 AATTAAAAATT
1 AATTAAAAATT
894 AATTAAAAATT
1 AATTAAAAATT
905 AA-TAAAAA
1 AATTAAAAA
913 CAAAAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AATTAAAAATT
Found at i:2543 original size:17 final size:16
Alignment explanation
Indices: 2508--2545 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2498 TATACTGTTG
* *
2508 AAAAAAGTTTAGGTTA
1 AAAAAAGCTTAAGTTA
2524 AAAAAAGCTTAAGTTA
1 AAAAAAGCTTAAGTTA
2540 AAAAAA
1 AAAAAA
2546 TTGTGGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.61, C:0.03, G:0.13, T:0.24
Consensus pattern (16 bp):
AAAAAAGCTTAAGTTA
Found at i:5269 original size:16 final size:15
Alignment explanation
Indices: 5226--5277 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 15
5216 ATAAATCAAA
5226 AATATTTAATTATTTTT
1 AATA-TTAA-TATTTTT
*
5243 AATATAAAATATTTTT
1 AATAT-TAATATTTTT
5259 AATTATTAATATTTATT
1 AA-TATTAATATTT-TT
5276 AA
1 AA
5278 AAAATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATATTAATATTTTT
Found at i:5381 original size:16 final size:16
Alignment explanation
Indices: 5362--5404 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
5352 TATTATTAAA
**
5362 TTAAAAAATTAATTTT
1 TTAAAAAATTAATAAT
*
5378 TTAAAATATTAATAAT
1 TTAAAAAATTAATAAT
*
5394 ATAAAAAATTA
1 TTAAAAAATTA
5405 TGTAAATACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAAAAATTAATAAT
Found at i:5656 original size:14 final size:16
Alignment explanation
Indices: 5632--5664 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5622 GTAAAAGACA
5632 TTAATTTC-AAAAAAT
1 TTAATTTCAAAAAAAT
5647 TTAA-TTCAAAAAAAT
1 TTAATTTCAAAAAAAT
5662 TTA
1 TTA
5665 TCTCAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAATTTCAAAAAAAT
Found at i:8046 original size:12 final size:13
Alignment explanation
Indices: 8024--8056 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
8014 TTACTATCGT
*
8024 TAATTTATTTATA
1 TAATATATTTATA
8037 TAA-ATATTTATA
1 TAATATATTTATA
8049 TAATATAT
1 TAATATAT
8057 GAAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATATATTTATA
Found at i:8899 original size:2 final size:2
Alignment explanation
Indices: 8892--8958 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
8882 TTGTTATAGT
8892 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8934 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
8959 TTGTTGGTAC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10561 original size:21 final size:21
Alignment explanation
Indices: 10535--10590 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
10525 TATATAAATG
*
10535 AATGTATCGATATATGCTTAA
1 AATGTATCGATACATGCTTAA
10556 AATGTATCGATACATGCTTAA
1 AATGTATCGATACATGCTTAA
10577 AATGTATCGATACA
1 AATGTATCGATACA
10591 AAACCACCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATGCTTAA
Found at i:10641 original size:20 final size:20
