Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3796
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: 39693
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:8500 original size:9 final size:9
Alignment explanation
Indices: 8486--8520 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
8476 ACATTAAAAT
8486 ATATATATA
1 ATATATATA
*
8495 ATATATAAA
1 ATATATATA
*
8504 ATACATATA
1 ATATATATA
8513 ATATATAT
1 ATATATAT
8521 TAGAAATGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (9 bp):
ATATATATA
Found at i:9672 original size:25 final size:22
Alignment explanation
Indices: 9609--9671 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
9599 CCAGTCCCAT
9609 GCAT-CAGATAATAACAACATG
1 GCATGCAGATAATAACAACATG
9630 GCATGCAGATAATAACAACATG
1 GCATGCAGATAATAACAACATG
9652 GCATGCAG-TAAATAACAACA
1 GCATGCAGAT-AATAACAACA
9672 ATCAAACATG
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
21 5 0.12
22 35 0.88
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.17
Consensus pattern (22 bp):
GCATGCAGATAATAACAACATG
Found at i:11195 original size:26 final size:26
Alignment explanation
Indices: 11159--11242 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
11149 CATGAAATTC
11159 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
11185 TTATCATGAAATATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
11211 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
11237 TTATCA
1 TTATCA
11243 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:11582 original size:19 final size:19
Alignment explanation
Indices: 11558--11594 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11548 TATAAATAAT
* *
11558 AATGATGTTGGAAATATAC
1 AATGATATTAGAAATATAC
11577 AATGATATTAGAAATATA
1 AATGATATTAGAAATATA
11595 TATAAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.32
Consensus pattern (19 bp):
AATGATATTAGAAATATAC
Found at i:11692 original size:24 final size:24
Alignment explanation
Indices: 11651--11706 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
11641 ACACAATAAT
*
11651 ATATATAACATACAATAT-TGAAAA
1 ATATAT-ACATACAATATACGAAAA
11675 CATATATACATA-ATATATACGAAAA
1 -ATATATACATACA-ATATACGAAAA
11700 ATATATA
1 ATATATA
11707 GATATACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 16 0.57
25 11 0.39
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (24 bp):
ATATATACATACAATATACGAAAA
Found at i:11731 original size:30 final size:30
Alignment explanation
Indices: 11678--11752 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
11668 TTGAAAACAT
*
11678 ATATACATAATATATACGAAAAATATATAG
1 ATATACATAATATATACGAAAAATATATAC
** *
11708 ATATACATAATATAATA-TTAAAATATTTAC
1 ATATACATAATAT-ATACGAAAAATATATAC
11738 ATAATACATAA-ATAT
1 AT-ATACATAATATAT
11753 TAGGGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 26 0.67
31 11 0.28
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.35
Consensus pattern (30 bp):
ATATACATAATATATACGAAAAATATATAC
Found at i:11834 original size:25 final size:23
Alignment explanation
Indices: 11790--11835 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
11780 CTACATAAGT
* *
11790 ATATACATAAATATATTAAAAAC
1 ATATACATAAATAAAATAAAAAC
11813 ATATACATATATATAAAATAAAA
1 ATATACATA-A-ATAAAATAAAA
11836 TAAAATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 1 0.05
25 9 0.47
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (23 bp):
ATATACATAAATAAAATAAAAAC
Found at i:13314 original size:24 final size:20
Alignment explanation
Indices: 13268--13334 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 20
13258 CTTTCTTTCC
*
13268 TTCTTTTCTTCTCTGTTTTCAT
1 TTCTTTTGTT-TCT-TTTTCAT
13290 TTCATATTCTGTTTCCTTTTTCAT
1 TTC-T-TT-TGTTT-CTTTTTCAT
13314 TTCTTTTGTTTCTTTTT-AT
1 TTCTTTTGTTTCTTTTTCAT
13333 TT
1 TT
13335 ATTATAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
19 4 0.10
20 6 0.15
21 5 0.12
22 5 0.12
