Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3686
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: 37939
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Found at i:1478 original size:93 final size:93
Alignment explanation
Indices: 1366--1537 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
1356 GCCCATAAGT
* *
1366 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1431 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
1459 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
1524 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
1538 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:1533 original size:46 final size:46
Alignment explanation
Indices: 1358--1533 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
1348 TGTAACCCGC
* *
1358 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
1404 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
1450 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
1497 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1534 TGCCCAAATA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:3938 original size:29 final size:29
Alignment explanation
Indices: 3901--3984 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
3891 GATAACAAGA
*
3901 AAACC-GAATAAAGAAATCCAAGATAGAG
1 AAACCAGAATAAAGAAATCCAAGATAAAG
3929 AAACCAGAATAAAGAAATCC-AGAATAAAG
1 AAACCAGAATAAAGAAATCCAAG-ATAAAG
* * *
3958 AGATCCAGGATAAAGAAACCCAAGATA
1 A-AACCAGAATAAAGAAATCCAAGATA
3985 CGATACTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.15
29 20 0.42
30 19 0.40
31 2 0.04
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (29 bp):
AAACCAGAATAAAGAAATCCAAGATAAAG
Found at i:3950 original size:15 final size:15
Alignment explanation
Indices: 3897--3975 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
3887 CAAAGATAAC
*
3897 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
3911 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
3926 GAGAAA-CCAGAATA
1 AAGAAATCCAGAATA
3940 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
3955 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
3970 AAGAAA
1 AAGAAA
3976 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
14 20 0.36
15 35 0.64
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:3984 original size:15 final size:15
Alignment explanation
Indices: 3908--3984 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
3898 AGAAAACCGA
3908 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
3923 ATAGAGAAA-CC-AG
1 ATAAAGAAATCCAAG
3936 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
3951 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
3967 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
3982 ATA
1 ATA
3985 CGATACTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
13 2 0.04
14 10 0.19
15 39 0.75
16 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:6969 original size:46 final size:46
Alignment explanation
Indices: 6902--7063 Score: 157
Period size: 46 Copynumber: 3.5 Consensus size: 46
6892 ACCAATAAGC
6902 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTATCCATATGT
1 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTATCCATATGT
* * * * * * *
6948 GAACTCAGACTCAACTCAACGAGCTC-AG-ATGCCTAGTTACATCTCT
1 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTA--TCCATATGT
* * * * * *
6994 CGAGCTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGT
1 -GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTATCCATATGT
*
7041 GAACTCGGACTCAACTGAACGAG
1 GAACTCGGACTCAACTCAACGAG