Alignment explanation
Indices: 10616--10694 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
10606 CTGCCAAGGA
* *
10616 AATGTATTGATACATTAATC
1 AATGTATCGATACATTTATC
10636 AATGTATCGATACATGCTTA-C
1 AATGTATCGATACAT--TTATC
* *
10657 AATTGTATTGATACATTTCTC
1 AA-TGTATCGATACATTTATC
*
10678 ATTGTATCGATACATTT
1 AATGTATCGATACATTT
10695 TGCATTTTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
20 30 0.61
21 5 0.10
22 14 0.29
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTTATC
Found at i:17640 original size:13 final size:13
Alignment explanation
Indices: 17620--17653 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
17610 AAGAAAATGC
17620 ACAAAAAATGAAAA
1 ACAAAAAA-GAAAA
17634 A-AAAAAAGAAAA
1 ACAAAAAAGAAAA
17646 ACAAAAAA
1 ACAAAAAA
17654 AAATGCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 12 0.63
14 1 0.05
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.03
Consensus pattern (13 bp):
ACAAAAAAGAAAA
Found at i:19055 original size:32 final size:32
Alignment explanation
Indices: 18963--20037 Score: 863
Period size: 32 Copynumber: 33.6 Consensus size: 32
18953 GGCACCATTT
* *
18963 TTCTCCAAAGTCCACACAAGCTGGTGGCAACC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
* *
18995 -T-TCTAAAGCCTACACAAG-TCGGTAGCAACC
1 TTCTCTAAAGCCCACACAAGCT-GGTGGCAACC
*
19025 TTCTCTAAAGCCCACATAAGCTGGTGGCAACC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
* *
19057 TTTCTCTAAAGCCCACACAAGCTAGTGGTAACC
1 -TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
* * *
19090 TTCTCCAAAGCCCACACAAGCTGATGGTAACC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
*
19122 -TCTCTAAAGCCCACACAAGCCGGTGGCAACC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
* * * *
19153 TTCTCCAAAACCAATACAAGCTGGTGGCAACC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
* * *
19185 -CCTCTAAAGCCCACACAAGTTGATGGCAACC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
* *
19216 TTCTCTAAACCCCACACAAGCTAGTGGCAACCC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAA-CC
* * * * *
19249 ATTTTC-AAAGCCCACAGAAGTTAGTGCCAACC
1 -TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
* ***
19281 TTCTCTAAAGCCCACATAAGCTGGTAAAAACCC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAA-CC
* * *
19314 TTGTTTAAAGCCCACACAAG-TCGATGGCAACCC
1 TTCTCTAAAGCCCACACAAGCT-GGTGGCAA-CC
19347 TTCTC-AAAGCCCACACAAG-TAGGTGGCAACC
1 TTCTCTAAAGCCCACACAAGCT-GGTGGCAACC
*
19378 TTCTCTAAAGCCCACACAAG-TCAGTGGCAACC
1 TTCTCTAAAGCCCACACAAGCT-GGTGGCAACC
19410 TT-TCTAAAGCCCACACAAGCTGGTGGCAACC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
* ** *
19441 TT-TTTCAAAGTTCATACAAGCTGGTGGCAACAC
1 TTCTCT-AAAGCCCACACAAGCTGGTGGCAAC-C
*
19474 --CTCTAAAGCCCACACAAGTTGGTGGCAACC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
* * * *
