Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold894
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: 24977
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5781 original size:52 final size:52
Alignment explanation
Indices: 5703--5857 Score: 222
Period size: 52 Copynumber: 3.0 Consensus size: 52
5693 CGAAATATGA
5703 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
5755 AAATTTGCCTGTATGTATCGATACATTTTATAGTGTATCGACACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *** *
5807 AAATTTGTCTGCATGTATCGATACA-AAGATCAGTGTATCGATACATTTGGG
1 AAATTTGCCTGCATGTATCGATACATTTCAT-AGTGTATCGATACATCTGGG
5858 TAATGTATCG
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 2 0.02
52 90 0.98
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:5914 original size:13 final size:13
Alignment explanation
Indices: 5896--5978 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
5886 AGCTTCGTAG
5896 CGATACATTGTAT
1 CGATACATTGTAT
5909 CGATACAAACTTATGTAT
1 CGATAC--A--T-TGTAT
5927 CGATACATTGTAT
1 CGATACATTGTAT
5940 CGATACAACACTTGTTTAT
1 CGAT---ACA-TTG--TAT
*
5959 CTATACATTGTAT
1 CGATACATTGTAT
5972 CGATACA
1 CGATACA
5979 ACATTTTGGT
Statistics
Matches: 57, Mismatches: 2, Indels: 22
0.70 0.02 0.27
Matches are distributed among these distances:
13 24 0.42
14 1 0.02
15 4 0.07
16 7 0.12
17 4 0.07
18 11 0.19
19 6 0.11
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:5970 original size:32 final size:32
Alignment explanation
Indices: 5896--5997 Score: 145
Period size: 32 Copynumber: 3.2 Consensus size: 32
5886 AGCTTCGTAG
5896 CGATACATTGTATCGATACAA-ACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* *
5927 CGATACATTGTATCGATACAACACTTGTTTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* *
5959 CTATACATTGTATCGATACAACA-TTTTGGTAT
1 CGATACATTGTATCGATACAACACTTAT-GTAT
5991 CGATACA
1 CGATACA
5998 AATTGTTGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
31 24 0.38
32 39 0.62
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:8444 original size:13 final size:13
Alignment explanation
Indices: 8426--8451 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8416 ACATTTAGTC
8426 ATGTATCGATACA
1 ATGTATCGATACA
8439 ATGTATCGATACA
1 ATGTATCGATACA
8452 TCTTGTATGT
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:8446 original size:33 final size:32
Alignment explanation
Indices: 8404--8471 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
8394 CGTTACAAGC
8404 CAATGTATCGATACAT-TTAGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
8437 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
8469 CAA
1 CAA
8472 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:8558 original size:13 final size:13
Alignment explanation
Indices: 8540--8564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8530 TACAATGGTC
8540 ATGTATCGATACA
1 ATGTATCGATACA
8553 ATGTATCGATAC
1 ATGTATCGATAC
8565 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:8614 original size:19 final size:20
Alignment explanation
Indices: 8574--8615 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
8564 CTGTGCATTA
8574 TGTATCGATACATCTGAAGG
1 TGTATCGATACATCTGAAGG
*
8594 TGTATCGATACAT-TTAAGG
1 TGTATCGATACATCTGAAGG
8613 TGT
1 TGT
8616 CGCAACGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATCTGAAGG
Found at i:9705 original size:79 final size:79
Alignment explanation
Indices: 9588--9789 Score: 212
Period size: 79 Copynumber: 2.6 Consensus size: 79
9578 GAGATAATAA
* * * * ** *
9588 CGGGGTTGGAGTGTCCCCTTGAAAATGACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCGAT-A
9653 -TTAGAGAA-AAA-C
65 TTTAGAGAATAAAGC
* * * *
9665 ATCGGGATTGGAGTATCCTCTCGAAAATAACGGGGTTGGAGTATCCCTAATTATGAGAAATTGAT
1 --CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCGAT
* *
9730 ATTTTGGGAATAAAGC
64 ATTTAGAGAATAAAGC
* **
9746 CGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCC
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCC
