Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013124.1 Corchorus capsularis cultivar CVL-1 contig13145, whole genome shotgun sequence
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: 89542
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1088 original size:16 final size:16
Alignment explanation
Indices: 1055--1107 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 16
1045 GTTGTCGGAG
*
1055 AAGAAGAAGTGAAGAA
1 AAGAAAAAGTGAAGAA
1071 AAGAAAAAG-GAAGAA
1 AAGAAAAAGTGAAGAA
*
1086 AA-AAAAAGAGAA-AA
1 AAGAAAAAGTGAAGAA
*
1100 AATAAAAA
1 AAGAAAAA
1108 AAGGGCGGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.29
15 16 0.47
16 8 0.24
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (16 bp):
AAGAAAAAGTGAAGAA
Found at i:3134 original size:2 final size:2
Alignment explanation
Indices: 3127--3157 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3117 AAAAAGAGTA
3127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3158 ACTGTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7599 original size:30 final size:30
Alignment explanation
Indices: 7563--7820 Score: 308
Period size: 30 Copynumber: 8.6 Consensus size: 30
7553 AATAGTGTAT
* *
7563 ATGACAACTTCTTGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
7593 ATGACAAC--AT-GTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
7620 ATGACAACTTCTGGTGTCCATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* **
7650 ATGACATCTAT-AAGTGTCAATTGCAAAATC
1 ATGACAACT-TCTGGTGTCAATTGCAAAATC
*
7680 ATGACAACTTATGGTGTCAATTGCAAAAAATC
1 ATGACAACTTCTGGTGTCAATTGC--AAAATC
* *
7712 ATGACAACTTATGGTGTTAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * *
7742 TTGACAAATTATGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
**
7772 ATGACAACTTCTATTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
7802 ATGACAATTTCTGGTGTCA
1 ATGACAACTTCTGGTGTCA
7821 TTTGGAGAGT
Statistics
Matches: 198, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
27 25 0.13
28 1 0.01
29 2 0.01
30 140 0.71
31 1 0.01
32 29 0.15
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAAATC
Found at i:7741 original size:92 final size:88
Alignment explanation
Indices: 7576--7820 Score: 318
Period size: 92 Copynumber: 2.7 Consensus size: 88
7566 ACAACTTCTT
* * *
7576 GTGTCAATTGCAAGATCATGACAAC--ATGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCC
1 GTGTCAATTGCAAAATCATGACAACTTATGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCA
7639 ATTGCAAAATCATGAC-ATCTATAA
66 ATTGCAAAATCATGACAAT-TAT-A
*
7663 GTGTCAATTGCAAAATCATGACAACTTATGGTGTCAATTGCAAAAAATCATGACAACTTATGGTG
1 GTGTCAATTGCAAAATCATGACAACTTAT-GTGTCAATTGC--AAAATCATGACAACTTCTGGTG
* * *
7728 TTAATTGCAAAATCTTGACAAATTATG
63 TCAATTGCAAAATCATGAC-AATTATA
*
7755 GTGTCAATTGCAAAATCATGACAACTTCTAT-TGTCAATTGCAAAATCATGACAATTTCTGGTGT
1 GTGTCAATTGCAAAATCATGACAAC-T-TATGTGTCAATTGCAAAATCATGACAACTTCTGGTGT
7819 CA
64 CA
7821 TTTGGAGAGT
Statistics
Matches: 139, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
87 24 0.17
89 2 0.01
90 33 0.24
92 71 0.51
93 4 0.03
94 5 0.04
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (88 bp):
GTGTCAATTGCAAAATCATGACAACTTATGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCA
ATTGCAAAATCATGACAATTATA
Found at i:16872 original size:41 final size:41
Alignment explanation
Indices: 16727--16873 Score: 206
Period size: 41 Copynumber: 3.6 Consensus size: 41
16717 CTGGACTAAC
*
16727 ACTTCTGGTGTCAAATGTAATTTTAATTTACCAAAGTGACA
1 ACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAAGTGACA
* * *
16768 AATTCTGGTGTCAAAGGTAATTTTAATTTACCAATGTGACA
1 ACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAAGTGACA
* ** *
16809 ACTTCTAGTGTCAGCAGTAATTTTAATTTACCAAAATGACA
1 ACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAAGTGACA
16850 ACTTCTGGTGTCAAAAAG-AATTTT
1 ACTTCTGGTGTC-AAAAGTAATTTT
16874 CAATGTTATT
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 89 0.97
42 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (41 bp):
ACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAAGTGACA
Found at i:20401 original size:22 final size:22
Alignment explanation
Indices: 20376--20568 Score: 115
Period size: 22 Copynumber: 8.7 Consensus size: 22