23 2 0.05
24 13 0.32
25 5 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.70
Consensus pattern (20 bp):
TTCTTTTGTTTCTTTTTCAT
Found at i:16268 original size:44 final size:44
Alignment explanation
Indices: 16218--16301 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
16208 AAATAAAAAG
16218 AAAATCTAATAAAATTTGAGAATAATTTAT-TATAGGATGATCCT
1 AAAATCTAATAAAATTTGAGAATAATTTATAT-TAGGATGATCCT
16262 AAAATCTAATAAAATTTGAGAATAATTTATATTAGGATGA
1 AAAATCTAATAAAATTTGAGAATAATTTATATTAGGATGA
16302 AATTATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.36
Consensus pattern (44 bp):
AAAATCTAATAAAATTTGAGAATAATTTATATTAGGATGATCCT
Found at i:16978 original size:21 final size:21
Alignment explanation
Indices: 16931--16978 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
16921 ACAAAAATAA
**
16931 ATAAAAAAATATTAAATTTTG
1 ATAAAAAAATATTAAAAATTG
*
16952 AAAAAAAAATGATTAAAAATTG
1 ATAAAAAAAT-ATTAAAAATTG
16974 -TAAAA
1 ATAAAA
16979 GAAGAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (21 bp):
ATAAAAAAATATTAAAAATTG
Found at i:16978 original size:22 final size:21
Alignment explanation
Indices: 16933--16988 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
16923 AAAAATAAAT
**
16933 AAAAAAATATTAAATTTTGAA
1 AAAAAAATATTAAAAATTGAA
16954 AAAAAAATGATTAAAAATTGTAA
1 AAAAAAAT-ATTAAAAATTG-AA
16977 AAGAAGAAATAT
1 AA-AA-AAATAT
16989 GTTTGTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 8 0.28
22 9 0.31
23 4 0.14
24 4 0.14
25 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAAAAATATTAAAAATTGAA
Found at i:17493 original size:29 final size:30
Alignment explanation
Indices: 17441--17498 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
17431 ACCTAACTTT
17441 TAGTAAATTTCTTTTTTGTCACCCAACTAG
1 TAGTAAATTTCTTTTTTGTCACCCAACTAG
*
17471 TAGTTAATTT-TTTTTTGTCACCCAACTA
1 TAGTAAATTTCTTTTTTGTCACCCAACTA
17499 TGAACAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.47
Consensus pattern (30 bp):
TAGTAAATTTCTTTTTTGTCACCCAACTAG
Found at i:18136 original size:60 final size:57
Alignment explanation
Indices: 18030--18154 Score: 135
Period size: 60 Copynumber: 2.1 Consensus size: 57
18020 GACAAAATTG
* **
18030 AATAGTTAGGTGATCATTTTGTAACTTTTAATAATGGGGTGACCAAAAAAGAAATTTACT
1 AATAGTTAGATGATCATTTTGTAACTTTTAATAATGAAGTGACC-AAAAA-AAA-TTACT
* * * * *
18090 AATAGTTAGATGA-CTATTTTGTAAGTTTTAATAGTTAAGTGGCCAAAAAAAATTATT
1 AATAGTTAGATGATC-ATTTTGTAACTTTTAATAATGAAGTGACCAAAAAAAATTACT
18147 AATAGTTA
1 AATAGTTA
18155 AGCAGGCAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
57 12 0.21
58 3 0.05
59 6 0.11
60 35 0.62
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (57 bp):
AATAGTTAGATGATCATTTTGTAACTTTTAATAATGAAGTGACCAAAAAAAATTACT
Found at i:18946 original size:35 final size:35
Alignment explanation
Indices: 18900--18968 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
18890 TCTACAGATA
18900 AAATTATATAGATAAGCATGGAAGAACAGTTCTTC
1 AAATTATATAGATAAGCATGGAAGAACAGTTCTTC
18935 AAATTATATAGATAAGCATGGAAGAACAGTTCTT
1 AAATTATATAGATAAGCATGGAAGAACAGTTCTT
18969 GTTATGAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.29
Consensus pattern (35 bp):
AAATTATATAGATAAGCATGGAAGAACAGTTCTTC
Found at i:20037 original size:20 final size:21
Alignment explanation
Indices: 20012--20054 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
20002 TTTATTTTCC
*
20012 TATTAAAATTTTATTAT-TTT
1 TATTAAAATATTATTATCTTT
20032 TATTAAAATATTATTATCTTT
1 TATTAAAATATTATTATCTTT
20053 TA
1 TA
20055 CAGGAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTAAAATATTATTATCTTT
Found at i:20131 original size:57 final size:57
Alignment explanation
Indices: 20065--20179 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 57
20055 CAGGAAATTC
*
20065 ATGATAATAATTATTTTAAAATTTATGAG-T-TAATAAATCTATTTTAAAATTTAAGAG
1 ATGATAATAATTATTTTAAAATTTAAGAGATATAAT-AAT-TATTTTAAAATTTAAGAG
* *