9790 TCGATGAAAT
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
78 1 0.01
79 97 0.95
80 3 0.03
81 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCGATAT
TTAGAGAATAAAGC
Found at i:9802 original size:28 final size:26
Alignment explanation
Indices: 9746--9819 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 26
9736 GGAATAAAGC
**
9746 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTAT--CCTCGGAAATAA
9774 CGGGGTTGGAGTATCCTCGATGAAATAA
1 CGGGGTTGGAGTATCCTCG--GAAATAA
*
9802 CGAGGTTGGAGTATCCTC
1 CGGGGTTGGAGTATCCTC
9820 AATTGTGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
26 5 0.12
28 36 0.88
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCTCGGAAATAA
Found at i:9802 original size:107 final size:108
Alignment explanation
Indices: 9667--9999 Score: 284
Period size: 107 Copynumber: 3.1 Consensus size: 108
9657 AGAAAAACAT
* *
9667 CGGGATTGGAGTATCCTCTCGAAAATAACGGGGTTGGAGTATCC-CTAATTATGAGAAATTGAT-
1 CGGGATTGGAGTATCCTCTCGAAAATAACGAGGTTGGAGTATCCTC-AATTATGAAAAATTGATG
* * *
9730 ATTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAA
65 ATTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAGGTAA
* * *
9774 CGGGGTTGGAGTAT-C-CTCGATGAAATAACGAGGTTGGAGTATCCTCAATTGTGAAAAATTGGT
1 CGGGATTGGAGTATCCTCTCGA--AAATAACGAGGTTGGAGTATCCTCAATTATGAAAAATTGAT
* * *
9837 GTTTTTGGAAATAAAATCGGAGTTGGAGTAT-CCC-C-GA-TTAA
64 GATTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAGGTAA
* * * * * * * *
9878 AGGAAAATTGGTGT-T--T-T-GAAAATAAAGTCGGGGTTGGAGTATCCCCGATT-CGAAAAATC
1 CGG--GATTGGAGTATCCTCTCGAAAAT-AA--CGAGGTTGGAGTATCCTCAATTATGAAAAATT
*
9937 GATGA-TTTGGAAATAAAACCTGG-GTTGGAGTATCCCCTCGGAGATAA
61 GATGATTTTGGAAATAAAACC-GGAGTTGGAGTATCCCCTCGGAGGTAA
*
9984 CGGGGTTGGAGTATCC
1 CGGGATTGGAGTATCC
10000 CCGATTATGA
Statistics
Matches: 180, Mismatches: 28, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
101 4 0.02
102 26 0.14
103 17 0.09
104 32 0.18
105 11 0.06
106 13 0.07
107 51 0.28
108 26 0.14
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (108 bp):
CGGGATTGGAGTATCCTCTCGAAAATAACGAGGTTGGAGTATCCTCAATTATGAAAAATTGATGA
TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAGGTAA
Found at i:9895 original size:52 final size:49
Alignment explanation
Indices: 9805--9973 Score: 176
Period size: 52 Copynumber: 3.3 Consensus size: 49
9795 GAAATAACGA
* * *
9805 GGTTGGAGTATCCTCAATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATT-AGAAAAATTGGTG-TTTTGGAAATAAAATCG
* * *
9856 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAGTCGG
1 G-GTTGGAGTATCCCCGATT--AGAAAAATTGGTGTTTTGGAAATAAAATC-G
* * * * *
9909 GGTTGGAGTATCCCCGATTCGAAAAATCGATGATTTGGAAATAAAACCTG
1 GGTTGGAGTATCCCCGATTAGAAAAATTGGTGTTTTGGAAATAAAATC-G
9959 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
9974 TCGGAGATAA
Statistics
Matches: 99, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
50 37 0.37
51 1 0.01
52 48 0.48
53 13 0.13
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (49 bp):
GGTTGGAGTATCCCCGATTAGAAAAATTGGTGTTTTGGAAATAAAATCG
Found at i:9962 original size:50 final size:50
Alignment explanation
Indices: 9840--9973 Score: 153
Period size: 50 Copynumber: 2.6 Consensus size: 50
9830 AATTGGTGTT
* * * *
9840 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGT
1 TTTGGAAATAAAATCGG-GTTGGAGTATCCCCGATT-AAGAAAAATCGATGA
* * *
9892 TTTGAAAATAAAGTCGGGGTTGGAGTATCCCCGATT-CGAAAAATCGATGA
1 TTTGGAAATAAAATC-GGGTTGGAGTATCCCCGATTAAGAAAAATCGATGA
*
9942 TTTGGAAATAAAACCTGGGTTGGAGTATCCCC
1 TTTGGAAATAAAATC-GGGTTGGAGTATCCCC
9974 TCGGAGATAA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
50 37 0.53
52 31 0.44
53 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (50 bp):
TTTGGAAATAAAATCGGGTTGGAGTATCCCCGATTAAGAAAAATCGATGA
Found at i:9999 original size:78 final size:80
Alignment explanation
Indices: 9906--10080 Score: 241
Period size: 80 Copynumber: 2.2 Consensus size: 80