20366 ATAACCAGAT
*
20376 TATGAAATTTTGATAACCTTGC
1 TATGAAATTTTGATAACCTTCC
* * * *
20398 TATGCAATATTAATAACTTGATCC
1 TATGAAATTTTGATAACCT--TCC
* * * * *
20422 TATAAAAATTCGGTAACCTTGC
1 TATGAAATTTTGATAACCTTCC
* * **
20444 TATGAAATTTTGGTAACCATAT
1 TATGAAATTTTGATAACCTTCC
* *
20466 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
**
20488 TACCAAATTTT-ATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
*
20508 ATATGAAATTTGGATAACC-TCC
1 -TATGAAATTTTGATAACCTTCC
* * *
20530 AATTGAAATTTTGATTACC-ACAC
1 TA-TGAAATTTTGATAACCTTC-C
20553 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
20569 TCACACAAAA
Statistics
Matches: 127, Mismatches: 38, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
20 2 0.02
21 15 0.12
22 95 0.75
23 2 0.02
24 13 0.10
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:21458 original size:20 final size:20
Alignment explanation
Indices: 21433--21470 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
21423 ACCTCCTTAT
21433 GAAATTTTGATAACCACACC
1 GAAATTTTGATAACCACACC
21453 GAAATTTTGATAACCACA
1 GAAATTTTGATAACCACA
21471 TTATGAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (20 bp):
GAAATTTTGATAACCACACC
Found at i:21484 original size:22 final size:22
Alignment explanation
Indices: 21367--21487 Score: 84
Period size: 22 Copynumber: 5.6 Consensus size: 22
21357 CTACAATGTA
* * **
21367 GAAATATTGATAACCATATCGT
1 GAAATTTTGATAACCACATTAT
* * * *
21389 GAAAATATGATAAGCTCATTAT
1 GAAATTTTGATAACCACATTAT
** * * *
21411 GAAATTTCAATTACCTCCTTAT
1 GAAATTTTGATAACCACATTAT
**
21433 GAAATTTTGATAACCACA--CC
1 GAAATTTTGATAACCACATTAT
21453 GAAATTTTGATAACCACATTAT
1 GAAATTTTGATAACCACATTAT
*
21475 GAAATCTTGATAA
1 GAAATTTTGATAA
21488 TCTCCTTATG
Statistics
Matches: 72, Mismatches: 25, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
20 18 0.25
22 54 0.75
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (22 bp):
GAAATTTTGATAACCACATTAT
Found at i:21500 original size:22 final size:22
Alignment explanation
Indices: 21429--21487 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 22
21419 AATTACCTCC
*
21429 TTATGAAATTTTGATAACCACA
1 TTATGAAATCTTGATAACCACA
** *
21451 --CCGAAATTTTGATAACCACA
1 TTATGAAATCTTGATAACCACA
21471 TTATGAAATCTTGATAA
1 TTATGAAATCTTGATAA
21488 TCTCCTTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 18 0.60
22 12 0.40
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (22 bp):
TTATGAAATCTTGATAACCACA
Found at i:21635 original size:22 final size:22
Alignment explanation
Indices: 21610--21864 Score: 124
Period size: 22 Copynumber: 11.6 Consensus size: 22
21600 CTCTTTATGT
*
21610 AATTTTGATAATCTCTCTATAA
1 AATTTTGATAACCTCTCTATAA
** * * *
21632 AATTTCCAAAACCTCCCTATGA
1 AATTTTGATAACCTCTCTATAA
*
21654 AATTTTGTTAACCTC-CTTATAA
1 AATTTTGATAACCTCTC-TATAA
* * *
21676 AATTTTGATAACCACACTAAAA
1 AATTTTGATAACCTCTCTATAA
* * * *
21698 AATTTCGATAACCTTTGTATGA
1 AATTTTGATAACCTCTCTATAA
* * * *
21720 AATTTTGTTAATCTCCCTAAAA
1 AATTTTGATAACCTCTCTATAA
* * * *
21742 AACTTTGATAACCTTTTTATGA
1 AATTTTGATAACCTCTCTATAA
* * * *
21764 AATTTTGGTAACC-CTTGTGTTA
1 AATTTTGATAACCTC-TCTATAA
* *
21786 AATTTTGATAA-CTACACTATGA
1 AATTTTGATAACCT-CTCTATAA
* *
21808 AGTTTTGATAACCTC-CATATGA
1 AATTTTGATAACCTCTC-TATAA
* * * * *
21830 AATTTTGGTAAACACACTAT-G
1 AATTTTGATAACCTCTCTATAA
21851 AATTTTGATAACCT
1 AATTTTGATAACCT
21865 TCCTAAGTAA
Statistics
Matches: 168, Mismatches: 57, Indels: 17
0.69 0.24 0.07
Matches are distributed among these distances:
21 14 0.08
22 149 0.89
23 5 0.03
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
AATTTTGATAACCTCTCTATAA
Found at i:21700 original size:66 final size:66
Alignment explanation
Indices: 21610--21754 Score: 173
Period size: 66 Copynumber: 2.2 Consensus size: 66
21600 CTCTTTATGT
* * * * * *
21610 AATTTTGATAATCTCTCTATAAAATTTCCAAAACCTCCCTATGAAATTTTGTTAACCTCCTTATA
1 AATTTTGATAACCACACTAAAAAATTTCCAAAACCTCCCTATGAAATTTTGTTAACCTCCCTAAA
21675 A
66 A
* * *** *
21676 AATTTTGATAACCACACTAAAAAATTTCGATAACCTTTGTATGAAATTTTGTTAATCTCCCTAAA
1 AATTTTGATAACCACACTAAAAAATTTCCAAAACCTCCCTATGAAATTTTGTTAACCTCCCTAAA
21741 A
66 A
*
21742 AACTTTGATAACC
1 AATTTTGATAACC
21755 TTTTTATGAA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.37
