Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1858
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: 124052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:535 original size:58 final size:58
Alignment explanation
Indices: 468--587 Score: 240
Period size: 58 Copynumber: 2.1 Consensus size: 58
458 ATTTCTTCAC
468 TTTGAAAATTTGAAGGTTTTATCAAAGTTGGTAGGTTTAAGGATAACAATATTTGACT
1 TTTGAAAATTTGAAGGTTTTATCAAAGTTGGTAGGTTTAAGGATAACAATATTTGACT
526 TTTGAAAATTTGAAGGTTTTATCAAAGTTGGTAGGTTTAAGGATAACAATATTTGACT
1 TTTGAAAATTTGAAGGTTTTATCAAAGTTGGTAGGTTTAAGGATAACAATATTTGACT
584 TTTG
1 TTTG
588 GTAAATGTCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (58 bp):
TTTGAAAATTTGAAGGTTTTATCAAAGTTGGTAGGTTTAAGGATAACAATATTTGACT
Found at i:7673 original size:52 final size:52
Alignment explanation
Indices: 7528--7656 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
7518 CGAAATATGA
*
7528 AAATTTGCCTACATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
7580 AAATTTGCCTGTATGTATCGATACATTTCATAATGTATCGATCCATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
7632 AAATTTGCCTGCATGTATCAATACA
1 AAATTTGCCTGCATGTATCGATACA
7657 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:7683 original size:13 final size:13
Alignment explanation
Indices: 7665--7689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7655 CAAAGATCAG
7665 TGTATCGATACAA
1 TGTATCGATACAA
7678 TGTATCGATACA
1 TGTATCGATACA
7690 TTTGAGTAAT
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):
TGTATCGATACAA
Found at i:7766 original size:19 final size:19
Alignment explanation
Indices: 7742--7793 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
7732 AGCGATACAT
7742 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
7761 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
7780 TGTATCGATACAAA
1 TGTATCGATACAAA
7794 TCATTGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:8769 original size:49 final size:49
Alignment explanation
Indices: 8631--8929 Score: 310
Period size: 49 Copynumber: 6.1 Consensus size: 49
8621 CTTAGGAATG
*
8631 TTAAAGATGAAGGTGCCAATGTGCTGA-TCAAGGCTAGCGACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * * * *
8679 TTAAAAGGTGAAAAAAGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TT-AAAGATG---AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
*
8732 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * * * **
8781 TTAAAAAAGAA--TGCCAATGTGTTGATTCAAGGCCAACGACATTTGGGTT
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACA-TT-GGAC
* * *
8830 TTAAAGATGAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* *
8879 TT--A-A--AA-GTGTCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
8922 TTAGAAGA
1 TTA-AAGA
8930 AGATGCCACC
Statistics
Matches: 207, Mismatches: 31, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
43 36 0.17
44 2 0.01
46 2 0.01
47 29 0.14
48 4 0.02
49 65 0.31
50 2 0.01
51 25 0.12
52 21 0.10
53 21 0.10
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.25
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
Found at i:9028 original size:30 final size:30
Alignment explanation
Indices: 8946--9284 Score: 390
Period size: 30 Copynumber: 11.6 Consensus size: 30
8936 CACCAACTTG
* **
8946 TGTGGGCTTTTG-AAAGGGTTG-CACCAACT
1 TGTGGGCTTTGGAAAAGGG-TGCCACTGACT
* * *
8975 TGTGTGCTTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
*
9003 TGTGGGTTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
*
9033 TGTGGGCTTTGGAAAAGGGTGCCATTGACT
1 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
* * *
9063 TCTGGGCTTTGGAAAA-GATGCCACTAACT
1 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
9092 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
**** * *
9122 TGTGGGCTTT-TTCTAGGATGCCACTAACT
1 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
9151 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
* *
9181 TGTAGGCTTTGGAAAA-GATGCCACTGACT
1 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
9210 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
*** *
9240 TGTGGGCTTT--TCTAGGTTGCCACTGACT
1 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
*
9268 TGTGGGCTTTTGAAAAG
1 TGTGGGCTTTGGAAAAG
9285 TGAGGAATGT
Statistics
Matches: 262, Mismatches: 40, Indels: 15
0.83 0.13 0.05
Matches are distributed among these distances:
27 2 0.01
28 43 0.16
29 86 0.33
30 131 0.50
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (30 bp):
TGTGGGCTTTGGAAAAGGGTGCCACTGACT
Found at i:9102 original size:59 final size:59
Alignment explanation
Indices: 8971--9284 Score: 400
Period size: 59 Copynumber: 5.4 Consensus size: 59
8961 GGGTTGCACC
* * * * *
8971 AACTTGTGTGCTTTTG--AAGGTTGCCACTGACTTGTGGGTTTTGGAAAAGGGTGCCACT
1 AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAA-GATGCCACT
* * *
9029 GACTTGTGGGCTTTGGAAAAGGGTGCCATTGACTTCTGGGCTTTGGAAAAGATGCCACT
1 AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACT
**** *
9088 AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTTCTAGGATGCCACT
1 AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACT
*
9147 AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTAGGCTTTGGAAAAGATGCCACT
1 AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACT
* *** * *
9206 GACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTT-TCTAGGTTGCCACT
1 AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACT
* *