7064 TTTGGATGCC
Statistics
Matches: 88, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
44 5 0.06
45 1 0.01
46 51 0.58
47 27 0.31
49 4 0.05
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTATCCATATGT
Found at i:11949 original size:28 final size:30
Alignment explanation
Indices: 11916--11974 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
11906 AATACATTTC
*
11916 ACATATTCTCT-ATTCATTTG-CACATATA
1 ACATATTCTCTCATACATTTGTCACATATA
* *
11944 ACATATTTTCTCATACTTTTGTCACATATA
1 ACATATTCTCTCATACATTTGTCACATATA
11974 A
1 A
11975 TCACTTGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 10 0.38
29 7 0.27
30 9 0.35
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.44
Consensus pattern (30 bp):
ACATATTCTCTCATACATTTGTCACATATA
Found at i:19018 original size:27 final size:27
Alignment explanation
Indices: 18977--19053 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 27
18967 GGGCAAAACA
* *
18977 GTCATTTTACCCTACAGGGGTATGTCG
1 GTCATTTTACACTACAAGGGTATGTCG
*
19004 GTCATTTTACACTACAAGGGTATTTCG
1 GTCATTTTACACTACAAGGGTATGTCG
* * * *
19031 ATAATTGTACAGTACAAGGGTAT
1 GTCATTTTACACTACAAGGGTAT
19054 TTTGATAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (27 bp):
GTCATTTTACACTACAAGGGTATGTCG
Found at i:19054 original size:27 final size:27
Alignment explanation
Indices: 19018--19305 Score: 296
Period size: 27 Copynumber: 10.7 Consensus size: 27
19008 TTTTACACTA
* *
19018 CAAGGGTATTTCGATAATTGTAC-AGT
1 CAAGGGTATTTCGATAATTTTACAAAT
*
19044 ACAAGGGTATTTTGATAATTTTACAAAT
1 -CAAGGGTATTTCGATAATTTTACAAAT
*
19072 CGAGGGTATTTCGATAATTTTACAAAT
1 CAAGGGTATTTCGATAATTTTACAAAT
*
19099 CAAGGGTATTTCGACAATTTTACAAAT
1 CAAGGGTATTTCGATAATTTTACAAAT
* *
19126 TAAGGGTGTTTCGATAATTTTACAAAT
1 CAAGGGTATTTCGATAATTTTACAAAT
* *
19153 TAAGGGTATTTCAATAATTTTACAAAT
1 CAAGGGTATTTCGATAATTTTACAAAT
* * * * *
19180 CGATGATA-TTCAATAATTTCAC-AAT
1 CAAGGGTATTTCGATAATTTTACAAAT
* *
19205 CGATGGTATTTCGATAATTTTACAAAT
1 CAAGGGTATTTCGATAATTTTACAAAT
** * *
19232 CGGGGGTATTTC-AGTAATTATACAAAC
1 CAAGGGTATTTCGA-TAATTTTACAAAT
* * *
19259 CGAGGGTATTTCGATAAATTTACAAAC
1 CAAGGGTATTTCGATAATTTTACAAAT
** *
19286 CGGGGGTATTTCGGTAATTT
1 CAAGGGTATTTCGATAATTT
19306 CTCTTTATTA
Statistics
Matches: 226, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
25 10 0.04
26 26 0.12
27 187 0.83
28 3 0.01
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (27 bp):
CAAGGGTATTTCGATAATTTTACAAAT
Found at i:19708 original size:27 final size:28
Alignment explanation
Indices: 19622--19712 Score: 112
Period size: 28 Copynumber: 3.3 Consensus size: 28
19612 TAGCCCCTTT
* * * *
19622 AGGCCCAATCTCGTTCACATGGCCCATC
1 AGGCCCAATCACATTCAAATAGCCCATC
* * *
19650 AAGCCTAATCACATTCATATAGCCCATC
1 AGGCCCAATCACATTCAAATAGCCCATC
19678 AGGCCCAATCACATTCAAAT-GCCCATC
1 AGGCCCAATCACATTCAAATAGCCCATC
19705 AGGCCCAA
1 AGGCCCAA
19713 CTACTTCTCA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 15 0.28
28 39 0.72
ACGTcount: A:0.31, C:0.36, G:0.13, T:0.20
Consensus pattern (28 bp):
AGGCCCAATCACATTCAAATAGCCCATC
Found at i:22602 original size:27 final size:27
Alignment explanation
Indices: 22528--22604 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 27
22518 AAAAATAATC
* * * * *
22528 ATTTTACCCTATAGGGGTATGTCAGTC
1 ATTTTACACTACAAGGGTATTTCAGTA
* *
22555 ATTTTACACTACTAGGGTATTTTAGTA
1 ATTTTACACTACAAGGGTATTTCAGTA
22582 ATTTTACACTACAAGGGTATTTC
1 ATTTTACACTACAAGGGTATTTC
22605 GATAAATTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCAGTA
Found at i:22625 original size:27 final size:27