Consensus pattern (66 bp):
AATTTTGATAACCACACTAAAAAATTTCCAAAACCTCCCTATGAAATTTTGTTAACCTCCCTAAA
A
Found at i:21877 original size:43 final size:44
Alignment explanation
Indices: 21785--21881 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 44
21775 CCCTTGTGTT
* *
21785 AAATTTTGATAACTACACTATGAAGTTTTGATAACCTCCATATG
1 AAATTTTGGTAACTACACTATGAAGTTTTGATAACCTCCATAAG
21829 AAATTTTGGTAAAC-ACACTATGAA-TTTTGATAACCTTCC-TAAG
1 AAATTTTGGT-AACTACACTATGAAGTTTTGATAACC-TCCATAAG
*
21872 TAATTTTGGT
1 AAATTTTGGT
21882 TTGATTGTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
43 23 0.48
44 22 0.46
45 3 0.06
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (44 bp):
AAATTTTGGTAACTACACTATGAAGTTTTGATAACCTCCATAAG
Found at i:22272 original size:2 final size:2
Alignment explanation
Indices: 22265--22293 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22255 GGTAAATTAC
22265 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22294 CATGTGGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22795 original size:33 final size:33
Alignment explanation
Indices: 22753--22819 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
22743 GCTTATTTTG
*
22753 TTTGATTACAAAGAAATCAATGGAAATGAAGTA
1 TTTGATTACAAAGAAATCAATGAAAATGAAGTA
22786 TTTGATTACAAAGAAATCAATGAAAATGAAGTA
1 TTTGATTACAAAGAAATCAATGAAAATGAAGTA
22819 T
1 T
22820 GGCAAATAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.28
Consensus pattern (33 bp):
TTTGATTACAAAGAAATCAATGAAAATGAAGTA
Found at i:23987 original size:5 final size:5
Alignment explanation
Indices: 23977--24034 Score: 88
Period size: 5 Copynumber: 12.4 Consensus size: 5
23967 TATATAGTAG
23977 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T-AG- TAAGA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA
24025 T-AG- TAAGA TA
1 TAAGA TAAGA TA
24035 TTTCTTTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
3 2 0.04
4 8 0.16
5 39 0.80
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:24752 original size:2 final size:2
Alignment explanation
Indices: 24745--24780 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
24735 CTATCAAGAT
24745 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24781 TGGTGTGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26080 original size:5 final size:5
Alignment explanation
Indices: 26070--26096 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
26060 TTAGTCGTGT
26070 ACACG ACACG ACACG ACACG ACACG AC
1 ACACG ACACG ACACG ACACG ACACG AC
26097 TAAACACGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.41, G:0.19, T:0.00
Consensus pattern (5 bp):
ACACG
Found at i:27199 original size:26 final size:25
Alignment explanation
Indices: 27156--27211 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
27146 GAAAAGGAAA
27156 GAAAAGAAAAGAAAAAGGG-AAATAG
1 GAAAAGAAAAGAAAAAGGGAAAAT-G
27181 GAAAA-AATAAGAAATAAGGGAAAATG
1 GAAAAGAA-AAGAAA-AAGGGAAAATG
27207 GAAAA
1 GAAAA
27212 TTTGGGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 2 0.07
25 11 0.39
26 11 0.39
27 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.25, T:0.07
Consensus pattern (25 bp):
GAAAAGAAAAGAAAAAGGGAAAATG
Found at i:27329 original size:18 final size:18
Alignment explanation
Indices: 27306--27341 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27296 CTCAATTAGT
*
27306 GAATCATTGAACGCGGTC
1 GAATCAGTGAACGCGGTC
27324 GAATCAGTGAACGCGGTC
1 GAATCAGTGAACGCGGTC
27342 ATATTTCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.19
Consensus pattern (18 bp):
GAATCAGTGAACGCGGTC
Found at i:35180 original size:27 final size:27
Alignment explanation
Indices: 35150--35203 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
35140 CTGCATTCTA
35150 GCTTTTTGCTGCCATGACCTCTCAACC
1 GCTTTTTGCTGCCATGACCTCTCAACC
35177 GCTTTTTGCTGCCATGACCTCTCAACC
1 GCTTTTTGCTGCCATGACCTCTCAACC
35204 ATTCTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.37, G:0.15, T:0.33
Consensus pattern (27 bp):
GCTTTTTGCTGCCATGACCTCTCAACC
Found at i:47895 original size:130 final size:130
Alignment explanation
Indices: 47681--48416 Score: 985
Period size: 130 Copynumber: 5.7 Consensus size: 130
47671 ACAATAATTA
* * * * * * *