9264 GACTTGTGGGCTTTTGAAAAG
1 AACTTGTGGGCTTTGGAAAAG
9285 TGAGGAATGT
Statistics
Matches: 224, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
58 42 0.19
59 154 0.69
60 28 0.12
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (59 bp):
AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACT
Found at i:9162 original size:118 final size:118
Alignment explanation
Indices: 8971--9284 Score: 456
Period size: 118 Copynumber: 2.7 Consensus size: 118
8961 GGGTTGCACC
* * * *** *
8971 AACTTGTGTGCTTTTG--AAGGTTGCCACTGACTTGTGGG-TTTTGGAAAAGGGTGCCACTGACT
1 AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTT--TCTAGGATGCCACTGACT
* *
9033 TGTGGGCTTTGGAAAAGGGTGCCATTGACTTCTGGGCTTTGGAAAAGATGCCACT
64 TGTGGGCTTTGGAAAAGGGTGCCACTGACTTCTAGGCTTTGGAAAAGATGCCACT
*
9088 AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTTCTAGGATGCCACTAACTTG
1 AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTTCTAGGATGCCACTGACTTG
*
9153 TGGGCTTTGGAAAAGGGTGCCACTGACTTGTAGGCTTTGGAAAAGATGCCACT
66 TGGGCTTTGGAAAAGGGTGCCACTGACTTCTAGGCTTTGGAAAAGATGCCACT
* *
9206 GACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGC-TTTTCTAGGTTGCCACTGACTTG
1 AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTTCTAGGATGCCACTGACTTG
*
9270 TGGGCTTTTGAAAAG
66 TGGGCTTTGGAAAAG
9285 TGAGGAATGT
Statistics
Matches: 179, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
117 49 0.27
118 105 0.59
119 21 0.12
120 4 0.02
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (118 bp):
AACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTTCTAGGATGCCACTGACTTG
TGGGCTTTGGAAAAGGGTGCCACTGACTTCTAGGCTTTGGAAAAGATGCCACT
Found at i:10732 original size:14 final size:12
Alignment explanation
Indices: 10708--10803 Score: 68
Period size: 14 Copynumber: 7.4 Consensus size: 12
10698 ATCCGGACCC
10708 TTTTTGTTGTTGTT
1 TTTTTGTT-TT-TT
* *
10722 TTTTT-TCTGTT
1 TTTTTGTTTTTT
* *
10733 TGTTTGTTTGTT
1 TTTTTGTTTTTT
*
10745 TTTTTCTTCTTTT
1 TTTTTGTT-TTTT
10758 TTTTTGTTTCTTT
1 TTTTTGTTT-TTT
10771 TGTTTTGTTTTGTT
1 T-TTTTGTTTT-TT
10785 TTGTTTGTTTGTTT
1 TT-TTTGTTT-TTT
10799 TTTTT
1 TTTTT
10804 TTGCGGAGGA
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
11 6 0.09
12 13 0.19
13 20 0.30
14 27 0.40
15 1 0.01
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.81
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:10736 original size:4 final size:4
Alignment explanation
Indices: 10717--10798 Score: 51
Period size: 4 Copynumber: 19.5 Consensus size: 4
10707 CTTTTTGTTG
* * * *
10717 TTGT TT-T TT-T TCTGT TTGT TTGT TTGT TTTT TTCT TCTTT TTTT TTGT
1 TTGT TTGT TTGT T-TGT TTGT TTGT TTGT TTGT TTGT T-TGT TTGT TTGT
*
10765 TTCTT TTGTT TTGTT TTGTT TTGT TTGT TTGT TT
1 TT-GT TTG-T TTG-T TTG-T TTGT TTGT TTGT TT
10799 TTTTTTTGCG
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
3 5 0.07
4 40 0.60
5 22 0.33
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.80
Consensus pattern (4 bp):
TTGT
Found at i:10741 original size:19 final size:17
Alignment explanation
Indices: 10708--10805 Score: 81
Period size: 19 Copynumber: 5.4 Consensus size: 17
10698 ATCCGGACCC
*
10708 TTTTTGTTG-TTGTTTT
1 TTTTTTTTGTTTGTTTT
10724 TTTTCTGTTTGTTTGTTTGT
1 TTTT-T-TTTGTTTGTTT-T
* *
10744 TTTTTTCTTCTTTTTTTT
1 TTTTTT-TTGTTTGTTTT
10762 TGTTTCTTTTGTTTTGTTTT
1 T-TTT-TTTTG-TTTGTTTT
*
10782 GTTTTGTTTGTTTGTTTT
1 -TTTTTTTTGTTTGTTTT
10800 TTTTTT
1 TTTTTT
10806 GCGGAGGATG
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
16 4 0.06
17 6 0.09
18 14 0.21
19 24 0.36
20 17 0.26
21 1 0.02
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (17 bp):
TTTTTTTTGTTTGTTTT
Found at i:10771 original size:10 final size:9
Alignment explanation
Indices: 10717--10805 Score: 67
Period size: 9 Copynumber: 9.9 Consensus size: 9
10707 CTTTTTGTTG
10717 TTGTTTTTT
1 TTGTTTTTT
* *
10726 TTCTGTTTGT
1 TTGT-TTTTT
*
10736 TTGTTTGTT
1 TTGTTTTTT
*
10745 TT-TTTCTT
1 TTGTTTTTT
*
10753 CT-TTTTTT
1 TTGTTTTTT
*
10761 TTGTTTCTT
1 TTGTTTTTT
10770 TTGTTTTGTT
1 TTGTTTT-TT
*
10780 TTGTTTTGT
1 TTGTTTTTT
10789 TTGTTTGTTT
1 TTGTTT-TTT
10799 TT-TTTTT
1 TTGTTTTT
10806 GCGGAGGATG
Statistics
Matches: 63, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
8 14 0.22
9 29 0.46
10 20 0.32
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.82
Consensus pattern (9 bp):
TTGTTTTTT
Found at i:15233 original size:32 final size:32
Alignment explanation
Indices: 15192--15256 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
15182 AGGATGGTAC
15192 AGCCCCGGCTGAATGTATCCATGGTCTCGCTA
1 AGCCCCGGCTGAATGTATCCATGGTCTCGCTA
15224 AGCCCCGGCTGAATGTATCCATGGTCTCGCTA
1 AGCCCCGGCTGAATGTATCCATGGTCTCGCTA
15256 A
1 A
15257 TAGGCAATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.20, C:0.31, G:0.25, T:0.25
Consensus pattern (32 bp):
AGCCCCGGCTGAATGTATCCATGGTCTCGCTA
Found at i:16881 original size:23 final size:24
Alignment explanation
Indices: 16858--16935 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
16848 TTTTGACACT
16858 AATAAGGGTGGCTTTTGTTGACTA
1 AATAAGGGTGGCTTTTGTTGACTA
* **** *
16882 AA-GAGAGCCACCTTTT-TTGACATC
1 AATAAG-GGTGGCTTTTGTTGAC-TA
16906 AATAAGGGTGGCTTTTGTTGACTA
1 AATAAGGGTGGCTTTTGTTGACTA
16930 AATAAG
1 AATAAG
16936 CAATCCACCA
Statistics
Matches: 38, Mismatches: 12, Indels: 8
0.66 0.21 0.14
Matches are distributed among these distances:
23 7 0.18
24 24 0.63
25 7 0.18