Alignment explanation
Indices: 22595--22854 Score: 239
Period size: 27 Copynumber: 9.7 Consensus size: 27
22585 TTACACTACA
22595 AGGGTATTTCGATAAATTTT-CAAATTG
1 AGGGTATTTCGAT-AATTTTACAAATTG
* *
22622 AGGGTGTTTTGATAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATTG
* **
22649 AGGGTATTTCAATAATTTTACAAATCAA
1 AGGGTATTTCGATAATTTTACAAAT-TG
*
22677 AGGTGT-TTTAG-TAATTTTACAAATTG
1 AGG-GTATTTCGATAATTTTACAAATTG
* * * *
22703 AGGGTATTTTGGTAATTTCACAAATCG
1 AGGGTATTTCGATAATTTTACAAATTG
* * *
22730 AGGATATTT-TAGTAATTTCAC-AATTG
1 AGGGTATTTCGA-TAATTTTACAAATTG
*
22756 AGGGTATTT-TAGTAATTTTACAAATTG
1 AGGGTATTTCGA-TAATTTTACAAATTG
**
22783 AGGGTATTTC-AGTAATTTTACAAACCG
1 AGGGTATTTCGA-TAATTTTACAAATTG
**
22810 AGGGTATTTCGATAATTTTACAAATCA
1 AGGGTATTTCGATAATTTTACAAATTG
22837 AGGGTATTTC-AGTAATTT
1 AGGGTATTTCGA-TAATTT
22855 CTCTTTACTA
Statistics
Matches: 199, Mismatches: 24, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
25 2 0.01
26 37 0.19
27 151 0.76
28 7 0.04
29 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATTG
Found at i:22626 original size:54 final size:54
Alignment explanation
Indices: 22568--22854 Score: 314
Period size: 54 Copynumber: 5.3 Consensus size: 54
22558 TTACACTACT
* ** *
22568 AGGGTATTTTAGTAATTTTAC-ACTACAAGGGTATTTCGATAAATTTT-CAAATTG
1 AGGGTATTTTAGTAATTTTACAAAT-TGAGGGTATTTCGAT-AATTTTACAAATCG
* * *
22622 AGGGTGTTTT-GATAATTTTACAAATTGAGGGTATTTCAATAATTTTACAAATCA
1 AGGGTATTTTAG-TAATTTTACAAATTGAGGGTATTTCGATAATTTTACAAATCG
* * * * *
22676 AAGGTGTTTTAGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAAATCG
1 AGGGTATTTTAGTAATTTTACAAATTGAGGGTATTTCGATAATTTTACAAATCG
* * * *
22730 AGGATATTTTAGTAATTTCAC-AATTGAGGGTATTT-TAGTAATTTTACAAATTG
1 AGGGTATTTTAGTAATTTTACAAATTGAGGGTATTTCGA-TAATTTTACAAATCG
* ** *
22783 AGGGTATTTCAGTAATTTTACAAACCGAGGGTATTTCGATAATTTTACAAATCA
1 AGGGTATTTTAGTAATTTTACAAATTGAGGGTATTTCGATAATTTTACAAATCG
*
22837 AGGGTATTTCAGTAATTT
1 AGGGTATTTTAGTAATTT
22855 CTCTTTACTA
Statistics
Matches: 197, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
53 52 0.26
54 141 0.72
55 4 0.02
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (54 bp):
AGGGTATTTTAGTAATTTTACAAATTGAGGGTATTTCGATAATTTTACAAATCG
Found at i:22653 original size:81 final size:80
Alignment explanation
Indices: 22568--22854 Score: 284
Period size: 81 Copynumber: 3.6 Consensus size: 80
22558 TTACACTACT
*
22568 AGGGTATTTTAGTAATTTTAC-ACTACAAGGGTATTTCGATAAATTTT-CAAATTGAGGGTGTTT
1 AGGGTATTTTAGTAATTTTACAAAT-CAAGGGTATTTCGAT-AATTTTACAAATTGAGGGT-TTT
*
22631 TGATAATTTTACAAATTG
63 TGATAATTTTACAAATCG
* * *
22649 AGGGTATTTCAATAATTTTACAAATCAAAGGTGT-TTTAG-TAATTTTACAAATTGAGGGTATTT
1 AGGGTATTTTAGTAATTTTACAAATC-AAGG-GTATTTCGATAATTTTACAAATTGAGGGT-TTT
* *
22712 TGGTAATTTCACAAATCG
63 TGATAATTTTACAAATCG
* * ** * * *
22730 AGGATATTTTAGTAATTTCAC-AATTGAGGGTATTT-TAGTAATTTTACAAATTGAGGGTATTTC
1 AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTCGA-TAATTTTACAAATTGAGGGTTTTTG
*
22793 AGTAATTTTACAAACCG
65 A-TAATTTTACAAATCG
*
22810 AGGGTA-TTTCGATAATTTTACAAATCAAGGGTATTTC-AGTAATTT
1 AGGGTATTTTAG-TAATTTTACAAATCAAGGGTATTTCGA-TAATTT
22855 CTCTTTACTA
Statistics
Matches: 170, Mismatches: 25, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
78 2 0.01
79 13 0.08
80 55 0.32
81 88 0.52
82 10 0.06
83 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (80 bp):
AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATTGAGGGTTTTTGA
TAATTTTACAAATCG
Found at i:22797 original size:107 final size:108
Alignment explanation
Indices: 22634--22855 Score: 293