47681 AAAGTCGTTGTCTTAGAGATTTTGATGGTATTTTACCCAACGACTTTTTAAATTGGTGCCAATGC
1 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACACAAC-ACTTTTTTAGTTGTTGCCAATGC
* * * * * *
47746 TTACAGTTTTCGCAACAACAAAAACAAAATTGTTGAAAAATCATAATCTATTCGTAATAATTTTA
65 TTACAATTTTCGTAACAACAAAAACAAAGTCGTTGCAAAATCATAATCTATTCGTAACAATTTTA
47811 T
130 T
* * * *
47812 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTGATACAACACTTTTTTAATCGTTGCCAATGCT
1 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGCT
* *
47877 TACGATTTTTGTAACAACAAAAACAAAGTCGTTGCAAAATCATAAAT-TATTCGTAACAACTTTT
66 TACAATTTTCGTAACAACAAAAACAAAGTCGTTGCAAAATCAT-AATCTATTCGTAACAA-TTTT
47941 AT
129 AT
* *
47943 AAA-ACGTTGCCTAAGTGATTTTGATGGTATTTTAAACAACA-TTTTTCTAGTTGTTGCCAATGC
1 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTT-TAGTTGTTGCCAATGC
* * * *
48006 TTACAATTTTTGTAACAACAAAAACAAAGTCGCTGCGAAATCATAATTTATTCGTAACAATTTTA
65 TTACAATTTTCGTAACAACAAAAACAAAGTCGTTGCAAAATCATAATCTATTCGTAACAATTTTA
48071 T
130 T
* *
48072 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACGCAACACTTTTTTAGTCGTTGCCAATGCT
1 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGCT
* ** * *
48137 TACAATTTTCGTAACAACAAAAACAAAGTTGTTGTTAAATCATAAACTATTCGTAACAACTTTAT
66 TACAATTTTCGTAACAACAAAAACAAAGTCGTTGCAAAATCATAATCTATTCGTAACAATTTTAT
** * * *
48202 AAAAACGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACATTTTTAGTTGTTCCCCATGCT
1 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGCT
* * * *
48267 TACAATTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATAATCTATTTGTAAAAACTTTAT
66 TACAATTTTCGTAACAACAAAAACAAAGTCGTTGCAAAATCATAATCTATTCGTAACAATTTTAT
* * * * *
48332 AAAGTCATTGCCTAAGTGATTTTGAAGGTATTTTACACAACA-TTTATTAGTTGTTGTCAATGTT
1 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGCT
*
48396 TACAATATTCGTAACAACAAA
66 TACAATTTTCGTAACAACAAA
48417 TTTTTTAGTT
Statistics
Matches: 538, Mismatches: 61, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
129 53 0.10
130 433 0.80
131 52 0.10
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGCT
TACAATTTTCGTAACAACAAAAACAAAGTCGTTGCAAAATCATAATCTATTCGTAACAATTTTAT
Found at i:51921 original size:2 final size:2
Alignment explanation
Indices: 51914--51956 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
51904 TCAATGTGAT
* *
51914 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA CA 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
51956 T
1 T
51957 GATTCACTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53936 original size:133 final size:132
Alignment explanation
Indices: 53737--54188 Score: 366
Period size: 133 Copynumber: 3.4 Consensus size: 132
53727 TTTTACCTAC
* * * *
53737 AAAAGTATTTACAGCCAAAATA---ATGTTGTGTAATAATTTTGGCAACAACATTTTGTCATTTT
1 AAAAGTATTTACAACCAAAATACTGTTGTTGTGTAA-AATTTTGACAACAACATTTTGCCATTTT
* *
53799 AAAAAGTAAGTTGTAAC-AA-AAAATGTCGTTTTAAAAACCTTCACCCAA-TAATTAAAATATTG
65 AAAAAGTAAGTTGTAACTAACAAAATATCGTTATAAAAACCTTCACCCAACT-A-T-AAATATTG
* *
53861 TTATAT
127 TTACAG
* * * * *
53867 AAAAGTATTTACAACCAAAGTGA-TGTTGTTGTGTAAACATTTTGACAATATCCTTTTGCCGTTT
1 AAAAGTATTTACAACCAAAAT-ACTGTTGTTGTGTAAA-ATTTTGACAACAACATTTTGCCATTT
* * * * * *
53931 TAAAAAGTCATTTGTAACTAACTAGATATCGTTATAAAAACCTTTACGCAACTATAAATATTGTT
64 TAAAAAGTAAGTTGTAACTAACAAAATATCGTTATAAAAACCTTCACCCAACTATAAATATTGTT
* *
53996 GCCG
129 ACAG
* ** *
54000 AAAAGTATTTACAACCAAAATACTTTTGTTGTGTAAATATTTTGACAACAACATTTTTTCGTTTT
1 AAAAGTATTTACAACCAAAATACTGTTGTTGTGTAAA-ATTTTGACAACAACATTTTGCCATTTT
* *** * * * * * * *
54065 AAAACATTTTTTTGCAACCAACTAAATATCATTATAAAAAACTTTACACAACTAATAAATATTGT
65 AAAA-AGTAAGTTGTAACTAACAAAATATCGTTATAAAAACCTTCACCCAACT-ATAAATATTGT
*
54130 TACCG
128 TACAG
* * * * *
54135 AAAACTATTTACAACAAAAATAATTTTG-T-TGTAAACATTTTGTCAAC-ACATTTT
1 AAAAGTATTTACAACCAAAATACTGTTGTTGTGTAAA-ATTTTGACAACAACATTTT
54189 ATCGTTTTAA
Statistics
Matches: 268, Mismatches: 44, Indels: 18
0.81 0.13 0.05
Matches are distributed among these distances:
130 19 0.07
131 1 0.00
132 9 0.03
133 131 0.49
134 43 0.16
135 64 0.24
136 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (132 bp):
AAAAGTATTTACAACCAAAATACTGTTGTTGTGTAAAATTTTGACAACAACATTTTGCCATTTTA
AAAAGTAAGTTGTAACTAACAAAATATCGTTATAAAAACCTTCACCCAACTATAAATATTGTTAC
AG
Found at i:54155 original size:135 final size:133