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (24 bp):
AATAAGGGTGGCTTTTGTTGACTA
Found at i:16900 original size:48 final size:48
Alignment explanation
Indices: 16839--16931 Score: 152
Period size: 48 Copynumber: 1.9 Consensus size: 48
16829 TAAAAAAATA
16839 AGCCACCAATTTTGACA-CTAATAAGGGTGGCTTTTGTTGACTAAAGAG
1 AGCCACCAATTTTGACATC-AATAAGGGTGGCTTTTGTTGACTAAAGAG
**
16887 AGCCACCTTTTTTGACATCAATAAGGGTGGCTTTTGTTGACTAAA
1 AGCCACCAATTTTGACATCAATAAGGGTGGCTTTTGTTGACTAAA
16932 TAAGCAATCC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
48 41 0.98
49 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (48 bp):
AGCCACCAATTTTGACATCAATAAGGGTGGCTTTTGTTGACTAAAGAG
Found at i:22370 original size:2 final size:2
Alignment explanation
Indices: 22358--22392 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
22348 AATTTTCCCT
*
22358 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22393 CCTATGAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:24199 original size:45 final size:45
Alignment explanation
Indices: 24117--24207 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
24107 AGTTCTAACC
* * *
24117 ACACTTCCATCCTTGTTTCACATTTCCTAAACGATTTA-ATTTCAT
1 ACACTTCCATCCTTATTTCACATTTCATAAACAATTTACA-TTCAT
** *
24162 ACACTTCCATCCTTATTTGGCATTTCATGAACAATTTACATTCAT
1 ACACTTCCATCCTTATTTCACATTTCATAAACAATTTACATTCAT
24207 A
1 A
24208 GAGGTAAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 38 0.97
46 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.41
Consensus pattern (45 bp):
ACACTTCCATCCTTATTTCACATTTCATAAACAATTTACATTCAT
Found at i:24471 original size:2 final size:2
Alignment explanation
Indices: 24464--24489 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24454 AAATGAACTA
24464 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
24490 TTGAATGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26454 original size:24 final size:25
Alignment explanation
Indices: 26407--26454 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
26397 TTTTTAATAA
* **
26407 TTATTATGTATTATATTTTCTTTAT
1 TTATTATGTATTATATCTAATTTAT
26432 TTATTATGT-TTATATCTAATTTA
1 TTATTATGTATTATATCTAATTTA
26455 CAATTATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (25 bp):
TTATTATGTATTATATCTAATTTAT
Found at i:26628 original size:29 final size:28
Alignment explanation
Indices: 26581--26643 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
26571 TATCGTGCTC
26581 ATATTA-TTTTTATATTATATCATATTTT
1 ATATTATTTTTTATATTATATC-TATTTT
*
26609 A-ATTATTTTTTCATGTTATATCTATTTT
1 ATATTATTTTTT-ATATTATATCTATTTT
26637 ATATTAT
1 ATATTAT
26644 CATACTACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 4 0.13
28 13 0.42
29 14 0.45
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (28 bp):
ATATTATTTTTTATATTATATCTATTTT
Found at i:29268 original size:17 final size:17
Alignment explanation
Indices: 29234--29356 Score: 63
Period size: 15 Copynumber: 7.8 Consensus size: 17
29224 GAGGATTTAA
29234 ATTATAATTATAAATAT
1 ATTATAATTATAAATAT
*
29251 ATTATCAATTA-AATTAT
1 ATTAT-AATTATAAATAT
*
29268 ATT-TAATTATAAACAT
1 ATTATAATTATAAATAT
* *
29284 A--ATAAATAT-TATCAT
1 ATTATAATTATAAAT-AT
* *
29299 AAT-TAATTATAAAAAT
1 ATTATAATTATAAATAT
*
29315 A-T-TAATAATAAATAT
1 ATTATAATTATAAATAT
* *
29330 -TAATTATTA-AAA-A-
1 ATTATAATTATAAATAT
29343 ATTATAATTATAAA
1 ATTATAATTATAAA
29357 ATAATAATAA
Statistics
Matches: 79, Mismatches: 16, Indels: 24
0.66 0.13 0.20
Matches are distributed among these distances:
14 9 0.11
15 32 0.41
16 19 0.24
17 14 0.18
18 5 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTATAATTATAAATAT
Found at i:29318 original size:15 final size:15
Alignment explanation
Indices: 29300--29357 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 15
29290 TATTATCATA
29300 ATTAATTATAAAAAT
1 ATTAATTATAAAAAT
*
29315 ATTAA-TA-ATAAAT
1 ATTAATTATAAAAAT
29328 ATTAATTATTAAAAA-
1 ATTAATTA-TAAAAAT
29343 ATTATAATTATAAAA
1 A-T-TAATTATAAAA
29358 TAATAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 10 0.28
14 4 0.11
15 6 0.17
16 10 0.28
17 6 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTAATTATAAAAAT
Found at i:29361 original size:28 final size:31
Alignment explanation
Indices: 29238--29369 Score: 82
Period size: 31 Copynumber: 4.3 Consensus size: 31
29228 ATTTAAATTA
* *
29238 TAATTATAAATATATT-ATCAATTAAATTATATT
1 TAATTATAAAAATATTAAT-AA-TAAA-TATAAT
* * *
29271 TAATTATAAACATAAT-A-AATATTATCATAAT
1 TAATTATAAAAATATTAATAATA-AAT-ATAAT
29302 TAATTATAAAAATATTAATAATAAATATTAAT
1 TAATTATAAAAATATTAATAATAAATA-TAAT
*
29334 T-ATTA-AAAAAT-TATAATTATAAA-ATAA-
1 TAATTATAAAAATAT-TAATAATAAATATAAT
*
29361 TAATAATAA
1 TAATTATAA
29370 TAACACCACA
Statistics
Matches: 82, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
27 1 0.01
28 6 0.07
29 4 0.05
30 18 0.22
31 26 0.32
32 8 0.10
33 19 0.23
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (31 bp):
TAATTATAAAAATATTAATAATAAATATAAT
Found at i:29366 original size:17 final size:16
Alignment explanation
Indices: 29319--29372 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
29309 AAAAATATTA
* *
29319 ATAATAAATATTAATT
1 ATAAAAAATAATAATT
*
29335 ATTAAAAAATTATAATT
1 A-TAAAAAATAATAATT
*
29352 ATAAAATAATAATAATA
1 ATAAAA-AATAATAATT
29369 ATAA
1 ATAA
29373 CACCACAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 6 0.19
17 25 0.81
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAAAAATAATAATT
Found at i:29369 original size:14 final size:14
Alignment explanation
Indices: 29310--29369 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
29300 ATTAATTATA
*
29310 AAAATATTAATAAT
1 AAAATAATAATAAT
*
29324 AAATATTAATTATTAA-
1 AAA-A-TAA-TAATAAT
* *
29340 AAAATTATAATTAT
1 AAAATAATAATAAT
29354 AAAATAATAATAAT
1 AAAATAATAATAAT
29368 AA
1 AA
29370 TAACACCACA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
13 4 0.11
14 19 0.54
15 2 0.06
16 5 0.14
17 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:32930 original size:6 final size:6
Alignment explanation
Indices: 32915--32945 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
32905 TATATTTTTG
32915 AAAT-A AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AA
32946 GTAACTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:33420 original size:42 final size:42
Alignment explanation
Indices: 33357--33454 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 42
33347 ACAAAAATTA
* * *
33357 TTTTAGAAGATATTCGTGTATCTTATGAATATGTAAATCTTG
1 TTTTAGAAGATTTTCGTGTATCTTATGAACATGCAAATCTTG
* * *
33399 TTTTAAAAGATTTTC-TCGTATCTTGTGAACGTGCAAATCTTG
1 TTTTAGAAGATTTTCGT-GTATCTTATGAACATGCAAATCTTG
33441 TTTTAGAAGATTTT
1 TTTTAGAAGATTTT
33455 TCACATATCC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (42 bp):
TTTTAGAAGATTTTCGTGTATCTTATGAACATGCAAATCTTG
Found at i:37604 original size:15 final size:16
Alignment explanation
Indices: 37584--37617 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
37574 AGTAGGTTAA
*
37584 GAGGAAGA-AATAAAG
1 GAGGAAGAGAACAAAG
37599 GAGGAAGAGAACAAAG
1 GAGGAAGAGAACAAAG
37615 GAG
1 GAG
37618 TCAAAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.56, C:0.03, G:0.38, T:0.03
Consensus pattern (16 bp):
GAGGAAGAGAACAAAG
Found at i:40326 original size:17 final size:18
Alignment explanation
Indices: 40304--40337 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
40294 TGATTATTAA
40304 TTTTAATTTT-AATATTC
1 TTTTAATTTTGAATATTC
40321 TTTTAATTTTGAATATT
1 TTTTAATTTTGAATATT
40338 TTATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTAATTTTGAATATTC
Found at i:40344 original size:5 final size:5
Alignment explanation
Indices: 40334--40359 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40324 TAATTTTGAA
40334 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
40360 TTAACTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:40555 original size:2 final size:2
Alignment explanation
Indices: 40550--40580 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40540 TTAATTAATA
40550 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
40581 AGCTTTTAAC
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:42065 original size:29 final size:29
Alignment explanation
Indices: 42023--42186 Score: 170
Period size: 29 Copynumber: 5.7 Consensus size: 29
42013 AGGTTAACAG
* * * *
42023 GTAATTTTGGAAAGTTGAGGGGTCAAAAC
1 GTAATTTTGAAAAGTTTAGAGGTCAAAGC
*
42052 GTAATTTTGAAAAGTGTTAGAAGTCAAAGC
1 GTAATTTTGAAAAGT-TTAGAGGTCAAAGC
* *
42082 GTAATTTTGATAAGTTTAGAGGTC-AAGT
1 GTAATTTTGAAAAGTTTAGAGGTCAAAGC
* *
42110 GTAATTTTGAAAAGTTTA-AGGGTCAATGT
1 GTAATTTTGAAAAGTTTAGA-GGTCAAAGC
* * * * *
42139 TTAATTTTGAAATGTTTATAAGTCAAAGT
1 GTAATTTTGAAAAGTTTAGAGGTCAAAGC
42168 GTAATTTTGAAAAGTTTAG
1 GTAATTTTGAAAAGTTTAG
42187 GGATTTAATA
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.01
28 24 0.21
29 64 0.56
30 25 0.22
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (29 bp):
GTAATTTTGAAAAGTTTAGAGGTCAAAGC
Found at i:60850 original size:33 final size:33
Alignment explanation
Indices: 60813--60879 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
60803 TTCAACGATT
60813 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
60846 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
60879 T
1 T
60880 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:60851 original size:13 final size:13
Alignment explanation
Indices: 60833--60857 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60823 CATAAAATGT
60833 TGTATCGATACAA
1 TGTATCGATACAA
60846 TGTATCGATACA
1 TGTATCGATACA
60858 TATTTTTTTG
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):
TGTATCGATACAA
Found at i:60939 original size:13 final size:13
Alignment explanation
Indices: 60921--60945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60911 ATTACTCAAA
60921 TGTATCGATACAT
1 TGTATCGATACAT
60934 TGTATCGATACA
1 TGTATCGATACA
60946 CCGATCTTTG
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:67699 original size:4 final size:4
Alignment explanation
Indices: 67692--67718 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
67682 AAATAAAAAA
67692 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAA
67719 AAGGGGTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:68999 original size:28 final size:28
Alignment explanation
Indices: 68965--69316 Score: 384
Period size: 28 Copynumber: 12.5 Consensus size: 28
68955 CGTTCATCTC
*
68965 TTCAAAGCCCACAGGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
68993 TTTAAAGCTCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
69021 TTCAAAGTCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
69049 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
69077 TTTAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
69105 TTCAAAGCCCATAAGTTAGTGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
69133 TTCAAAGCCCACAAGTCGGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
69161 TTTAAAGCCCACACAAATCAGTGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
* * *
69191 TCCAAAGCCCACAAGTCAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
69219 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* ** * *
69247 TTCAAA-CTCACAAGTTGGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGG-CA-TCCT
*
69276 TTCAAAGCCAACAAGTCAGTGGCATCTCT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
69305 TT-AAAGCCCACA
1 TTCAAAGCCCACA
69317 TAAGTTAGTG
Statistics
Matches: 273, Mismatches: 45, Indels: 12
0.83 0.14 0.04
Matches are distributed among these distances:
27 12 0.04
28 212 0.78
29 16 0.06
30 33 0.12
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:69556 original size:48 final size:48
Alignment explanation
Indices: 69440--69618 Score: 279
Period size: 48 Copynumber: 3.8 Consensus size: 48
69430 GGCACCTTTA
* *
69440 TTAGCTCAATGTCGTTGGCCTTGGATCAGCACATTGTCCACTTTT-CC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
69487 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* *
69535 TTAGCTCAATATCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* * **
69583 TTAGCTCGATGTCGTTGGCCTTGAATTGGCACATTG
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTG
69619 GCACTCCTCT
Statistics
Matches: 121, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
47 43 0.36
48 78 0.64
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (48 bp):
TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
Found at i:69556 original size:95 final size:96
Alignment explanation
Indices: 69440--69618 Score: 279
Period size: 95 Copynumber: 1.9 Consensus size: 96
69430 GGCACCTTTA
* * * *
69440 TTAGCTCAATGTCGTTGGCCTTGGATCAGCACATTGTCCACTTTT-CCTTAGCTCAATGTCGCTG
1 TTAGCTCAATATCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCCTTAGCTCAATGTCGCTG
69504 GCCTTGAATCAGCACATTGTCCACTTTTCCC
66 GCCTTGAATCAGCACATTGTCCACTTTTCCC
* *
69535 TTAGCTCAATATCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCCTTAGCTCGATGTCGTTG
1 TTAGCTCAATATCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCCTTAGCTCAATGTCGCTG
**
69600 GCCTTGAATTGGCACATTG
66 GCCTTGAATCAGCACATTG
69619 GCACTCCTCT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 41 0.55
96 34 0.45
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (96 bp):
TTAGCTCAATATCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCCTTAGCTCAATGTCGCTG
GCCTTGAATCAGCACATTGTCCACTTTTCCC
Found at i:78758 original size:41 final size:39
Alignment explanation
Indices: 78713--78837 Score: 128
Period size: 40 Copynumber: 3.1 Consensus size: 39
78703 GACTTATCGG
* *
78713 TTTTATCCTAGTGAACCTTTTACTCTTAGTTGACTTGTCTA
1 TTTTATCCTAGTCAACC-TTTACTCTTTGTTGACTTGTC-A
* * *
78754 TTTTATCCTAGTCAACCCTT-CTCATTTCTTAACTTGTCA
1 TTTTATCCTAGTCAACCTTTACTC-TTTGTTGACTTGTCA
*
78793 GTTTTGTCCTAGTCAACCTTTACT-TATTGTTGACTTGTCAA
1 -TTTTATCCTAGTCAACCTTTACTCT-TTGTTGACTTGTC-A
78834 TTTT
1 TTTT
78838 GTCTCGGTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
39 5 0.07
40 46 0.66
41 19 0.27
ACGTcount: A:0.19, C:0.22, G:0.10, T:0.49
Consensus pattern (39 bp):
TTTTATCCTAGTCAACCTTTACTCTTTGTTGACTTGTCA
Found at i:78803 original size:40 final size:40
Alignment explanation
Indices: 78741--79150 Score: 226
Period size: 40 Copynumber: 10.2 Consensus size: 40
78731 TTTACTCTTA
*
78741 GTTGACTTGTCTA-TTTTATCCTAGTCAACCCTTCTCATTT
1 GTTGACTTGTC-AGTTTTGTCCTAGTCAACCCTTCTCATTT
* * * *
78781 CTTAACTTGTCAGTTTTGTCCTAGTCAACCTTTACTTA-TT
1 GTTGACTTGTCAGTTTTGTCCTAGTCAACCCTT-CTCATTT
* * * * * *
78821 GTTGACTTGTCAATTTTGT-CTCGGTTAACCCTTTTTATCT
1 GTTGACTTGTCAGTTTTGTCCT-AGTCAACCCTTCTCATTT
* * * ** * *** *
78861 ATTAACTTATC-GATTTCAT-CTCGATCAATTTTTTTCATTT
1 GTTGACTTGTCAG-TTTTGTCCTAG-TCAACCCTTCTCATTT
* * *
78901 GTTGACTTGTCAGTTTTGTCCCAGTCAACCCTTTTTATTT
1 GTTGACTTGTCAGTTTTGTCCTAGTCAACCCTTCTCATTT
* * * * * *
78941 GTTAACTTGTTAGTTTTCT-CTCGGTTAACCCTTTTCATTT
1 GTTGACTTGTCAGTTTTGTCCT-AGTCAACCCTTCTCATTT
* * * * *
78981 GTTAACTTGTTAGTTTTGTCC-CGATCAACTCTTCTTATTT
1 GTTGACTTGTCAGTTTTGTCCTAG-TCAACCCTTCTCATTT
* ** * * *
79021 GTTGACTTGTCGGTTTCAT-CTCGATCAACCTTTACTTA-TT
1 GTTGACTTGTCAGTTTTGTCCTAG-TCAACCCTT-CTCATTT
* * *
79061 GTTGACTTTTCAGTTTTGTCCTAATCAACCTCTTTTTCATTT
1 GTTGACTTGTCAGTTTTGTCCTAGTCAACC-C-TTCTCATTT
* * * *
79103 GTTGACTTGACAGTTTTATCCTGGTCAACCTTTCTCATTT
1 GTTGACTTGTCAGTTTTGTCCTAGTCAACCCTTCTCATTT
79143 GTTGACTT
1 GTTGACTT
79151 ATTGATTTCA
Statistics
Matches: 280, Mismatches: 73, Indels: 34
0.72 0.19 0.09
Matches are distributed among these distances:
39 10 0.04
40 226 0.81
41 15 0.05
42 29 0.10
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.49
Consensus pattern (40 bp):
GTTGACTTGTCAGTTTTGTCCTAGTCAACCCTTCTCATTT
Found at i:78866 original size:80 final size:81
Alignment explanation
Indices: 78712--78868 Score: 176
Period size: 80 Copynumber: 2.0 Consensus size: 81
78702 AGACTTATCG
* *
78712 GTTTTATCCTAGTGAACCTTTTACTCTTAGTTGACTTGTCTATTTTATCCTAGTCAACCCTTCTC
1 GTTTTATCCTAGTCAACCTTTTACTCTTAGTTGACTTGTCAATTTTATCCTAGTCAACCCTTCTC
* *
78777 ATTTCTTAACTTGTCA
66 ATCTATTAACTTGTCA
* * * * * *
78793 GTTTTGTCCTAGTCAACC-TTTACT-TATTGTTGACTTGTCAATTTTGT-CTCGGTTAACCCTTT
1 GTTTTATCCTAGTCAACCTTTTACTCT-TAGTTGACTTGTCAATTTTATCCT-AGTCAACCCTTC
*
78855 TTATCTATTAACTT
64 TCATCTATTAACTT
78869 ATCGATTTCA