Period size: 107 Copynumber: 2.1 Consensus size: 108
22624 GGTGTTTTGA
* * *
22634 TAATTTTACAAATTGAGGGTATTTCAATAATTTTACAAATCAAAGGTGTTTTAGTAATTTTACAA
1 TAATTTCACAAATTGAGGGTATTTCAATAATTTTACAAATCAAAGGTATTTCAGTAATTTTACAA
** * * * *
22699 ATTGAGGGTATTTTGGTAATTTCACAAATCGAGGATATTTTAG
66 ACCGAGGGTATTTCGATAATTTCACAAATCAAGGATATTTCAG
* * ** *
22742 TAATTTCAC-AATTGAGGGTATTTTAGTAATTTTACAAATTGAGGGTATTTCAGTAATTTTACAA
1 TAATTTCACAAATTGAGGGTATTTCAATAATTTTACAAATCAAAGGTATTTCAGTAATTTTACAA
* *
22806 ACCGAGGGTATTTCGATAATTTTACAAATCAAGGGTATTTCAG
66 ACCGAGGGTATTTCGATAATTTCACAAATCAAGGATATTTCAG
22849 TAATTTC
1 TAATTTC
22856 TCTTTACTAT
Statistics
Matches: 98, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
107 90 0.92
108 8 0.08
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (108 bp):
TAATTTCACAAATTGAGGGTATTTCAATAATTTTACAAATCAAAGGTATTTCAGTAATTTTACAA
ACCGAGGGTATTTCGATAATTTCACAAATCAAGGATATTTCAG
Found at i:24604 original size:27 final size:27
Alignment explanation
Indices: 24530--24637 Score: 107
Period size: 27 Copynumber: 4.0 Consensus size: 27
24520 TGGCTGCCAT
* * *
24530 AACAGATA-ATGTGACAGAGTCACCAG
1 AACAGAAATATGTGGCAGAGCCACCAG
24556 ATAC--AAATAATCGTGGCAGAGCCACCAG
1 A-ACAGAAAT-AT-GTGGCAGAGCCACCAG
24584 AACAGAAATATGTGGCAGAGCCACCAG
1 AACAGAAATATGTGGCAGAGCCACCAG
* *
24611 ATCAGATAAT-TGTGGCATAGCCACCAG
1 AACAGA-AATATGTGGCAGAGCCACCAG
24638 GACGCTTCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
25 2 0.03
26 1 0.01
27 43 0.61
28 20 0.29
29 4 0.06
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (27 bp):
AACAGAAATATGTGGCAGAGCCACCAG
Found at i:24626 original size:54 final size:54
Alignment explanation
Indices: 24530--24637 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
24520 TGGCTGCCAT
* *
24530 AACAGATAATGTGACAGAGTCACCAGATACAAATAATCGTGGCAGAGCCACCAG
1 AACAGAAAATGTGACAGAGCCACCAGATACAAATAATCGTGGCAGAGCCACCAG
* * * *
24584 AACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCACCAG
1 AACAGAAA-ATGTGACAGAGCCACCAGATACAAATAATCGTGGCAGAGCCACCAG
24638 GACGCTTCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 29 0.62
55 18 0.38
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (54 bp):
AACAGAAAATGTGACAGAGCCACCAGATACAAATAATCGTGGCAGAGCCACCAG
Found at i:26082 original size:24 final size:24
Alignment explanation
Indices: 26055--26101 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
26045 CTAGATTTCC
**
26055 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
26079 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
26102 CTCCTGACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.02, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:30033 original size:40 final size:40
Alignment explanation
Indices: 29960--30167 Score: 274
Period size: 40 Copynumber: 5.2 Consensus size: 40
29950 CCTTCTGGGT
* * * *
29960 TTAG-CCGGATATAGTTACTCGCTCAAATTCCTTCGGGAC
1 TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC
** * *
29999 TTAGCCCGGTTATAGTAATTCGCACAATTGCCTTCGGGAC
1 TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC
* *
30039 TTAGCCCGAAAATAGCAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC
* *
30079 TTAGCTCAGAAATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC
* *
30119 TTAGCCCGAAAATAGTAACTCGCACAAATACCTTCGGGAC
1 TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC
*
30159 TTCGCCCGG
1 TTAGCCCGG
30168 TTATCATCCA
Statistics
Matches: 146, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 4 0.03
40 142 0.97
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC
Done.