Alignment explanation
Indices: 53853--54225 Score: 421
Period size: 133 Copynumber: 2.8 Consensus size: 133
53843 CCAATAATTA
*** * * * * * * *
53853 AAATATTGTTATATAAAAGTATTTACAACCAAAGTGATGTTGTTGTGTAAACATTTTGACAATAT
1 AAATATTGTTACCGAAAACTATTTACAACAAAAATAATTTTGTTGTGTAAACATTTTGACAACAA
* ** * * * * * * * *
53918 CCTTTTGCCGTTTTAAAAAGTCATTTGTAACTAACTAGATATCGTTATAAAAACCTTTACGCAAC
66 CATTTTATCGTTTTAAAAATTTATTTGCAACCAACTAAATATCATTATAAAAAACTTTACACAAC
53983 TAT
131 TAT
* * * * *
53986 AAATATTGTTGCCGAAAAGTATTTACAACCAAAATACTTTTGTTGTGTAAATATTTTGACAACAA
1 AAATATTGTTACCGAAAACTATTTACAACAAAAATAATTTTGTTGTGTAAACATTTTGACAACAA
* *
54051 CATTTTTTCGTTTTAAAACATTTTTTTGCAACCAACTAAATATCATTATAAAAAACTTTACACAA
66 CATTTTATCGTTTTAAAA-ATTTATTTGCAACCAACTAAATATCATTATAAAAAACTTTACACAA
54116 CTAAT
130 CT-AT
*
54121 AAATATTGTTACCGAAAACTATTTACAACAAAAATAATTTTG-T-TGTAAACATTTTGTCAAC-A
1 AAATATTGTTACCGAAAACTATTTACAACAAAAATAATTTTGTTGTGTAAACATTTTGACAACAA
*
54183 CATTTTATCGTTTT-AAAATGTTATTCGCAACCAACTAAATATC
66 CATTTTATCGTTTTAAAAAT-TTATTTGCAACCAACTAAATATC
54226 GTTGTAAATA
Statistics
Matches: 205, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
130 2 0.01
131 24 0.12
132 14 0.07
133 85 0.41
134 40 0.20
135 40 0.20
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (133 bp):
AAATATTGTTACCGAAAACTATTTACAACAAAAATAATTTTGTTGTGTAAACATTTTGACAACAA
CATTTTATCGTTTTAAAAATTTATTTGCAACCAACTAAATATCATTATAAAAAACTTTACACAAC
TAT
Found at i:54246 original size:34 final size:34
Alignment explanation
Indices: 54188--54256 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
54178 CAACACATTT
* * *
54188 TATCGTTTTAAAATGTTATTCGCAACCAACTAAA
1 TATCGTTGTAAAATATTATTCGCAACCAAATAAA
54222 TATCGTTGT-AAATATTATTACGCAACCAAATAAA
1 TATCGTTGTAAAATATTATT-CGCAACCAAATAAA
54256 T
1 T
54257 GTTGTCACGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 9 0.29
34 22 0.71
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.35
Consensus pattern (34 bp):
TATCGTTGTAAAATATTATTCGCAACCAAATAAA
Found at i:59195 original size:29 final size:29
Alignment explanation
Indices: 59153--59277 Score: 125
Period size: 29 Copynumber: 4.3 Consensus size: 29
59143 TTACCAAGTT
* *
59153 TTTTTACTTTCTTTTTTTACTTAATACTCT
1 TTTTTACTCTCTTTTTTTACTTAATAC-CA
59183 TTTTTACTC-C---TTTTACTTAATTACCA
1 TTTTTACTCTCTTTTTTTACTTAA-TACCA
* *
59209 TTTTTACTCTCCTTTTTTACTTAATAACA
1 TTTTTACTCTCTTTTTTTACTTAATACCA
* *
59238 TTTTTACTCTCTTTTTCTAC-TGATCACCA
1 TTTTTACTCTCTTTTTTTACTTAAT-ACCA
59267 TTTCTTACTCT
1 TTT-TTACTCT
59278 TTACTACTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
26 20 0.25
27 4 0.05
28 3 0.04
29 29 0.36
30 25 0.31
ACGTcount: A:0.19, C:0.22, G:0.01, T:0.58
Consensus pattern (29 bp):
TTTTTACTCTCTTTTTTTACTTAATACCA
Found at i:59196 original size:26 final size:25
Alignment explanation
Indices: 59167--59252 Score: 91
Period size: 26 Copynumber: 3.2 Consensus size: 25
59157 TACTTTCTTT
*
59167 TTTTACTTAATACTCTTTTTTACTCC
1 TTTTACTTAATAC-CATTTTTACTCC
59193 TTTTACTTAATTACCATTTTTACTCTCC
1 TTTTACTTAA-TACCATTTTTA--CTCC
*
59221 TTTTTTACTTAATAACATTTTTACTCTC
1 --TTTTACTTAATACCATTTTTACTC-C
59249 TTTT
1 TTTT
59253 TCTACTGATC
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
26 21 0.40
27 6 0.12
28 5 0.10
29 10 0.19
30 10 0.19
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTTACTTAATACCATTTTTACTCC
Found at i:59220 original size:28 final size:28
Alignment explanation
Indices: 59081--59253 Score: 105
Period size: 27 Copynumber: 6.1 Consensus size: 28
59071 TATTTTTTGA
59081 TTAC-TAATTACCAATTTTTACT-T-CTT
1 TTACTTAATTACC-ATTTTTACTCTCCTT
*
59107 TGTAC-TGATTACCATATTTTACTCT-C-T
1 T-TACTTAATTACCAT-TTTTACTCTCCTT
**
59134 TTACTTTAATTACCAAGTTTTTTTACTTTCTTTTT
1 TTAC-TTAATTACC-A---TTTTTAC--TCTCCTT
*
59169 TTACTTAA-TACTCTTTTTTA--CTCCTT
1 TTACTTAATTAC-CATTTTTACTCTCCTT
59195 TTACTTAATTACCATTTTTACTCTCCTTTT
1 TTACTTAATTACCATTTTTACTCTCC--TT
* *
59225 TTACTTAA-TAACATTTTTACTCTCTTT
1 TTACTTAATTACCATTTTTACTCTCCTT
59252 TT
1 TT
59254 CTACTGATCA
Statistics
Matches: 119, Mismatches: 9, Indels: 37
0.72 0.05 0.22
Matches are distributed among these distances:
26 25 0.21
27 26 0.22
28 13 0.11
29 16 0.13
30 16 0.13
31 6 0.05
32 1 0.01
33 6 0.05
34 5 0.04