9896 AAAATAAAGT
* * *
9906 CGGGGTTGGAGTATCCCCGATT-CGA-AAAATCGATGA-TTTGGAAATAAAACCTG-GGTTGGAG
1 CGGGGTTGGAGTATCCCCGATTACGAGAAAAT-AAT-ATTTTAGAAATAAAACCGGAGGTTGGAG
* *
9967 TATCCCCTCGGAGATAA
64 TATCCCCTCGAAAATAA
* *
9984 CGGGGTTGGAGTATCCCCGATTATGAGAAAATAATATTTTAGAAATAAAGCCGGAGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTACGAGAAAATAATATTTTAGAAATAAAACCGGAGGTTGGAGTA
10049 TCCCCTCGAAAATAA
66 TCCCCTCGAAAATAA
10064 CGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
10081 TGATGATTAA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
78 23 0.27
79 18 0.21
80 45 0.52
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (80 bp):
CGGGGTTGGAGTATCCCCGATTACGAGAAAATAATATTTTAGAAATAAAACCGGAGGTTGGAGTA
TCCCCTCGAAAATAA
Found at i:10091 original size:27 final size:27
Alignment explanation
Indices: 10039--10114 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
10029 TAAAGCCGGA
*
10039 GGTTGGAGTATCCCCTCGA-AAATAACGG
1 GGTTGGAGTAT-CCCT-GATGAATAACGG
*
10067 GGTTGGAGTATCCCTGATGATTAACGG
1 GGTTGGAGTATCCCTGATGAATAACGG
*
10094 GGTTGGAGTATCCCCGATGAA
1 GGTTGGAGTATCCCTGATGAA
10115 AAATTGATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 2 0.05
27 30 0.70
28 11 0.26
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (27 bp):
GGTTGGAGTATCCCTGATGAATAACGG
Found at i:12661 original size:19 final size:19
Alignment explanation
Indices: 12637--12767 Score: 136
Period size: 19 Copynumber: 7.8 Consensus size: 19
12627 TAGTAGCTAA
12637 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
12656 TTATGTATCGATAC---A-
1 TTATGTATCGATACAATAC
12671 -T-TGTATCGATACAATAC
1 TTATGTATCGATACAATAC
12688 TTATGTATCGATAC---A-
1 TTATGTATCGATACAATAC
12703 -T-TGTATCGATACAATAC
1 TTATGTATCGATACAATAC
12720 TTATGTATCGATAC---A-
1 TTATGTATCGATACAATAC
12735 -T-TGTATCGATACAATAC
1 TTATGTATCGATACAATAC
12752 TTATGTATCGATACAA
1 TTATGTATCGATACAA
12768 ATTGTTGAAT
Statistics
Matches: 94, Mismatches: 0, Indels: 36
0.72 0.00 0.28
Matches are distributed among these distances:
13 33 0.35
14 3 0.03
16 6 0.06
18 3 0.03
19 49 0.52
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (19 bp):
TTATGTATCGATACAATAC
Found at i:12677 original size:13 final size:13
Alignment explanation
Indices: 12659--12747 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
12649 ACAATACTTA
12659 TGTATCGATACAT
1 TGTATCGATACAT
12672 TGTATCGATACAATACTT
1 TGTATCGATAC---A--T
12690 ATGTATCGATACAT
1 -TGTATCGATACAT
12704 TGTATCGATACAATACTT
1 TGTATCGATAC---A--T
12722 ATGTATCGATACAT
1 -TGTATCGATACAT
12736 TGTATCGATACA
1 TGTATCGATACA
12748 ATACTTATGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
14 2 0.03
16 4 0.06
18 2 0.03
19 22 0.34
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12681 original size:32 final size:32
Alignment explanation
Indices: 12640--12766 Score: 254
Period size: 32 Copynumber: 4.0 Consensus size: 32
12630 TAGCTAATTA
12640 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
12672 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
12704 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
12736 TGTATCGATACAATACTTATGTATCGATACA
1 TGTATCGATACAATACTTATGTATCGATACA
12767 AATTGTTGAA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 95 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAATACTTATGTATCGATACAT
Found at i:12847 original size:21 final size:21
Alignment explanation
Indices: 12823--12876 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
12813 ACATTTGTAG
*
12823 AATGTATCGATACTTTCCACA
1 AATGTATCGATACATTCCACA
*
12844 AATGTATCGATACATTCTACA
1 AATGTATCGATACATTCCACA
12865 AATGTATCGATA
1 AATGTATCGATA
12877 TATTTGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
AATGTATCGATACATTCCACA
Found at i:19242 original size:3 final size:3
Alignment explanation
Indices: 19229--19262 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
19219 ACCATCCAAA
*
19229 ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