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
79 3 0.05
80 44 0.70
81 16 0.25
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (81 bp):
GTTTTATCCTAGTCAACCTTTTACTCTTAGTTGACTTGTCAATTTTATCCTAGTCAACCCTTCTC
ATCTATTAACTTGTCA
Found at i:78927 original size:120 final size:121
Alignment explanation
Indices: 78765--79080 Score: 340
Period size: 120 Copynumber: 2.6 Consensus size: 121
78755 TTTATCCTAG
* * * *
78765 TCAACCCTTC-TCATTTCTTAACTTGTCAGTTTTGTCCTAGTCAACCTTTACTTATTGTTGACTT
1 TCAACTCTTCTTCATTTGTTGACTTGTCAGTTTTGTCCCAGTCAACCTTTACTTATTGTTGACTT
* * *
78829 GTCAATTTTGTCTCGGTTAACCCTTTTTATCTATTAACTTATCGA-TTTCATCTCGA
66 GTCAGTTTTGTCTCGGTTAACCCTTTTCATCTATTAACTTAT-GAGTTTCATCCCGA
* * *
78885 TCAA-TTTTTTTCATTTGTTGACTTGTCAGTTTTGTCCCAGTCAACCCTTT--TTATTTGTTAAC
1 TCAACTCTTCTTCATTTGTTGACTTGTCAGTTTTGTCCCAGTCAA-CCTTTACTTA-TTGTTGAC
* * * * * * **
78947 TTGTTAGTTTTCTCTCGGTTAACCCTTTTCATTTGTTAACTTGTTAGTTTTGTCCCGA
64 TTGTCAGTTTTGTCTCGGTTAACCCTTTTCATCTATTAACTTATGAGTTTCATCCCGA
* ** *
79005 TCAACTCTTCTT-ATTTGTTGACTTGTCGGTTTCATCTC-GATCAACCTTTACTTATTGTTGACT
1 TCAACTCTTCTTCATTTGTTGACTTGTCAGTTTTGTCCCAG-TCAACCTTTACTTATTGTTGACT
*
79068 TTTCAGTTTTGTC
65 TGTCAGTTTTGTC
79081 CTAATCAACC
Statistics
Matches: 160, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
119 12 0.08
120 135 0.84
121 13 0.08
ACGTcount: A:0.17, C:0.21, G:0.12, T:0.49
Consensus pattern (121 bp):
TCAACTCTTCTTCATTTGTTGACTTGTCAGTTTTGTCCCAGTCAACCTTTACTTATTGTTGACTT
GTCAGTTTTGTCTCGGTTAACCCTTTTCATCTATTAACTTATGAGTTTCATCCCGA
Found at i:78963 original size:80 final size:80
Alignment explanation
Indices: 78741--79111 Score: 274
Period size: 80 Copynumber: 4.6 Consensus size: 80
78731 TTTACTCTTA
* * * * * * * *
78741 GTTGACTTGTCTA-TTTTATCCTAGTCAACCCTTCTCATTTCTTAACTTGTCAGTTTT-GTC-CT
1 GTTGACTTGTC-AGTTTTGTCCCAGTCAACCCTTTTTATTTGTTAACTTGTTAGTTTTCATCTCG
78803 AGTCAACCTTTACTTATT
65 A-TCAA-CTTTACTTATT
* * * * * * * * *
78821 GTTGACTTGTCAATTTTGTCTCGGTTAACCCTTTTTATCTATTAACTT-ATCGATTTCATCTCGA
1 GTTGACTTGTCAGTTTTGTCCCAGTCAACCCTTTTTATTTGTTAACTTGTTAGTTTTCATCTCGA
**
78885 TCAA-TTTTTTTCATTT
66 TCAACTTTACTT-A-TT
*
78901 GTTGACTTGTCAGTTTTGTCCCAGTCAACCCTTTTTATTTGTTAACTTGTTAGTTTTC-TCTCGG
1 GTTGACTTGTCAGTTTTGTCCCAGTCAACCCTTTTTATTTGTTAACTTGTTAGTTTTCATCTCGA
* * *
78965 TTAACCCTTTTCAT-TT
66 TCAA--CTTTACTTATT
* * * * * * *
78981 GTTAACTTGTTAGTTTTGTCCC-GATCAACTCTTCTTATTTGTTGACTTG-TCGGTTTCATCTCG
1 GTTGACTTGTCAGTTTTGTCCCAG-TCAACCCTTTTTATTTGTTAACTTGTTAGTTTTCATCTCG
79044 ATCAACCTTTACTTATT
65 ATCAA-CTTTACTTATT
* * * *
79061 GTTGACTTTTCAGTTTTGTCCTAATCAACCTCTTTTTCATTTGTTGACTTG
1 GTTGACTTGTCAGTTTTGTCCCAGTCAACC-CTTTTT-ATTTGTTAACTTG
79112 ACAGTTTTAT
Statistics
Matches: 228, Mismatches: 48, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
78 5 0.02
79 20 0.09
80 172 0.75
81 13 0.06
82 13 0.06
83 5 0.02
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.49
Consensus pattern (80 bp):
GTTGACTTGTCAGTTTTGTCCCAGTCAACCCTTTTTATTTGTTAACTTGTTAGTTTTCATCTCGA
TCAACTTTACTTATT
Found at i:79143 original size:122 final size:121
Alignment explanation
Indices: 78967--79253 Score: 371
Period size: 122 Copynumber: 2.4 Consensus size: 121
78957 TCTCTCGGTT
* ** * * *
78967 AACC-CTTTTCATTTGTTAACTTGTTAGTTTTGTCCCGATCAACTCTTCTTATTTGTTGACTTGT
1 AACCTCTTTTCATTTGTTGACTTGACAGTTTTATCCCGATCAACTCTTCTCATTTGTTGACTTAT
* * * ** *
79031 CGGTTTCATCTCGATCAACCTTTACTTATTGTTGACTTTTCAGTTTTGTCCTAATC
66 CGATTTCATCTCAATCAACCTTTACTTATTGTTGACTTGTCAGTTTCATCCCAATC
* *
79087 AACCTCTTTTTCATTTGTTGACTTGACAGTTTTATCCTGGTCAAC-CTTTCTCATTTGTTGACTT
1 AACCTC-TTTTCATTTGTTGACTTGACAGTTTTATCCCGATCAACTC-TTCTCATTTGTTGACTT
* *
79151 ATTGATTTCATCTCAATCAACCTTTACTTATTGTTGACTTGTCGGTTTCATCCCAATC
64 ATCGATTTCATCTCAATCAACCTTTACTTATTGTTGACTTGTCAGTTTCATCCCAATC
* * *
79209 AACCTCTTTTCATCTGTTGACTTGACAGTTTTGTCTCGATCAACT
1 AACCTCTTTTCATTTGTTGACTTGACAGTTTTATCCCGATCAACT
79254 TTTATTCTTA
Statistics
Matches: 142, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
120 4 0.03
121 35 0.25
122 103 0.73
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.46
Consensus pattern (121 bp):
AACCTCTTTTCATTTGTTGACTTGACAGTTTTATCCCGATCAACTCTTCTCATTTGTTGACTTAT
CGATTTCATCTCAATCAACCTTTACTTATTGTTGACTTGTCAGTTTCATCCCAATC
Found at i:79171 original size:40 final size:40
Alignment explanation
Indices: 78999--79231 Score: 136
Period size: 40 Copynumber: 5.8 Consensus size: 40
78989 GTTAGTTTTG
* * * *
78999 TCCCGATCAA-CTCTTCTTATTTGTTGACTTGTCGGTTTCA
1 TCCCAATCAACCT-TTCTCATTTGTTGACTTATCGATTTCA
* * * * **
79039 TCTCGATCAACCTTTACTTA-TTGTTGACTTTTC-AGTTTTG
1 TCCCAATCAACCTTT-CTCATTTGTTGACTTATCGA-TTTCA
* * *
79079 TCCTAATCAACCTCTTTTTCATTTGTTGACTTGA-C-AGTTTTA
1 TCCCAATCAA-C-CTTTCTCATTTGTTGACTT-ATCGA-TTTCA
*** *
79121 TCCTGGTCAACCTTTCTCATTTGTTGACTTATTGATTTCA
1 TCCCAATCAACCTTTCTCATTTGTTGACTTATCGATTTCA
* * * *
79161 TCTCAATCAACCTTTACTTA-TTGTTGACTTGTCGGTTTCA
1 TCCCAATCAACCTTT-CTCATTTGTTGACTTATCGATTTCA
* *
79201 TCCCAATCAACCTCTTTTCATCTGTTGACTT
1 TCCCAATCAACCT-TTCTCATTTGTTGACTT
79232 GACAGTTTTG
Statistics
Matches: 152, Mismatches: 29, Indels: 23
0.75 0.14 0.11
Matches are distributed among these distances:
39 1 0.01
40 97 0.64
41 25 0.16
42 29 0.19
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.46
Consensus pattern (40 bp):
TCCCAATCAACCTTTCTCATTTGTTGACTTATCGATTTCA
Found at i:79292 original size:121 final size:122
Alignment explanation