35 5 0.04
ACGTcount: A:0.22, C:0.20, G:0.02, T:0.57
Consensus pattern (28 bp):
TTACTTAATTACCATTTTTACTCTCCTT
Found at i:59277 original size:28 final size:27
Alignment explanation
Indices: 59236--59338 Score: 84
Period size: 27 Copynumber: 3.7 Consensus size: 27
59226 TACTTAATAA
*
59236 CATTTTTACTCTCTTTTTCTACTGATCAC
1 CATTTTTA--CTCTTTTTCTACTGATTAC
* *
59265 CATTTCTTACTC-TTTACTACTAATTAC
1 CATTT-TTACTCTTTTTCTACTGATTAC
* *
59292 CCTCTTTTACT-TTTTTTTATCTGATTAC
1 CAT-TTTTACTCTTTTTCTA-CTGATTAC
*
59320 CACTTTTTACTCTTCTTCT
1 CA-TTTTTACTCTTTTTCT
59339 TTTCCTCTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
27 24 0.41
28 20 0.34
29 11 0.19
30 3 0.05
ACGTcount: A:0.17, C:0.26, G:0.02, T:0.54
Consensus pattern (27 bp):
CATTTTTACTCTTTTTCTACTGATTAC
Found at i:59301 original size:27 final size:28
Alignment explanation
Indices: 59263--59333 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
59253 TCTACTGATC
59263 ACCA-TTTCTTACTCTTTACTA-CTAATT
1 ACCACTTT-TTACTCTTTACTATCTAATT
* ** *
59290 ACC-CTCTTTTACTTTTTTTTATCTGATT
1 ACCACT-TTTTACTCTTTACTATCTAATT
59318 ACCACTTTTTACTCTT
1 ACCACTTTTTACTCTT
59334 CTTCTTTTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
27 14 0.40
28 19 0.54
29 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.01, T:0.54
Consensus pattern (28 bp):
ACCACTTTTTACTCTTTACTATCTAATT
Found at i:59651 original size:55 final size:55
Alignment explanation
Indices: 59581--60109 Score: 738
Period size: 55 Copynumber: 9.6 Consensus size: 55
59571 GATTACTATC
* * *
59581 TTTTACCTGATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTGTTACCTTAACTCTGATTAATCTCT
* * * * *
59636 TTTTACTTAATTACTGATTTACTGATTACTGCTACTTTGACTCTGATTTACCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTGTTACCTTAACTCTGATTAATCTCT
* * * *
59691 TTTTACTTAATTACTGATTTGCTGGTTACCGTTACCTTAACTCTGATTAATTTCT
1 TTTTACTTAATTACTGATTTACTGATTACTGTTACCTTAACTCTGATTAATCTCT
* * * * * *
59746 TTTTACTTAATTACTGATTTAATGATTACTGTTACTTTGACTCTGATTTACCCCTT
1 TTTTACTTAATTACTGATTTACTGATTACTGTTACCTTAACTCTGATTAATCTC-T
* * * *
59802 TTTTACTTAATTACTGATTTGCTGGTTACTGTAACCTTAACTCTGATTAATTTCT
1 TTTTACTTAATTACTGATTTACTGATTACTGTTACCTTAACTCTGATTAATCTCT
* * *
59857 TTTTACTTAATTACTGATTTACTGATCACTATTACCTTAACTCTAATTAATCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTGTTACCTTAACTCTGATTAATCTCT
* *
59912 TTTTACTTAATTACTGATTTACTGATTACTGTTACTTTAACTCTGATTGATCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTGTTACCTTAACTCTGATTAATCTCT
* *
59967 TTTTACTTAATTACTGATTTACTGATTACTGTTA-CTCTGACTCTGGTTAATCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTGTTACCT-TAACTCTGATTAATCTCT
* *
60022 TTTTACTTAATTACTGATTTACTGATTACTGTTA-CTCTGACTCTGATTGATCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTGTTACCT-TAACTCTGATTAATCTCT
60077 TTTTACTTAATTACTGATTTACTGATTACTGTT
1 TTTTACTTAATTACTGATTTACTGATTACTGTT
60110 CGGATTGATC
Statistics
Matches: 417, Mismatches: 55, Indels: 4
0.88 0.12 0.01
Matches are distributed among these distances:
54 1 0.00
55 371 0.89
56 45 0.11
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (55 bp):
TTTTACTTAATTACTGATTTACTGATTACTGTTACCTTAACTCTGATTAATCTCT
Found at i:59890 original size:276 final size:275
Alignment explanation
Indices: 59581--60108 Score: 842
Period size: 276 Copynumber: 1.9 Consensus size: 275
59571 GATTACTATC
* * *
59581 TTTTACCTGATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTACTTAA
1 TTTTACCTAATTACTGATTTACTGATCACTATTACCTTAACTCTAATTAATCTCTTTTTACTTAA
* *
59646 TTACTGATTTACTGATTACTGCTACTTTGACTCTGATTTACCTCTTTTTACTTAATTACTGATTT
66 TTACTGATTTACTGATTACTGCTACTTTAACTCTGATTGACCTCTTTTTACTTAATTACTGATTT
* * *
59711 GCTGGTTACCGTTAC-CTTAACTCTGATTAATTTCTTTTTACTTAATTACTGATTTAATGATTAC
131 ACTGATTACCGTTACTC-TAACTCTGATTAATCTCTTTTTACTTAATTACTGATTTAATGATTAC
* * * *
59775 TGTTACTTTGACTCTGATTTACCCCTTTTTTACTTAATTACTGATTTGCTGGTTACTGTAACCTT
195 TGTTACTCTGACTCTGATTGACCCC-TTTTTACTTAATTACTGATTTACTGATTACTGTAACCTT
59840 AACTCTGATTAATTTCT
259 AACTCTGATTAATTTCT
*
59857 TTTTACTTAATTACTGATTTACTGATCACTATTACCTTAACTCTAATTAATCTCTTTTTACTTAA
1 TTTTACCTAATTACTGATTTACTGATCACTATTACCTTAACTCTAATTAATCTCTTTTTACTTAA
* *
59922 TTACTGATTTACTGATTACTGTTACTTTAACTCTGATTGATCTCTTTTTACTTAATTACTGATTT