19504 TTCTCCAAAGCCCATATAAGCTAGTGGCAACC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
* * * *
19536 --CTCTAAAACTCACACAAGTTTGTGGCAACC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
* * * *
19566 TTCTCTAAAACCCACACAAACTGCTAGCAACCC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAA-CC
* * * *
19599 TTTTTTCAAAGCCCACATAAG-TCGATGGCAACCC
1 TTCTCT-AAAGCCCACACAAGCT-GGTGGCAA-CC
* *
19633 TTATC-AAAGCCCACACAAG-TCGGTGGTAACC
1 TTCTCTAAAGCCCACACAAGCT-GGTGGCAACC
* * *
19664 TTCTCTAAAGCCTACACAAGCTAGTAGCAAGCC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAA-CC
* * * *
19697 TTCTTTAAAGCCCACACAAGTTAGTGACAACCC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAA-CC
* * *
19730 TTCTC-AAAGCCCACATAAGCCGGTGGTAACTC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAAC-C
* *
19762 TTCTC-AAAGCCCACACAAAC-CGTGGCAACCC
1 TTCTCTAAAGCCCACACAAGCTGGTGGCAA-CC
19793 TTCTC-AAAGCCCACACAAG-TCGGTGGCAACC
1 TTCTCTAAAGCCCACACAAGCT-GGTGGCAACC
* * * *
19824 -CCTCTTAAAAGCTCACATAAGCCGGTGGCAACC
1 TTCTC-T-AAAGCCCACACAAGCTGGTGGCAACC
* *
19857 TCTCTCAAAAGCCCACACAA-ATAGGTGGCAACCC
1 T-TCTCTAAAGCCCACACAAGCT-GGTGGCAA-CC
* *
19891 TT-T-TAAAGCCCACACAAG-TCGATGGTAACCC
1 TTCTCTAAAGCCCACACAAGCT-GGTGGCAA-CC
*
19922 TTTTC-AAAGCCCACACAAG-TCGGTGGCAACCC
1 TTCTCTAAAGCCCACACAAGCT-GGTGGCAA-CC
*
19954 TTCTCTAAAGCCCACACAAG-TCGATGGCAACC
1 TTCTCTAAAGCCCACACAAGCT-GGTGGCAACC
*
19986 --CTCTAAAAGCCCACACAA-ATCGGTGGCAACCCC
1 TTCTCT-AAAGCCCACACAAGCT-GGTGGCAA--CC
*
20019 TT-TCAAAAGCCCACACAAG
1 TTCTCTAAAGCCCACACAAG
20038 TCGGTGACAT
Statistics
Matches: 850, Mismatches: 143, Indels: 98
0.78 0.13 0.09
Matches are distributed among these distances:
29 1 0.00
30 54 0.06
31 196 0.23
32 361 0.42
33 203 0.24
34 32 0.04
35 3 0.00
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.20
Consensus pattern (32 bp):
TTCTCTAAAGCCCACACAAGCTGGTGGCAACC
Found at i:19158 original size:63 final size:63
Alignment explanation
Indices: 18963--20043 Score: 801
Period size: 63 Copynumber: 16.9 Consensus size: 63
18953 GGCACCATTT
* * *
18963 TTCTCCAAAGTCCACACAAGCTGGTGGCAACCT-TCTAAAGCCTACACAAGTCGGTAGCAACC
1 TTCTCCAAAGCCCACACAAGCTGGTGGCAACCTCTCTAAAGCCCACACAAGTCGGTGGCAACC
* * * *
19025 TTCTCTAAAGCCCACATAAGCTGGTGGCAACCTTTCTCTAAAGCCCACACAAG-CTAGTGGTAAC
1 TTCTCCAAAGCCCACACAAGCTGGTGGCAACC--TCTCTAAAGCCCACACAAGTC-GGTGGCAAC
19089 C
63 C
* * *
19090 TTCTCCAAAGCCCACACAAGCTGATGGTAACCTCTCTAAAGCCCACACAAGCCGGTGGCAACC
1 TTCTCCAAAGCCCACACAAGCTGGTGGCAACCTCTCTAAAGCCCACACAAGTCGGTGGCAACC
* * * * * *
19153 TTCTCCAAAACCAATACAAGCTGGTGGCAACCCCTCTAAAGCCCACACAAGTTGATGGCAACC
1 TTCTCCAAAGCCCACACAAGCTGGTGGCAACCTCTCTAAAGCCCACACAAGTCGGTGGCAACC
* * * * * ** *
19216 TTCTCTAAACCCCACACAAGCTAGTGGCAACC-CATTTTCAAAGCCCACAGAAGTTAGTGCCAAC
1 TTCTCCAAAGCCCACACAAGCTGGTGGCAACCTC--TCT-AAAGCCCACACAAGTCGGTGGCAAC
19280 C
63 C
* * *** * * *
