Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2230
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: 35289
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4850 original size:76 final size:78
Alignment explanation
Indices: 4749--4952 Score: 218
Period size: 76 Copynumber: 2.6 Consensus size: 78
4739 GAGATAATAA
* * * * *
4749 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
4813 A-TT-AGAA-AAAAT
64 ATTTGAGAATAAAAC
* * **
4825 CGGGATTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* *
4890 TTTGGGAATAAAGC
65 TTTGAGAATAAAAC
* * *
4904 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
4953 GAAATAACGA
Statistics
Matches: 104, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
75 7 0.07
76 47 0.45
77 2 0.02
78 3 0.03
79 45 0.43
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTGAGAATAAAAC
Found at i:4944 original size:28 final size:28
Alignment explanation
Indices: 4904--4975 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
4894 GGAATAAAGC
** *
4904 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
4932 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
4960 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
4976 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:5033 original size:52 final size:50
Alignment explanation
Indices: 4964--5133 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 50
4954 AAATAACGAG
* * *
4964 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
5016 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG-AAATAAAACC-GGA
*
5069 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
5120 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
5134 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 81 0.82
53 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:5152 original size:28 final size:28
Alignment explanation
Indices: 5107--5188 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
5097 AGTGTTTTAA
* *
5107 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
5134 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
5161 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
5189 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:7625 original size:13 final size:13
Alignment explanation
Indices: 7607--7632 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7597 ACAAAGATCC
7607 ATGTATCGATACA
1 ATGTATCGATACA
7620 ATGTATCGATACA
1 ATGTATCGATACA
7633 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:7628 original size:33 final size:33
Alignment explanation
Indices: 7586--7652 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
7576 AAAATTTCCA
***
7586 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
7619 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
7652 A
1 A
7653 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:7696 original size:19 final size:18
Alignment explanation
Indices: 7672--7739 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
7662 CAGTAGCTAA
7672 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
7691 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
7706 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
7723 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
7740 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:7712 original size:13 final size:13
Alignment explanation
Indices: 7694--7718 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7684 ACAATACTTA
7694 TGTATCGATACAT
1 TGTATCGATACAT
7707 TGTATCGATACA
1 TGTATCGATACA
7719 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7716 original size:32 final size:32
Alignment explanation
Indices: 7675--7737 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
7665 TAGCTAATTA
*
7675 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
7707 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
7738 AATTGTTGAA
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:7819 original size:21 final size:21
Alignment explanation
Indices: 7795--7851 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
7785 CATTTGTAGG
7795 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