66 TTACTGATTTACTGATTACTGCTACTTTAACTCTGATTGACCTCTTTTTACTTAATTACTGATTT
* * * *
59987 ACTGATTACTGTTACTCTGACTCTGGTTAATCTCTTTTTACTTAATTACTGATTTACTGATTACT
131 ACTGATTACCGTTACTCTAACTCTGATTAATCTCTTTTTACTTAATTACTGATTTAATGATTACT
* *
60052 GTTACTCTGACTCTGATTGATCTCTTTTTACTTAATTACTGATTTACTGATTACTGT
196 GTTACTCTGACTCTGATTGACCCCTTTTTACTTAATTACTGATTTACTGATTACTGT
60109 TCGGATTGAT
Statistics
Matches: 230, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
275 31 0.13
276 198 0.86
277 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (275 bp):
TTTTACCTAATTACTGATTTACTGATCACTATTACCTTAACTCTAATTAATCTCTTTTTACTTAA
TTACTGATTTACTGATTACTGCTACTTTAACTCTGATTGACCTCTTTTTACTTAATTACTGATTT
ACTGATTACCGTTACTCTAACTCTGATTAATCTCTTTTTACTTAATTACTGATTTAATGATTACT
GTTACTCTGACTCTGATTGACCCCTTTTTACTTAATTACTGATTTACTGATTACTGTAACCTTAA
CTCTGATTAATTTCT
Found at i:65627 original size:70 final size:70
Alignment explanation
Indices: 65514--65652 Score: 269
Period size: 70 Copynumber: 2.0 Consensus size: 70
65504 TAATCAACAC
65514 GGGTTAGATCGAGTGGTAAGTGTCTCGTTTCAGCTTAAGCACGTCTTAGGTTCGAAACCTTACGT
1 GGGTTAGATCGAGTGGTAAGTGTCTCGTTTCAGCTTAAGCACGTCTTAGGTTCGAAACCTTACGT
65579 ACGCG
66 ACGCG
*
65584 GGGTTAGATCGAGTGGTAAGTGTCTCGTTTCAGCTTAAGCACGTCTTAGGTTCGAAACCTTACTT
1 GGGTTAGATCGAGTGGTAAGTGTCTCGTTTCAGCTTAAGCACGTCTTAGGTTCGAAACCTTACGT
65649 ACGC
66 ACGC
65653 AAATAGCCTA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (70 bp):
GGGTTAGATCGAGTGGTAAGTGTCTCGTTTCAGCTTAAGCACGTCTTAGGTTCGAAACCTTACGT
ACGCG
Found at i:68230 original size:37 final size:37
Alignment explanation
Indices: 68186--68256 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
68176 CTTGATCAAC
* *
68186 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
68223 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
68257 ATAATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:70740 original size:37 final size:37
Alignment explanation
Indices: 70697--70767 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
70687 CTTGATCAAC
* * * *
70697 ATACATGTCTTTTCATATAGATATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTCTATGATCA
70734 ATACATGTCTTTCCAAATAGACATAACTCTATGA
1 ATACATGTCTTTCCAAATAGACATAACTCTATGA
70768 ATAGTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTCTATGATCA
Found at i:72981 original size:17 final size:17
Alignment explanation
Indices: 72959--72994 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
72949 CCAAAAGAAA
72959 AACACCAGCAGACAAAC
1 AACACCAGCAGACAAAC
72976 AACACCAGCAGACAAAC
1 AACACCAGCAGACAAAC
72993 AA
1 AA
72995 GCTAAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.33, G:0.11, T:0.00
Consensus pattern (17 bp):
AACACCAGCAGACAAAC
Found at i:77281 original size:19 final size:19
Alignment explanation
Indices: 77241--77278 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
77231 GATTTATCCT
77241 ATCTATCTGTTGAATTTGA
1 ATCTATCTGTTGAATTTGA
*
77260 ATCT-TCTGTTGGATTTGA
1 ATCTATCTGTTGAATTTGA
77278 A
1 A
77279 ATCCTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (19 bp):
ATCTATCTGTTGAATTTGA
Found at i:81859 original size:16 final size:16
Alignment explanation
Indices: 81838--81871 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
81828 TTTCTTTGCC
81838 AACAAAAAGAAAATGT
1 AACAAAAAGAAAATGT
81854 AACAAAAAGAAAATGT
1 AACAAAAAGAAAATGT
81870 AA
1 AA
81872 GAAATTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.12
Consensus pattern (16 bp):
AACAAAAAGAAAATGT
Found at i:82219 original size:17 final size:17
Alignment explanation
Indices: 82197--82232 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
82187 TCTTCAACGG
82197 AGTGGTTGATTCTTTGT
1 AGTGGTTGATTCTTTGT
82214 AGTGGTTGATTCTTTGT
1 AGTGGTTGATTCTTTGT
82231 AG
1 AG
82233 ATCGAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.50
Consensus pattern (17 bp):
AGTGGTTGATTCTTTGT
Found at i:82387 original size:30 final size:30
Alignment explanation
Indices: 82351--82412 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
82341 TTGATGGAGA
*
82351 TGTTGATGGAGAAGAACTTTGCTTCAGATT
1 TGTTGATGGAGAAGAACTTTGCTTCAAATT
82381 TGTTGATGGAGAAGAACTTTGCTTCAAATT
1 TGTTGATGGAGAAGAACTTTGCTTCAAATT
82411 TG
1 TG
82413 CTTTGCTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.37