20122 ATGATAATAATTATTTTAAACTTTAAGAGATCATAATAATTATTTTAAATTTTAAGAG
1 ATGATAATAATTATTTTAAAATTTAAGAGAT-ATAATAATTATTTTAAAATTTAAGAG
20180 GGAATTATGA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
57 27 0.52
58 18 0.35
59 3 0.06
60 4 0.08
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (57 bp):
ATGATAATAATTATTTTAAAATTTAAGAGATATAATAATTATTTTAAAATTTAAGAG
Found at i:20146 original size:29 final size:29
Alignment explanation
Indices: 20065--20179 Score: 155
Period size: 29 Copynumber: 4.0 Consensus size: 29
20055 CAGGAAATTC
*
20065 ATGATAATAATTATTTTAAAATTTATGAG
1 ATGATAATAATTATTTTAAAATTTAAGAG
20094 -T--TAATAAATCTATTTTAAAATTTAAGAG
1 ATGATAAT-AAT-TATTTTAAAATTTAAGAG
*
20122 ATGATAATAATTATTTTAAACTTTAAGAG
1 ATGATAATAATTATTTTAAAATTTAAGAG
* *
20151 ATCATAATAATTATTTTAAATTTTAAGAG
1 ATGATAATAATTATTTTAAAATTTAAGAG
20180 GGAATTATGA
Statistics
Matches: 77, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.05
27 3 0.04
28 18 0.23
29 45 0.58
30 3 0.04
31 4 0.05
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (29 bp):
ATGATAATAATTATTTTAAAATTTAAGAG
Found at i:24210 original size:19 final size:19
Alignment explanation
Indices: 24186--24223 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24176 GAAATGAATA
*
24186 ATTTCAGGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
24205 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
24224 GCAATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Found at i:25135 original size:19 final size:20
Alignment explanation
Indices: 25102--25141 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
25092 GTATATATAT
25102 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
25121 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
25141 A
1 A
25142 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:25409 original size:16 final size:16
Alignment explanation
Indices: 25390--25425 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
25380 GTTTTTTTCT
25390 TTTTCTTCATTTTTTA
1 TTTTCTTCATTTTTTA
* *
25406 TTTTTTTTATTTTTTA
1 TTTTCTTCATTTTTTA
25422 TTTT
1 TTTT
25426 GGGTTGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCTTCATTTTTTA
Found at i:25774 original size:44 final size:44
Alignment explanation
Indices: 25716--27043 Score: 1506
Period size: 44 Copynumber: 30.4 Consensus size: 44
25706 CCCCGTCTAA
25716 TACAGAGACGCCAAAT-TCGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCT-GTTATCTTCGATCTGCTCTCCGCCGC
*
25760 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTTCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
25804 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
25848 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * * *
25892 TACGGAGACCCCAAATTTGTTATCTTCGATATGCTCTCCGTCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
25936 TACAGAGACGCCAAATCTGTTATCTTTGATCTGCTTTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
25980 TACAGAGATGCCAAATC----ATCTTCGATCTGTTCTTCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
26020 TACAGAGACGCCAAATCTGTTATCTTTGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
26064 TATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
26108 TACAGAGATGTCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * *
26152 TACAGAGATGCCAAATC----ATCTTTGATCTGCTCTTCGCCAC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
26192 TATAGAGACTCCAAATCTGTTATCTTTGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* ** * * * *
26236 TACAGAGACGCCAAATCACGGAGACGCTAAATCTGTTATCTTCGATCTGCTCTCTGC
1 TACAGAGACGCCAAAT--CTGTTA-TCT---TC-G--ATC-T-GCTCT-C-CGCCGC
** * ** * * * * *
26293 CGCTACAGA-GACGCAA-ATCATT-TATCTTTGATCTGCTCTCTGCCGC
1 TAC-AGAGACG-CCAAATCT-GTTATCT-T-CGATCTGCTCTCCGCCGC
*
26339 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
26383 TACGGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCAC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * *
26427 TACAGAGATGTCAAATC----ATCTTCGATCTACTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * * * * *
26467 TACAGAGATGCTAAATCTGTTATCTTCGATTTGTTCTCTGTCAC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
26511 TACAAAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
26555 TACAAAGACGCCAAATCTGTTATCTTCGATCTGCTCTTCACCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * **
26599 TACAGAGATGCCAAATC----ATCTTCGATCTGCTCTTCGCTAC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
26639 TACAGAGACGCCAAATCTGTTATCTTTGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
26683 TACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * *
26727 TATAGAGATGTCAAATCTGTTATCTTCGATCTGCTCTTCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
26771 TATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCAC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
26815 TACAGAGATGTCAAATC----ATCTTCGATCTGCTCTCCGCCAC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
26855 TACAGAGATGCCAAATC----ATCTTCGATCTGCTCTCCGCCAC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * * * *
26895 TACAGAGATGTCAAATCTGTTATCTTAGATCTGCTATCTGTCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
26939 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
26983 TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
27027 TATAAAGACGCCAAATC
1 TACAGAGACGCCAAATC
27044 ATCTTGGATT
Statistics
Matches: 1102, Mismatches: 141, Indels: 82
0.83 0.11 0.06
Matches are distributed among these distances:
40 218 0.20
44 824 0.75
45 11 0.01
46 11 0.01
47 3 0.00
48 4 0.00
49 1 0.00
50 4 0.00
51 1 0.00
52 2 0.00
53 3 0.00
54 2 0.00
55 4 0.00
56 1 0.00
57 6 0.01
58 7 0.01
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.30
Consensus pattern (44 bp):
TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
Found at i:26101 original size:172 final size:173
Alignment explanation
Indices: 25716--27057 Score: 1606
Period size: 172 Copynumber: 7.7 Consensus size: 173
25706 CCCCGTCTAA
25716 TACAGAGACGCCAAAT-TCGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGT
1 TACAGAGACGCCAAATCT-GTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGT
*
25780 TATCTTCGATCTGCTCTTCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGC
65 TATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC---TATCTTCGATCTGCTCTCCGC
*
25845 CGTTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
127 CGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * * *
25892 TACGGAGACCCCAAATTTGTTATCTTCGATATGCTCTCCGTCGCTACAGAGACGCCAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * * * *
25957 ATCTTTGATCTGCTTTCCGCCGCTACAGAGATGCCAAATC-ATCTTCGATCTGTTCTTCGCCGCT
66 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTATCTTCGATCTGCTCTCCGCCGCT
*
26021 ACAGAGACGCCAAATCTGTTATCTTTGATCTGCTCTCCGCCGC
131 ACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * *
26064 TATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGATGTCAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * * *
26129 ATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATC-ATCTTTGATCTGCTCTTCGCCACT
66 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTATCTTCGATCTGCTCTCCGCCGCT
* * *
26193 ATAGAGACTCCAAATCTGTTATCTTTGATCTGCTCTCCGCCGC
131 ACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
26236 TACAGAGACGCCAAATCACGGAGACGCTAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAG
1 TAC--AGA-G-------AC---G-C-C-AAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAG
* *
26301 AGACG-CAAATCAT-TTATCTTTGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCT
50 AGACGCCAAATC-TGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC---TATCT
* * *
26364 TCGATCTGCTCTCTGCCGCTACGGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCAC
111 TCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * * * *
26427 TACAGAGATGTCAAATC----ATCTTCGATCTACTCTCTGCCGCTACAGAGATGCTAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * * * * *
26488 ATCTTCGATTTGTTCTCTGTCACTACAAAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
66 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC---TATCTTCGATCTGCTCTCCGCC
* * *
26553 GCTACAAAGACGCCAAATCTGTTATCTTCGATCTGCTCTTCACCGC
128 GCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * **
26599 TACAGAGATGCCAAATC----ATCTTCGATCTGCTCTTCGCTACTACAGAGACGCCAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* *
26660 ATCTTTGATCTGCTCTCCGCCGCTACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
66 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC---TATCTTCGATCTGCTCTCCGCC
* * * *
26725 GCTATAGAGATGTCAAATCTGTTATCTTCGATCTGCTCTTCGCCGC
128 GCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * *
26771 TATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGATGTCAAATC----
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * *
26832 ATCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATC-ATCTTCGATCTGCTCTCCGCCACT
66 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTATCTTCGATCTGCTCTCCGCCGCT
* * * * * *
26896 ACAGAGATGTCAAATCTGTTATCTTAGATCTGCTATCTGTCGC
131 ACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
26939 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * * * * *
27004 ATCTTCGATCTACTCTCTGCCGCTATAAAGACGCCAAATC-ATCTTGGATTTGCT
66 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTATCTTCGATCTGCT
27058 TCAACGTAAA
Statistics
Matches: 1026, Mismatches: 108, Indels: 68
0.85 0.09 0.06
Matches are distributed among these distances:
168 116 0.11
171 32 0.03
172 577 0.56
174 3 0.00
175 6 0.01
176 132 0.13
177 1 0.00
178 1 0.00
181 1 0.00
182 2 0.00
185 1 0.00
186 1 0.00
187 46 0.04
188 43 0.04
189 3 0.00
191 61 0.06
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.30
Consensus pattern (173 bp):
TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTATCTTCGATCTGCTCTCCGCCGCT
ACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
Found at i:26349 original size:103 final size:104
Alignment explanation
Indices: 26169--26355 Score: 290
Period size: 103 Copynumber: 1.8 Consensus size: 104
26159 ATGCCAAATC
* *
26169 ATCTTTGATCTGCTCTTCGCCACTATAGAGACTCCAAATCTGTTATCTTTGATCTGCTCTCCGCC
1 ATCTTCGATCTGCTCTTCGCCACTACAGAGACTCCAAATCTGTTATCTTTGATCTGCTCTCCGCC
26234 GCTACAGAGACGCCAAATCACGGAGACGCTAAATCTGTT
66 GCTACAGAGACGCCAAATCACGGAGACGCTAAATCTGTT
* * *
26273 ATCTTCGATCTGCTC-TCTGCCGCTACAGAGAC-GCAAATCAT-TTATCTTTGATCTGCTCTCTG
1 ATCTTCGATCTGCTCTTC-GCCACTACAGAGACTCCAAATC-TGTTATCTTTGATCTGCTCTCCG
26335 CCGCTACAGAGACGCCAAATC
64 CCGCTACAGAGACGCCAAATC
26356 TGTTATCTTC
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
103 49 0.64
104 27 0.36
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (104 bp):
ATCTTCGATCTGCTCTTCGCCACTACAGAGACTCCAAATCTGTTATCTTTGATCTGCTCTCCGCC
GCTACAGAGACGCCAAATCACGGAGACGCTAAATCTGTT
Found at i:27367 original size:61 final size:64
Alignment explanation
Indices: 27250--27372 Score: 182
Period size: 61 Copynumber: 2.0 Consensus size: 64
27240 TTATGTATCC
27250 ATGCTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTG
* * *
27314 ATGCTTTATGTCAAATAATTTGGATG-T-T-A-TGAAATGAATCAAATGTTCCTAACTAAATG
1 ATGC-TTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATG
27373 AATGGTTATG
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
61 29 0.53
62 1 0.02
63 1 0.02
64 5 0.09
65 19 0.35
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTG
Found at i:39247 original size:19 final size:19
Alignment explanation
Indices: 39223--39260 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
39213 GAAATGAATA
*
39223 ATTTCAGGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
39242 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
39261 GCAATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Done.