Indices: 79036--79322 Score: 346
Period size: 121 Copynumber: 2.4 Consensus size: 122
79026 CTTGTCGGTT
* ** *
79036 TCATCTCGATCAACCTTTACTTATTGTTGACTTTTCAGTTTTGTCCTAATCAACCTCTTTTTCAT
1 TCATCTCGATCAACCTTTACTTATTGTTGACTTGTCAGTTTCATCCCAATCAACCTCTTTTTCAT
* * * * *
79101 TTGTTGACTTGACAGTTTTATCCTGGTCAACCTTTCTCATTTGTTGACTTATTGATT
66 CTGTTGACTTGACAGTTTTATCCTGATCAACCTTTCTCATTAGTTGACTGATTGATC
* *
79158 TCATCTCAATCAACCTTTACTTATTGTTGACTTGTCGGTTTCATCCCAATCAACCTC-TTTTCAT
1 TCATCTCGATCAACCTTTACTTATTGTTGACTTGTCAGTTTCATCCCAATCAACCTCTTTTTCAT
* * *
79222 CTGTTGACTTGACAGTTTTGT-CTCGATCAACTTTTATTC-TTAGTTGACTGATTGATC
66 CTGTTGACTTGACAGTTTTATCCT-GATCAACCTTT-CTCATTAGTTGACTGATTGATC
** * * * * *
79279 TGGTCTCGGTCAACCTTTACTAATTATTGATTTGTTAGTTTCAT
1 TCATCTCGATCAACCTTTACTTATTGTTGACTTGTCAGTTTCAT
79323 TTCGGTCAAT
Statistics
Matches: 140, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
120 2 0.01
121 85 0.61
122 53 0.38
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.46
Consensus pattern (122 bp):
TCATCTCGATCAACCTTTACTTATTGTTGACTTGTCAGTTTCATCCCAATCAACCTCTTTTTCAT
CTGTTGACTTGACAGTTTTATCCTGATCAACCTTTCTCATTAGTTGACTGATTGATC
Found at i:80736 original size:6 final size:6
Alignment explanation
Indices: 80717--80791 Score: 75
Period size: 6 Copynumber: 12.5 Consensus size: 6
80707 ATTTTGTTTA
* *
80717 TAATTAT TAATTT TACTTT TATTTT TAATTT TAATTT T-ATTT TAAAATTT
1 TAATT-T TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT T--AATTT
*
80767 TAATTT T-ATTT T-ATTT TATTTT TAA
1 TAATTT TAATTT TAATTT TAATTT TAA
80792 CTAGTTTTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
5 15 0.25
6 34 0.58
7 5 0.08
8 5 0.08
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:80755 original size:24 final size:23
Alignment explanation
Indices: 80707--80791 Score: 100
Period size: 25 Copynumber: 3.6 Consensus size: 23
80697 ATTTCTAAAA
* *
80707 ATTTTGTTTATAATTATTAATTTT
1 ATTTTATTTTTAATT-TTAATTTT
80731 ACTTTTATTTTTAATTTTAATTTT
1 A-TTTTATTTTTAATTTTAATTTT
*
80755 ATTTTAAAATTTTAATTTT-ATTTT
1 ATTTT--ATTTTTAATTTTAATTTT
80779 ATTTTATTTTTAA
1 ATTTTATTTTTAA
80792 CTAGTTTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
22 7 0.13
23 4 0.07
24 20 0.37
25 23 0.43
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (23 bp):
ATTTTATTTTTAATTTTAATTTT
Found at i:80765 original size:13 final size:14
Alignment explanation
Indices: 80739--80774 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
80729 TTACTTTTAT
80739 TTTTAATTTT--AA
1 TTTTAATTTTAAAA
80751 TTTT-ATTTTAAAA
1 TTTTAATTTTAAAA
80764 TTTTAATTTTA
1 TTTTAATTTTA
80775 TTTTATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 5 0.24
12 4 0.19
13 6 0.29
14 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTAATTTTAAAA
Found at i:80767 original size:19 final size:19
Alignment explanation
Indices: 80725--80779 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
80715 TATAATTATT
* *
80725 AATTTTACTTTTATTTT-T
1 AATTTTAATTTTATTTTAA
80743 AATTTTAATTTTATTTTAA
1 AATTTTAATTTTATTTTAA
80762 AATTTTAATTTTATTTTA
1 AATTTTAATTTTATTTTA
80780 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
18 16 0.47
19 18 0.53
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
AATTTTAATTTTATTTTAA
Found at i:81311 original size:13 final size:13
Alignment explanation
Indices: 81293--81317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
81283 ATAATGCACA
81293 GTATCGATACATT
1 GTATCGATACATT
81306 GTATCGATACAT
1 GTATCGATACAT
81318 GACCAAATGT
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):
GTATCGATACATT
Found at i:81436 original size:13 final size:13
Alignment explanation
Indices: 81418--81443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
81408 AAACACAATA
81418 TGTATCGATACAT
1 TGTATCGATACAT
81431 TGTATCGATACAT
1 TGTATCGATACAT
81444 CCCAAAATGT
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:81439 original size:32 final size:33
Alignment explanation
Indices: 81398--81465 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
81388 CCTTAACTGT
*
81398 TTGTATCGATA-AACACAATATGTATCGATACA
1 TTGTATCGATACAACACAAAATGTATCGATACA
* * *
81430 TTGTATCGATACATCCCAAAATGTATCTATACA
1 TTGTATCGATACAACACAAAATGTATCGATACA
81463 TTG
1 TTG
81466 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 11 0.35
33 20 0.65
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACAACACAAAATGTATCGATACA
Found at i:89087 original size:13 final size:13
Alignment explanation
Indices: 89069--89094 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89059 AGACACAATA
89069 TGTATCGATACAT
1 TGTATCGATACAT
89082 TGTATCGATACAT
1 TGTATCGATACAT
89095 CCCAAAATGT
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:89090 original size:32 final size:33
Alignment explanation
Indices: 89049--89115 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
89039 CCTTAACTGT
* *
89049 TTGTATCGATAGA-CACAATATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
* *
89081 TTGTATCGATACATCCCAAAATGTATCTATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
89114 TT
1 TT
89116 AGCTTGTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:91312 original size:58 final size:59
Alignment explanation
Indices: 91250--91440 Score: 221
Period size: 58 Copynumber: 3.3 Consensus size: 59
91240 GGAGGCAAAA
** *
91250 TGTAATTTTAAAAAGTTCAAAGGTCAAAGCATAATTTTGAAAATTTTAAAGG-TCAAAT-