Consensus pattern (30 bp):
TGTTGATGGAGAAGAACTTTGCTTCAAATT
Found at i:82434 original size:45 final size:45
Alignment explanation
Indices: 82381--82467 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
82371 GCTTCAGATT
82381 TGTTGATGGAGAAGAACTTTGCTTCAAATTTGCTTTGCTTGAAGA
1 TGTTGATGGAGAAGAACTTTGCTTCAAATTTGCTTTGCTTGAAGA
* * *
82426 TGTTGATGGAGGAGAACTTTGCTTCAGATTTGTTTTGCTTGA
1 TGTTGATGGAGAAGAACTTTGCTTCAAATTTGCTTTGCTTGA
82468 TGGAGAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.40
Consensus pattern (45 bp):
TGTTGATGGAGAAGAACTTTGCTTCAAATTTGCTTTGCTTGAAGA
Found at i:82440 original size:78 final size:73
Alignment explanation
Indices: 82301--82459 Score: 230
Period size: 78 Copynumber: 2.1 Consensus size: 73
82291 ATCGGCTTGC
*
82301 TTTGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGATGTTGATGGAGAAGA
1 TTTGTTGATGGAGAAGAACTTTGCTTCAAATTTGCTTTGCTTGA--GAGATGTTGAT-G-G-AGA
82366 ACTTTGCTTCAGA
61 ACTTTGCTTCAGA
82379 TTTGTTGATGGAGAAGAACTTTGCTTCAAATTTGCTTTGCTTGA-AGATGTTGATGGAGGAGAAC
1 TTTGTTGATGGAGAAGAACTTTGCTTCAAATTTGCTTTGCTTGAGAGATGTTGAT---GGAGAAC
82443 TTTGCTTCAGA
63 TTTGCTTCAGA
82454 TTTGTT
1 TTTGTT
82460 TTGCTTGATG
Statistics
Matches: 77, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
75 32 0.42
76 1 0.01
77 1 0.01
78 43 0.56
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (73 bp):
TTTGTTGATGGAGAAGAACTTTGCTTCAAATTTGCTTTGCTTGAGAGATGTTGATGGAGAACTTT
GCTTCAGA
Found at i:84465 original size:13 final size:13
Alignment explanation
Indices: 84447--84471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84437 TATCGCCATC
84447 AAGAATTTCACAG
1 AAGAATTTCACAG
84460 AAGAATTTCACA
1 AAGAATTTCACA
84472 AGAAAGTTGT
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:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (13 bp):
AAGAATTTCACAG
Found at i:84899 original size:119 final size:121
Alignment explanation
Indices: 84686--84925 Score: 432
Period size: 119 Copynumber: 2.0 Consensus size: 121
84676 AAGCCCCTGA
84686 ACTCTTAAAAAAGCCAAATAAATTATTTCGGCCAAATAAGCCCTTGAACTCTTAAAACACTAAAA
1 ACTCTTAAAAAAGCCAAATAAATTATTTCGGCCAAATAAGCCCTTGAACTCTTAAAACACTAAAA
84751 ACTCAAATAAGAACTAAAGAATTTTCATGACTGTCCAGTTTCTTTTATTAATGGCT
66 ACTCAAATAAGAACTAAAGAATTTTCATGACTGTCCAGTTTCTTTTATTAATGGCT
84807 ACTCTTAAAAAAGCCAAATAAATTATTTCGGCCAAAT-A-CCCTTGAACTCTTAAAA-AGCTAAA
1 ACTCTTAAAAAAGCCAAATAAATTATTTCGGCCAAATAAGCCCTTGAACTCTTAAAACA-CTAAA
**
84869 TGCTCAAATAAGAACTAAAGAATTTTCATGACTGTCCAGTTTCTTTTATTAATGGCT
65 AACTCAAATAAGAACTAAAGAATTTTCATGACTGTCCAGTTTCTTTTATTAATGGCT
84926 TTCACGACTG
Statistics
Matches: 116, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
118 1 0.01
119 77 0.66
120 1 0.01
121 37 0.32
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (121 bp):
ACTCTTAAAAAAGCCAAATAAATTATTTCGGCCAAATAAGCCCTTGAACTCTTAAAACACTAAAA
ACTCAAATAAGAACTAAAGAATTTTCATGACTGTCCAGTTTCTTTTATTAATGGCT
Found at i:85093 original size:13 final size:13
Alignment explanation
Indices: 85075--85099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85065 TATCGCCATC
85075 AAGAATTTCACAG
1 AAGAATTTCACAG
85088 AAGAATTTCACA
1 AAGAATTTCACA
85100 AGAAAGTTGT
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:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (13 bp):
AAGAATTTCACAG
Found at i:85976 original size:34 final size:34
Alignment explanation
Indices: 85938--86007 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
85928 TCACACATTA
85938 GTATTAACTTACATTGTATCCAGTTTTCTAATTT
1 GTATTAACTTACATTGTATCCAGTTTTCTAATTT
85972 GTATTAACTTACATTGTATCCAGTTTTCTAATTT
1 GTATTAACTTACATTGTATCCAGTTTTCTAATTT
86006 GT
1 GT
86008 TGAAATTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (34 bp):
GTATTAACTTACATTGTATCCAGTTTTCTAATTT
Found at i:86270 original size:2 final size:2
Alignment explanation
Indices: 86265--86311 Score: 69
Period size: 2 Copynumber: 23.0 Consensus size: 2
86255 TTTTTTTTTT
86265 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA CTA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
86308 TA TA
1 TA TA
86312 GCATTGTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.02
2 37 0.88
3 4 0.10
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Done.