19263 GCAAGAGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:19800 original size:21 final size:20
Alignment explanation
Indices: 19776--19827 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
19766 TTGCAAGAAG
*
19776 AAAACACAAAATTAACTAATA
1 AAAACA-AAAATTAACTAAGA
* *
19797 AAAACAATGAATTGACTAAGA
1 AAAACAA-AAATTAACTAAGA
19818 AAAACAAAAA
1 AAAACAAAAA
19828 CTTCCATGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15
Consensus pattern (20 bp):
AAAACAAAAATTAACTAAGA
Found at i:21169 original size:27 final size:27
Alignment explanation
Indices: 21131--21185 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
21121 ACTTCTCTAC
21131 TCCTAGAAATCCTCAACAAAATGGAGT
1 TCCTAGAAATCCTCAACAAAATGGAGT
21158 TCCTAGAAATCCTCAACAAAATGGAGT
1 TCCTAGAAATCCTCAACAAAATGGAGT
21185 T
1 T
21186 ATTGAAAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.24
Consensus pattern (27 bp):
TCCTAGAAATCCTCAACAAAATGGAGT
Found at i:23454 original size:6 final size:7
Alignment explanation
Indices: 23407--23453 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
23397 TTTAAAAAAT
23407 AATTTTA
1 AATTTTA
23414 AATTTTA
1 AATTTTA
23421 AATTTT-
1 AATTTTA
23427 AATATTTA
1 AAT-TTTA
23435 TAATTTT-
1 -AATTTTA
*
23442 TATTTTA
1 AATTTTA
23449 AATTT
1 AATTT
23454 ATGATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
6 8 0.24
7 20 0.59
8 3 0.09
9 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
AATTTTA
Found at i:23462 original size:21 final size:21
Alignment explanation
Indices: 23422--23469 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
23412 TAAATTTTAA
23422 ATTTTAATATTTATAATTTTT
1 ATTTTAATATTTATAATTTTT
*
23443 ATTTTAA-ATTTATGA-TTTT
1 ATTTTAATATTTATAATTTTT
23462 -TTTTAATA
1 ATTTTAATA
23470 AAATAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 5 0.20
20 7 0.28
21 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTAATATTTATAATTTTT
Found at i:23742 original size:24 final size:24
Alignment explanation
Indices: 23691--23765 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
23681 TTATAATGTA
23691 ATAATATTA-AAATA-TAATATATTAT
1 ATAA-ATTATAAATATTAATA-ATT-T
23716 ATAAATTATAAATATTAATAATTT
1 ATAAATTATAAATATTAATAATTT
* * *
23740 AT-ATTATATAAATTTTAATATTTT
1 ATAAAT-TATAAATATTAATAATTT
23764 AT
1 AT
23766 GTGCTTATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 2 0.05
24 25 0.57
25 12 0.27
26 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATAAATTATAAATATTAATAATTT
Found at i:23806 original size:20 final size:19
Alignment explanation
Indices: 23773--23836 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
23763 TATGTGCTTA
**
23773 TATTATTTCGTATTTTTTT
1 TATTATTTTATATTTTTTT
23792 ATATTATTTTATATTTTATTT
1 -TATTATTTTATATTTT-TTT
23813 TA-TATTTTA-ATTATTTTT
1 TATTATTTTATATT-TTTTT
23831 TATTAT
1 TATTAT
23837 ATTCATCTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.21
19 12 0.31
20 16 0.41
21 3 0.08
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TATTATTTTATATTTTTTT
Found at i:23831 original size:11 final size:10
Alignment explanation
Indices: 23783--23839 Score: 53
Period size: 10 Copynumber: 5.4 Consensus size: 10
23773 TATTATTTCG
*
23783 TATTTTTTTA
1 TATTTTATTA
23793 TATTATT-TTA
1 TATT-TTATTA
23803 TATTTTATTTTA
1 TATTTTA--TTA
23815 TATTTTAATTA
1 TATTTT-ATTA
*
23826 TTTTTTATTA
1 TATTTTATTA
23836 TATT
1 TATT
23840 CATCTTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 2 0.05
10 18 0.45
11 10 0.25
12 9 0.22
13 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TATTTTATTA
Found at i:23839 original size:12 final size:12
Alignment explanation
Indices: 23795--23834 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
23785 TTTTTTTATA
23795 TTATTTTATATT
1 TTATTTTATATT
23807 TTATTTTATATT
1 TTATTTTATATT
* *
23819 TTA-ATTATTTT
1 TTATTTTATATT
23830 TTATT
1 TTATT
23835 ATATTCATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTATTTTATATT
Done.