19281 TTCTCTAAAGCCCACATAAGCTGGTAAAAACCCTTGTTTAAAGCCCACACAAGTCGATGGCAACC
1 TTCTCCAAAGCCCACACAAGCTGGTGGCAA-CC-TCTCTAAAGCCCACACAAGTCGGTGGCAA-C
19346 C
63 C
*
19347 TTCT-CAAAGCCCACACAAG-TAGGTGGCAACCTTCTCTAAAGCCCACACAAGTCAGTGGCAACC
1 TTCTCCAAAGCCCACACAAGCT-GGTGGCAACC-TCTCTAAAGCCCACACAAGTCGGTGGCAACC
* * * ** *
19410 TT-TCTAAAGCCCACACAAGCTGGTGGCAACCTTTTTCAAAGTTCATACAAG-CTGGTGGCAACA
1 TTCTCCAAAGCCCACACAAGCTGGTGGCAACCTCTCT-AAAGCCCACACAAGTC-GGTGGCAAC-
19473 C
63 C
* * * * * *
19474 --CTCTAAAGCCCACACAAGTTGGTGGCAACCTTCTCCAAAGCCCATATAAG-CTAGTGGCAACC
1 TTCTCCAAAGCCCACACAAGCTGGTGGCAACC-TCTCTAAAGCCCACACAAGTC-GGTGGCAACC
* * * * * * * * *
19536 --CTCTAAAACTCACACAAGTTTGTGGCAACCTTCTCTAAAACCCACACAA-ACTGCTAGCAACC
1 TTCTCCAAAGCCCACACAAGCTGGTGGCAACC-TCTCTAAAGCCCACACAAGTC-GGTGGCAA-C
19598 C
63 C
* * * * * *
19599 TTTTTTCAAAGCCCACATAAG-TCGATGGCAACC-CTTATCAAAGCCCACACAAGTCGGTGGTAA
1 -TTCTCCAAAGCCCACACAAGCT-GGTGGCAACCTC-TCT-AAAGCCCACACAAGTCGGTGGCAA
19662 CC
62 CC
* * * * * ** *
19664 TTCTCTAAAGCCTACACAAGCTAGTAGCAAGCCTTCTTTAAAGCCCACACAAGTTAGTGACAACC
1 TTCTCCAAAGCCCACACAAGCTGGTGGCAA-CC-TCTCTAAAGCCCACACAAGTCGGTGGCAA-C
19729 C
63 C
* * * * *
19730 TTCT-CAAAGCCCACATAAGCCGGTGGTAA-CTCTTCTCAAAGCCCACACAA-ACCGTGGCAACC
1 TTCTCCAAAGCCCACACAAGCTGGTGGCAACCTC-TCT-AAAGCCCACACAAGTCGGTGGCAA-C
19792 C
63 C
* * * *
19793 TTCT-CAAAGCCCACACAAG-TCGGTGGCAACCCCTCTTAAAAGCTCACATAAGCCGGTGGCAAC
1 TTCTCCAAAGCCCACACAAGCT-GGTGGCAACCTCTC-T-AAAGCCCACACAAGTCGGTGGCAAC
19856 C
63 C
* * * * *
19857 TCTCTCAAAAGCCCACACAA-ATAGGTGGCAACC-CTTTTAAAGCCCACACAAGTCGATGGTAAC
1 T-TCTCCAAAGCCCACACAAGCT-GGTGGCAACCTC-TCTAAAGCCCACACAAGTCGGTGGCAA-
19920 CC
62 CC
* *
19922 TT-TTCAAAGCCCACACAAG-TCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGATGGCAAC
1 TTCTCCAAAGCCCACACAAGCT-GGTGGCAA-CC-TCTCTAAAGCCCACACAAGTCGGTGGCAAC
19985 C
63 C
* * * * *
19986 CTCT-AAAAGCCCACACAA-ATCGGTGGCAACCCCTTTCAAAAGCCCACACAAGTCGGTG
1 TTCTCCAAAGCCCACACAAGCT-GGTGGCAA--CCTCTCTAAAGCCCACACAAGTCGGTG
20044 ACATCTCTTT
Statistics
Matches: 823, Mismatches: 144, Indels: 102
0.77 0.13 0.10
Matches are distributed among these distances:
62 87 0.11
63 268 0.33
64 159 0.19
65 225 0.27
66 82 0.10
67 2 0.00
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.20
Consensus pattern (63 bp):
TTCTCCAAAGCCCACACAAGCTGGTGGCAACCTCTCTAAAGCCCACACAAGTCGGTGGCAACC
Found at i:19464 original size:288 final size:282
Alignment explanation
Indices: 18975--20025 Score: 1088
Period size: 288 Copynumber: 3.7 Consensus size: 282
18965 CTCCAAAGTC
* * * * *
18975 CACACAAGCTGGTGGCAACC-T-TCTAAAGCCTACACAAGTCGGTAGCAA-CCTTCTCTAAAGCC
1 CACACAAGTTAGTGGCAACCTTCTCTAAAGCCCACACAACT-GGTAGCAACCCTT-TTTAAAGCC
* * * * *
19037 CACATAAG-CTGGTGGCAACCTTTCTCTAAAGCCCACACAAGCTA-GTGGTAACCTTCTCCAAAG
64 CACACAAGTC-GATGGCAACCCTTCTC-AAAGCCCACACAAG-TAGGTGGCAACCTTCTCTAAAG