7816 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
7837 ATGTATCGATACATT
1 ATGTATCGATACATT
7852 TAAATTTTTT
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:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:10934 original size:17 final size:17
Alignment explanation
Indices: 10910--10951 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
10900 TTTAGTTTTG
10910 AAAC-TATTTTAACTTA
1 AAACATATTTTAACTTA
* *
10926 AAACATA-TTTAATTTT
1 AAACATATTTTAACTTA
10942 AAACATATTT
1 AAACATATTT
10952 AATTTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (17 bp):
AAACATATTTTAACTTA
Found at i:10936 original size:16 final size:16
Alignment explanation
Indices: 10917--10953 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
10907 TTGAAACTAT
10917 TTTAACTTAAAACATA
1 TTTAACTTAAAACATA
* *
10933 TTTAATTTTAAACATA
1 TTTAACTTAAAACATA
10949 TTTAA
1 TTTAA
10954 TTTTTTCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTAACTTAAAACATA
Found at i:10958 original size:17 final size:16
Alignment explanation
Indices: 10926--10957 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
10916 TTTTAACTTA
10926 AAACATATTTAATTTT
1 AAACATATTTAATTTT
10942 AAACATATTTAATTTT
1 AAACATATTTAATTTT
10958 TTCATCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
AAACATATTTAATTTT
Found at i:11007 original size:17 final size:18
Alignment explanation
Indices: 10985--11021 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
10975 TGGTCACTTT
10985 AATG-TTTTTCATCCAAA
1 AATGTTTTTTCATCCAAA
*
11002 AATGTTTTTTCATCTAAA
1 AATGTTTTTTCATCCAAA
11020 AA
1 AA
11022 AGGTAGCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (18 bp):
AATGTTTTTTCATCCAAA
Found at i:13333 original size:25 final size:25
Alignment explanation
Indices: 13299--13352 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
13289 TTGGTCTAAT
13299 CTTACCTTATTTCACTAACACTTAG
1 CTTACCTTATTTCACTAACACTTAG
13324 CTTACCTTATTTCACTAACACTTAG
1 CTTACCTTATTTCACTAACACTTAG
13349 CTTA
1 CTTA
13353 TAAATAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.41
Consensus pattern (25 bp):
CTTACCTTATTTCACTAACACTTAG
Found at i:14929 original size:13 final size:13
Alignment explanation
Indices: 14911--14971 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
14901 ACATTTGTGG
14911 AATGTATCGATAC
1 AATGTATCGATAC
14924 AATGTATCGATAC
1 AATGTATCGATAC
14937 -A--T-TC--TAC
1 AATGTATCGATAC
14944 AAATGTATCGATAC
1 -AATGTATCGATAC
14958 AATGTATCGATAC
1 AATGTATCGATAC
14971 A
1 A
14972 TTCTACAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
7 3 0.07
9 3 0.07
10 1 0.02
11 1 0.02
12 3 0.07
13 27 0.66
14 3 0.07
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:14933 original size:34 final size:34
Alignment explanation
Indices: 14911--14992 Score: 155
Period size: 34 Copynumber: 2.4 Consensus size: 34
14901 ACATTTGTGG
14911 AATGTATCGATACAATGTATCGATACATTCTACA
1 AATGTATCGATACAATGTATCGATACATTCTACA
14945 AATGTATCGATACAATGTATCGATACATTCTACA
1 AATGTATCGATACAATGTATCGATACATTCTACA
*
14979 AATGTATCAATACA
1 AATGTATCGATACA
14993 GGGTCCCAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (34 bp):
AATGTATCGATACAATGTATCGATACATTCTACA
Found at i:15121 original size:13 final size:13
Alignment explanation
Indices: 15103--15128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15093 TATTTTTCTG
15103 TGTATCGATACAT
1 TGTATCGATACAT
15116 TGTATCGATACAT
1 TGTATCGATACAT
15129 CTATTCTTTG
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:15146 original size:34 final size:33
Alignment explanation
Indices: 15083--15148 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
15073 GTCAAGGGAA
* *
15083 TGTATCGATATATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
15116 TGTATCGATACATCTATTCTTTGTATCGATACA
1 TGTATCGATACAT-TATTCTGTGTATCGATACA
15149 CCTAGGAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 12 0.41
34 17 0.59
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:17627 original size:27 final size:28
Alignment explanation
Indices: 17593--17668 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
17583 TTTCTTCACA