* * * *
19100 CCCACACAAGCTGATGGTAACCTCTCTAAAGCCCACACAAGCCGGTGGCAA-CCTTCTCCAAA-A
126 CCCACACAAGCAGATGGCAACCTCTCTAAAGCCCACACAAGCTGGTGGCAACCCTT-TTCAAAGA
* *
19163 CCAATACAAGCTGGTGGCAACCCCTCTAAAGCCCACACAAGTTGATGGCAACCTTCTCTAAACCC
190 CC-ATACAAGCTGGTGGCAACACCTCTAAAGCCCACACAAGTTG-TGGCAACCTTCTC-AAAGCC
*
19228 CACACAAGCTAGTGGCAACCCATTTTCAAAGCC
252 CACACAAGCTAGTGGCAACCC-TTTT-AAAGCT
* * * **
19261 CACAGAAGTTAGTGCCAACCTTCTCTAAAGCCCACATAAGCTGGTAAAAACCCTTGTTTAAAGCC
1 CACACAAGTTAGTGGCAACCTTCTCTAAAGCCCACACAA-CTGGTAGCAACCCTT-TTTAAAGCC
19326 CACACAAGTCGATGGCAACCCTTCTCAAAGCCCACACAAGTAGGTGGCAACCTTCTCTAAAGCCC
64 CACACAAGTCGATGGCAACCCTTCTCAAAGCCCACACAAGTAGGTGGCAACCTTCTCTAAAGCCC
* * **
19391 ACACAAGTCAG-TGGCAACCTTTCTAAAGCCCACACAAGCTGGTGGCAACCTTTTTCAAAGTTCA
129 ACACAAG-CAGATGGCAACCTCTCTAAAGCCCACACAAGCTGGTGGCAACCCTTTTCAAAGACCA
*
19455 TACAAGCTGGTGGCAACACCTCTAAAGCCCACACAAGTTGGTGGCAACCTTCTCCAAAGCCCATA
193 TACAAGCTGGTGGCAACACCTCTAAAGCCCACACAAGTT-GTGGCAACCTTCT-CAAAGCCCACA
* * *
19520 TAAGCTAGTGGCAACCC-TCTAAAACT
256 CAAGCTAGTGGCAACCCTTTTAAAGCT
* * *
19546 CACACAAGTTTGTGGCAACCTTCTCTAAAACCCACACAAACTGCTAGCAACCCTTTTTTCAAAGC
1 CACACAAGTTAGTGGCAACCTTCTCTAAAGCCCACAC-AACTGGTAGCAACCC-TTTTT-AAAGC
* * * *
19611 CCACATAAGTCGATGGCAACCCTTATCAAAGCCCACACAAGTCGGTGGTAACCTTCTCTAAAGCC
63 CCACACAAGTCGATGGCAACCCTTCTCAAAGCCCACACAAGTAGGTGGCAACCTTCTCTAAAGCC
* * * * * * * *
19676 TACACAAGCTAG-TAGCAAGCCTTCTTTAAAGCCCACACAAGTTAGTGACAACCCTTCTCAAAGC
128 CACACAAGC-AGATGGCAA-CC-TCTCTAAAGCCCACACAAGCTGGTGGCAACCCTTTTCAAAGA
* * * * * * ***
19740 CCACATAAGCCGGTGGTAACTCTTCTCAAAGCCCACACAAACCGTGGCAACCCTTCTCAAAGCCC
190 CCATACAAGCTGGTGGCAACACCTCT-AAAGCCCACACAAGTTGTGGCAA-CCTTCTCAAAGCCC
* *
19805 ACACAAG-TCGGTGGCAACCCCTCTTAAAAGCT
253 ACACAAGCT-AGTGGCAA-CCCT-TTTAAAGCT
* *** * * *
19837 CACATAAGCCGGTGGCAACCTCTCTCAAAAGCCCACACAAATAGGTGGCAACCC-TTTTAAAGCC
1 CACACAAGTTAGTGGCAACCT-TCTCTAAAGCCCACACAACT-GGTAGCAACCCTTTTTAAAGCC
* * *
19901 CACACAAGTCGATGGTAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCC
64 CACACAAGTCGATGGCAACCCTTCTCAAAGCCCACACAAGTAGGTGGCAA-CCTTCTCTAAAGCC
* *
19966 CACACAAGTC-GATGGCAACC-CTCTAAAAGCCCACACAA-ATCGGTGGCAACCCCTTTCAAA
128 CACACAAG-CAGATGGCAACCTCTCT-AAAGCCCACACAAGCT-GGTGGCAACCCTTTTCAAA
20026 AGCCCACACA
Statistics
Matches: 645, Mismatches: 90, Indels: 58
0.81 0.11 0.07
Matches are distributed among these distances:
285 50 0.08
286 102 0.16
287 10 0.02
288 283 0.44
289 119 0.18
290 31 0.05
291 27 0.04
292 23 0.04
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.20
Consensus pattern (282 bp):
CACACAAGTTAGTGGCAACCTTCTCTAAAGCCCACACAACTGGTAGCAACCCTTTTTAAAGCCCA
CACAAGTCGATGGCAACCCTTCTCAAAGCCCACACAAGTAGGTGGCAACCTTCTCTAAAGCCCAC
ACAAGCAGATGGCAACCTCTCTAAAGCCCACACAAGCTGGTGGCAACCCTTTTCAAAGACCATAC
AAGCTGGTGGCAACACCTCTAAAGCCCACACAAGTTGTGGCAACCTTCTCAAAGCCCACACAAGC
TAGTGGCAACCCTTTTAAAGCT
Found at i:20189 original size:52 final size:52
Alignment explanation
Indices: 20131--20308 Score: 164
Period size: 52 Copynumber: 3.4 Consensus size: 52
20121 AATGTTGTTG
*
20131 GCCTTGAATCAACATATTGGCA-CATTTTTCTTTCTTATGTCCAATATTGCTA
1 GCCTTGAATCAACATATTGGCACCATTTTTC-TTCTTAAGTCCAATATTGCTA
** * * ** **
20183 GCCTTGAATCAATGTATTGGCACCA-TTGTCATCTTTAAGTCTGATATCACTA
1 GCCTTGAATCAACATATTGGCACCATTTTTCTTC-TTAAGTCCAATATTGCTA
* * * * *
20235 GCCTTGAATCAGCATATTGGCATC-TTTATTATTCTTAAGCCCAATATTGTTA
1 GCCTTGAATCAACATATTGGCACCATTT-TTCTTCTTAAGTCCAATATTGCTA
* *
20287 GCCTTAAATCAGCATATTGGCA
1 GCCTTGAATCAACATATTGGCA
20309 TTCTTCTAAT
Statistics
Matches: 99, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
51 2 0.02
52 92 0.93
53 5 0.05
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (52 bp):
GCCTTGAATCAACATATTGGCACCATTTTTCTTCTTAAGTCCAATATTGCTA
Found at i:20324 original size:104 final size:105
Alignment explanation
Indices: 20131--20361 Score: 236
Period size: 104 Copynumber: 2.2 Consensus size: 105
20121 AATGTTGTTG
* * * * *
20131 GCCTTGAATCAACATATTGGCA-CATTTTTCTTTCTTATGTCCAATATTGCTAGCCTTGAATCAA
1 GCCTTGAATCAGCATATTGGCATCATTTTTCATTCTTAAGCCCAATATTGCTAGCCTTAAATCAA
** * * **
20195 TGTATTGGCACCATTGTCATCTTTAAGTCTGATATCACTA
66 CATATTGGCACCATTCTAATCTTTAAGTCCAATATCACTA
*
20235 GCCTTGAATCAGCATATTGGCATC-TTTATT-ATTCTTAAGCCCAATATTGTTAGCCTTAAATCA
1 GCCTTGAATCAGCATATTGGCATCATTT-TTCATTCTTAAGCCCAATATTGCTAGCCTTAAATCA
* * * * * *
20298 GCATATTGGCATTC-TTCTAATTTTTAAGTCCAATGTCGCTC
65 ACATATTGGCA-CCATTCTAATCTTTAAGTCCAATATCACTA
* *
20339 GCTTTGAATCAGCACATTGGCAT
1 GCCTTGAATCAGCATATTGGCAT
20362 TCTTCTCATC
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
104 100 0.96
105 4 0.04
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (105 bp):
GCCTTGAATCAGCATATTGGCATCATTTTTCATTCTTAAGCCCAATATTGCTAGCCTTAAATCAA
CATATTGGCACCATTCTAATCTTTAAGTCCAATATCACTA
Found at i:20325 original size:52 final size:53
Alignment explanation
Indices: 20226--20367 Score: 164
Period size: 52 Copynumber: 2.7 Consensus size: 53
20216 TTTAAGTCTG
*
20226 ATATCACTAGCCTTGAATCAGCATATTGGCA-TCTT-TATTATTCTTAAGCCCA
1 ATATCGCTAGCCTTGAATCAGCATATTGGCATTCTTCTA-TATTCTTAAGCCCA
* * * * *
20278 ATATTGTTAGCCTTAAATCAGCATATTGGCATTCTTCTA-ATTTTTAAGTCCA
1 ATATCGCTAGCCTTGAATCAGCATATTGGCATTCTTCTATATTCTTAAGCCCA
* * * *
20330 ATGTCGCTCGCTTTGAATCAGCACATTGGCATTCTTCT
1 ATATCGCTAGCCTTGAATCAGCATATTGGCATTCTTCT
20368 CATCTTCAAG
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
52 69 0.92
53 4 0.05
54 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (53 bp):
ATATCGCTAGCCTTGAATCAGCATATTGGCATTCTTCTATATTCTTAAGCCCA
Found at i:20379 original size:52 final size:52
Alignment explanation
Indices: 20293--20425 Score: 149