17593 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
17620 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
17648 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
17669 ACTTTATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:17831 original size:53 final size:52
Alignment explanation
Indices: 17651--17875 Score: 249
Period size: 51 Copynumber: 4.3 Consensus size: 52
17641 TTATTTCCGA
* * * * *
17651 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTTT-CGTAATC
1 GGGGATACTCCAACCCCGGCTTTATTTTCAAAACACTAATTTTTCCATAATC
* * *
17702 GGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGGCTTTATTTTC-AAAACACTAATTTTTCCATAATC
* * *
17754 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGCTTTATTTTCAAAACACTAATTTTTCC-ATAATC
** * * * * *
17807 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCT-CATAATT
1 GGGGATACTCCAACCCCGGCTTTATTTTCAAAACACTAATTTTTCCATAATC
17858 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
17876 TTATTTTCGA
Statistics
Matches: 148, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
50 3 0.02
51 56 0.38
52 46 0.31
53 43 0.29
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGCTTTATTTTCAAAACACTAATTTTTCCATAATC
Found at i:17991 original size:107 final size:107
Alignment explanation
Indices: 17864--18094 Score: 446
Period size: 107 Copynumber: 2.2 Consensus size: 107
17854 AATTGGGGAT
17864 ACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTCTAATCATCGATTTC
1 ACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTCTAATCATCGATTTC
17929 TCACAACCGGGGATACTTCAG-CCCTGTTATTTTCGAGGGAAC
66 TCACAACCGGGGATACTTCAGTCCC-GTTATTTTCGAGGGAAC
17971 ACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTCTAATCATCGATTTC
1 ACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTCTAATCATCGATTTC
18036 TCACAACCGGGGATACTTCAGTCCCGTTATTTTCGAGGGAAC
66 TCACAACCGGGGATACTTCAGTCCCGTTATTTTCGAGGGAAC
18078 ACTCCAACCCCGTTATT
1 ACTCCAACCCCGTTATT
18095 ATCTCCAAAA
Statistics
Matches: 123, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
107 120 0.98
108 3 0.02
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (107 bp):
ACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTCTAATCATCGATTTC
TCACAACCGGGGATACTTCAGTCCCGTTATTTTCGAGGGAAC
Found at i:18017 original size:28 final size:28
Alignment explanation
Indices: 17954--18010 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
17944 CTTCAGCCCT
17954 GTTATTTTCGAGGGAACACTCCAACCCC
1 GTTATTTTCGAGGGAACACTCCAACCCC
* * *
17982 GTTATTTTCGAGGGGATACTCCAATCCC
1 GTTATTTTCGAGGGAACACTCCAACCCC
18010 G
1 G
18011 ATTTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (28 bp):
GTTATTTTCGAGGGAACACTCCAACCCC
Found at i:23233 original size:15 final size:15
Alignment explanation
Indices: 23213--23244 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23203 TTCGATTAAC
*
23213 TAGTTTAAGTTAATT
1 TAGTTTAAGTAAATT
23228 TAGTTTAAGTAAATT
1 TAGTTTAAGTAAATT
23243 TA
1 TA
23245 ATCGATTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (15 bp):
TAGTTTAAGTAAATT
Found at i:26003 original size:2 final size:2
Alignment explanation
Indices: 25996--26025 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25986 TATAATATTC
25996 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
26026 ATTCTGTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28641 original size:17 final size:17
Alignment explanation
Indices: 28619--28663 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
28609 AATTATAATT
28619 TTTAAATATATTAAAAA
1 TTTAAATATATTAAAAA
*
28636 TTTAAAAAT-TTAAAAA
1 TTTAAATATATTAAAAA
*
28652 TTTTAATATATT
1 TTTAAATATATT
28664 TATGGCCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATATATTAAAAA
Found at i:28650 original size:7 final size:8
Alignment explanation
Indices: 28619--28654 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
28609 AATTATAATT
*
28619 TTTAAATA
1 TTTAAAAA
28627 TATTAAAAA
1 T-TTAAAAA
28636 TTTAAAAA
1 TTTAAAAA
28644 TTTAAAAA
1 TTTAAAAA
28652 TTT
1 TTT
28655 TAATATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
TTTAAAAA
Found at i:28660 original size:33 final size:35
Alignment explanation