Period size: 52 Copynumber: 2.6 Consensus size: 52
20283 GTTAGCCTTA
* * * * * ** **
20293 AATCAGCATATTGGCATTCTTCTAATTTTTAAGTCCAATGTCGCTCGCTTTG
1 AATCAGCACATTGGCATTCTTCTCATCTTCAAGTCCAATGTCACTAACCGTG
*
20345 AATCAGCACATTGGCATTCTTCTCATCTTCAAGTCTAATGTCACTAACCGTG
1 AATCAGCACATTGGCATTCTTCTCATCTTCAAGTCCAATGTCACTAACCGTG
* * *
20397 AATCAGCACGTTGGCACTCTTATCATCTT
1 AATCAGCACATTGGCATTCTTCTCATCTT
20426 TAAAGTCTGA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (52 bp):
AATCAGCACATTGGCATTCTTCTCATCTTCAAGTCCAATGTCACTAACCGTG
Found at i:20687 original size:52 final size:51
Alignment explanation
Indices: 20631--20788 Score: 174
Period size: 52 Copynumber: 3.1 Consensus size: 51
20621 ACACTTTTAC
* * *
20631 CATTTTTAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTAGTATTCTTCT
1 CATTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATT-GGAATCTTCT
* * * * * *
20683 CATTTTTATGCCCAATGTCGCTGACCTTGAATCAGCACAATGGCACCTTTAT
1 CATTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGAATC-TTCT
* * *
20735 CA-TTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCATATTGGAACTCTTCT
1 CATTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGAA-TCTTCT
20786 CAT
1 CAT
20789 CCTTATCAAC
Statistics
Matches: 85, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
51 42 0.49
52 43 0.51
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (51 bp):
CATTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGAATCTTCT
Found at i:21488 original size:20 final size:21
Alignment explanation
Indices: 21447--21495 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
21437 TTATAATTTA
*
21447 TATTGATACAATAAGAGTATG
1 TATTGATACAATAAGAGAATG
21468 TATTGATAC-ATAA-ATGAATG
1 TATTGATACAATAAGA-GAATG
*
21488 TATCGATA
1 TATTGATA
21496 TATGCCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 15 0.60
21 9 0.36
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (21 bp):
TATTGATACAATAAGAGAATG
Found at i:21566 original size:20 final size:20
Alignment explanation
Indices: 21541--21618 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
21531 ATGCCAAGGA
*
21541 AATGTATCAATACATTAATC
1 AATGTATCAATACATTTATC
*
21561 AATGTATCGATACATGCTTA-C
1 AATGTATCAATACAT--TTATC
*
21582 AATTGTATCAATACATTTCTC
1 AA-TGTATCAATACATTTATC
* *
21603 ACTGTATCGATACATT
1 AATGTATCAATACATT
21619 CTGGGTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 29 0.60
21 5 0.10
22 14 0.29
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (20 bp):
AATGTATCAATACATTTATC
Found at i:29030 original size:2 final size:2
Alignment explanation
Indices: 29023--29054 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29013 AATTTTTCTT
29023 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29055 ATGAAAGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29301 original size:2 final size:2
Alignment explanation
Indices: 29294--29338 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
29284 GAACATGTTT
29294 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29336 TA T
1 TA T
29339 GTATGTGTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35838 original size:13 final size:13
Alignment explanation
Indices: 35820--35844 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35810 CAAAGATCAG
35820 TGTATCGATACAA
1 TGTATCGATACAA
35833 TGTATCGATACA
1 TGTATCGATACA
35845 TTTGAGTAAT
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:36190 original size:13 final size:13
Alignment explanation
Indices: 36172--36196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36162 CATAAAGTGT
36172 TGTATCGATACAA
1 TGTATCGATACAA
36185 TGTATCGATACA
1 TGTATCGATACA
36197 TAAGTTTTGT
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:36212 original size:32 final size:33
Alignment explanation
Indices: 36152--36217 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
36142 TTCAATGATT
36152 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
36185 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
36217 T
1 T
36218 TTAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:36280 original size:34 final size:34
Alignment explanation
Indices: 36237--36316 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
36227 TGCCAAAAAA
*
36237 TGTATCGATACATTACTCAAATGTATCGATATAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
36271 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
36305 TGTATCGATACA
1 TGTATCGATACA
36317 CTGATCTTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (34 bp):
TGTATCGATACATTACTCAAATGTATCGATACAT
Found at i:36310 original size:13 final size:12
Alignment explanation
Indices: 36236--36316 Score: 61
Period size: 13 Copynumber: 7.1 Consensus size: 12
36226 CTGCCAAAAA
36236 ATGTATCGATAC
1 ATGTATCGATAC
36248 AT-TACTC-A-A-
1 ATGTA-TCGATAC
*
36257 ATGTATCGATAT
1 ATGTATCGATAC
36269 ATTGTATCGATAC
1 A-TGTATCGATAC
36282 AT-TACTC-A-A-
1 ATGTA-TCGATAC
36291 ATGTATCGATAC
1 ATGTATCGATAC
36303 ATTGTATCGATAC
1 A-TGTATCGATAC
36316 A
1 A
36317 CTGATCTTTG
Statistics
Matches: 56, Mismatches: 1, Indels: 23
0.70 0.01 0.29
Matches are distributed among these distances:
9 8 0.14
10 8 0.14
11 8 0.14
12 9 0.16
13 23 0.41
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:36381 original size:52 final size:52
Alignment explanation
Indices: 36325--36453 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
36315 CACTGATCTT
* *
36325 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
36377 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
36429 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
36454 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Done.