Indices: 28591--28663 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 35
28581 CGTTCAATAG
* *
28591 ATATTAAAAATAATATAAAATTATAATTTTTAAAT
1 ATATTAAAAATAATATAAAATTAAAAATTTTAAAT
*
28626 ATATTAAAAAT-TTA-AAAATTTAAAAATTTT-AAT
1 ATATTAAAAATAATATAAAA-TTAAAAATTTTAAAT
28659 ATATT
1 ATATT
28664 TATGGCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 12 0.35
34 11 0.32
35 11 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
ATATTAAAAATAATATAAAATTAAAAATTTTAAAT
Found at i:29255 original size:15 final size:17
Alignment explanation
Indices: 29229--29272 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
29219 ATAAAATTAT
29229 TTATAA-TTAATTT-AA
1 TTATAATTTAATTTAAA
29244 TT-TAATTTAATTTAAA
1 TTATAATTTAATTTAAA
*
29260 TTATTATTTAATT
1 TTATAATTTAATT
29273 AATAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 9 0.36
16 4 0.16
17 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATAATTTAATTTAAA
Found at i:29272 original size:11 final size:11
Alignment explanation
Indices: 29229--29273 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
29219 ATAAAATTAT
29229 TTATAA-TTAA
1 TTATAATTTAA
29239 TT-TAATTTAA
1 TTATAATTTAA
29249 TT-TAATTTAAA
1 TTATAATTT-AA
*
29260 TTATTATTTAA
1 TTATAATTTAA
29271 TTA
1 TTA
29274 ATAAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 3 0.10
10 14 0.45
11 9 0.29
12 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTATAATTTAA
Found at i:29567 original size:19 final size:19
Alignment explanation
Indices: 29539--29601 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
29529 CATTATCTTA
*
29539 TTTTATAATATTAATTAAT
1 TTTTAAAATATTAATTAAT
*
29558 TTTTAAAATATTACATATGAT
1 TTTTAAAATATTA-AT-TAAT
* *
29579 ATTTAAAA-A-TAATAAAT
1 TTTTAAAATATTAATTAAT
29596 TTTTAA
1 TTTTAA
29602 TAATTAATAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 7 0.19
18 2 0.06
19 14 0.39
20 3 0.08
21 10 0.28
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TTTTAAAATATTAATTAAT
Found at i:29791 original size:22 final size:21
Alignment explanation
Indices: 29761--29801 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
29751 TTAAAATAAA
* *
29761 TTTAAATTAATATTTATATTT
1 TTTAAATTAAAAATTATATTT
29782 TTTAATATTAAAAATTATAT
1 TTTAA-ATTAAAAATTATAT
29802 GAATAATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAAATTAAAAATTATATTT
Found at i:30253 original size:34 final size:34
Alignment explanation
Indices: 30213--30395 Score: 251
Period size: 34 Copynumber: 5.4 Consensus size: 34
30203 TTTTGTTAAG
30213 TGTATTTGGTGAGAATGTTAGATGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGATGTGTTAGGTGA
* *
30247 TATATTTGGTGAGAATGTTA-AGTATGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGA-TGTGTTAGGTGA
*
30281 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGATGTGTTAGGTGA
* *
30315 TGTATTTGGTGAGAATATTAGATGTGTTAGGTAA
1 TGTATTTGGTGAGAATGTTAGATGTGTTAGGTGA
* * * *
30349 TGTATTTGGTGAAAATATTAGGTGTGTTAGGTAA
1 TGTATTTGGTGAGAATGTTAGATGTGTTAGGTGA
* *
30383 TGTGTTAGGTGAG
1 TGTATTTGGTGAG
30396 TAAGATATTT
Statistics
Matches: 134, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
33 1 0.01
34 133 0.99
ACGTcount: A:0.26, C:0.00, G:0.33, T:0.41
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGATGTGTTAGGTGA
Found at i:35144 original size:35 final size:34
Alignment explanation
Indices: 35098--35266 Score: 175
Period size: 35 Copynumber: 4.9 Consensus size: 34
35088 CTTTGTTAAG
*
35098 TGTATTTGGTGAGAATGTTAGGTGTGTTTAGGTGA
1 TGTATTTGGTGAGAATATTAGGTGTG-TTAGGTGA
* *
35133 TGTATTTGGTGAGAATATTAAGTGTGTTAGGGTGG
1 TGTATTTGGTGAGAATATTAGGTGTGTTA-GGTGA
* * *
35168 TGGTA-TTGGTGAGACTGTTAGGTGTGTTCGGTGA
1 T-GTATTTGGTGAGAATATTAGGTGTGTTAGGTGA
* *
35202 TGTAATTTGGTGAGAATATTCGATGTGTTAGGT-A
1 TGT-ATTTGGTGAGAATATTAGGTGTGTTAGGTGA
* *
35236 CTGTATTTGGTGA-CATCTT-GGTGTGTTAGGT
1 -TGTATTTGGTGAGAATATTAGGTGTGTTAGGT
35267 CCGTGTTCGG
Statistics
Matches: 113, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
32 11 0.10
33 6 0.05
34 19 0.17
35 74 0.65
36 3 0.03
ACGTcount: A:0.20, C:0.04, G:0.36, T:0.41
Consensus pattern (34 bp):
TGTATTTGGTGAGAATATTAGGTGTGTTAGGTGA
Done.