1 TGTAATTTTAAAAAGTTCAAAGGTCAAAGTGTAATTTTGAAAAGTTT-AAGGATCAAATG
* * * * * * *
91308 TGTAATTTTGATAAGTTTAAGGGTCAATGTGTAATTTTGAAAAGTTTAGGGAT-TAATG
1 TGTAATTTTAAAAAGTTCAAAGGTCAAAGTGTAATTTTGAAAAGTTTAAGGATCAAATG
* *
91366 TGTAATTTTAAAAAGTTC-AAGGATCAAAGTGTAATTTTTAAAAGTTTATGGATC-AATG
1 TGTAATTTTAAAAAGTTCAAAGG-TCAAAGTGTAATTTTGAAAAGTTTAAGGATCAAATG
91424 TGTAATTTTAAAAAGTT
1 TGTAATTTTAAAAAGTT
91441 TAGGTACTTA
Statistics
Matches: 112, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
57 9 0.08
58 103 0.92
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (59 bp):
TGTAATTTTAAAAAGTTCAAAGGTCAAAGTGTAATTTTGAAAAGTTTAAGGATCAAATG
Found at i:91345 original size:87 final size:87
Alignment explanation
Indices: 91250--91440 Score: 215
Period size: 87 Copynumber: 2.2 Consensus size: 87
91240 GGAGGCAAAA
** *
91250 TGTAATTTTAAAAAGTTCAAAGG-TCAAAGCATAATTTTGAAAATTTTAAAGG-TCAAATTGTAA
1 TGTAATTTTAAAAAGTT-AAAGGATCAAAGCATAATTTT-AAAAAGTTAAAGGATCAAAGTGTAA
* *
91313 TTTTGATAAGTTTAAGGGTCAATG
64 TTTTGAAAAGTTTAAGGATCAATG
* * * * * ** *
91337 TGTAATTTTGAAAAGTTTAGGGATTAATGTGTAATTTTAAAAAGTTCAAGGATCAAAGTGTAATT
1 TGTAATTTTAAAAAGTTAAAGGATCAAAGCATAATTTTAAAAAGTTAAAGGATCAAAGTGTAATT
* *
91402 TTTAAAAGTTTATGGATCAATG
66 TTGAAAAGTTTAAGGATCAATG
91424 TGTAATTTTAAAAAGTT
1 TGTAATTTTAAAAAGTT
91441 TAGGTACTTA
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
86 13 0.15
87 73 0.85
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (87 bp):
TGTAATTTTAAAAAGTTAAAGGATCAAAGCATAATTTTAAAAAGTTAAAGGATCAAAGTGTAATT
TTGAAAAGTTTAAGGATCAATG
Found at i:91441 original size:29 final size:29
Alignment explanation
Indices: 91250--91442 Score: 194
Period size: 29 Copynumber: 6.7 Consensus size: 29
91240 GGAGGCAAAA
* *
91250 TGTAATTTTAAAAAGTTCAAAGG-TCAAAG
1 TGTAATTTTAAAAAGTT-TAAGGATCAATG
** * *
91279 CATAATTTTGAAAATTTTAAAGG-TCAAAT-
1 TGTAATTTTAAAAAGTTT-AAGGATC-AATG
* * *
91308 TGTAATTTTGATAAGTTTAAGGGTCAATG
1 TGTAATTTTAAAAAGTTTAAGGATCAATG
* * *
91337 TGTAATTTTGAAAAGTTTAGGGATTAATG
1 TGTAATTTTAAAAAGTTTAAGGATCAATG
* *
91366 TGTAATTTTAAAAAGTTCAAGGATCAAAG
1 TGTAATTTTAAAAAGTTTAAGGATCAATG
* *
91395 TGTAATTTTTAAAAGTTTATGGATCAATG
1 TGTAATTTTAAAAAGTTTAAGGATCAATG
91424 TGTAATTTTAAAAAGTTTA
1 TGTAATTTTAAAAAGTTTA
91443 GGTACTTAAT
Statistics
Matches: 136, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
28 7 0.05
29 127 0.93
30 2 0.01
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (29 bp):
TGTAATTTTAAAAAGTTTAAGGATCAATG
Found at i:91460 original size:87 final size:86
Alignment explanation
Indices: 91298--91462 Score: 224
Period size: 87 Copynumber: 1.9 Consensus size: 86
91288 GAAAATTTTA
* * * *
91298 AAGGTCAAATTGTAATTTTGATAAGTTTAAGGGTCAATGTGTAATTTTGAAAAGTTTAGGGATTA
1 AAGGTCAAAGTGTAATTTTGAAAAGTTTAAGGATCAATGTGTAATTTTAAAAAGTTTAGGGATTA
* *
91363 ATGTGTAATTTTAAAAAGTTC
66 ATGAGCAATTTTAAAAAGTTC
* * *
91384 AAGGATCAAAGTGTAATTTTTAAAAGTTTATGGATCAATGTGTAATTTTAAAAAGTTTAGGTACT
1 AAGG-TCAAAGTGTAATTTTGAAAAGTTTAAGGATCAATGTGTAATTTTAAAAAGTTTAGGGA-T
91449 TAAT-AGCAATTTTA
64 TAATGAGCAATTTTA
91463 CCACTTGTGT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
86 4 0.06
87 59 0.87
88 5 0.07
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (86 bp):
AAGGTCAAAGTGTAATTTTGAAAAGTTTAAGGATCAATGTGTAATTTTAAAAAGTTTAGGGATTA
ATGAGCAATTTTAAAAAGTTC
Found at i:95086 original size:53 final size:53
Alignment explanation
Indices: 95023--95123 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
95013 CATGTGCTAC
* * *
95023 TGGGGTGAGTAGACCT-TTGAAGTCTTAATGAGTGACTTAGTGTCACATTCCGT
1 TGGGGCGAGTAGACCTGGTG-AGTCTTAATGAATGACTTAGTGTCACATTCCGT
* *
95076 TGGGGCGAGTAGACCTGGTGTGTCTTAATGAATGACTTGGTGTCACAT
1 TGGGGCGAGTAGACCTGGTGAGTCTTAATGAATGACTTAGTGTCACAT
95124 CGTATTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 40 0.95
54 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.33
Consensus pattern (53 bp):
TGGGGCGAGTAGACCTGGTGAGTCTTAATGAATGACTTAGTGTCACATTCCGT
Found at i:98945 original size:16 final size:16
Alignment explanation
Indices: 98902--98951 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
98892 AACTCTAAAA
*
98902 TAAATTATAAAAGAATT
1 TAAATT-TAAAACAATT
**
98919 TAAATACAAAACAATT
1 TAAATTTAAAACAATT
*
98935 TAAATTTAAAATAATT
1 TAAATTTAAAACAATT
98951 T
1 T
98952 GACTTTTAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAATTTAAAACAATT
Found at i:106039 original size:20 final size:19
Alignment explanation
Indices: 106014--106051 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
106004 TAAATTGGTT
*
106014 TTTTTTTTTAATTTAATATA
1 TTTTTTATTAA-TTAATATA
106034 TTTTTTATTAATTAATAT
1 TTTTTTATTAATTAATAT
106052 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTATTAATTAATATA
Found at i:107167 original size:17 final size:17
Alignment explanation
Indices: 107145--107196 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
107135 TATTTAAAAT
107145 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
107162 ATTTTA-ATATA-AT-A
1 ATTTTATATTTATATAA
107176 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
107191 ATTTTA
1 ATTTTA
107197 ATATAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 6 0.21
14 5 0.17
15 4 0.14
16 8 0.28
17 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:107178 original size:14 final size:14
Alignment explanation
Indices: 107161--107208 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
107151 TATTTATATA
107161 AATTTTAATATAAT
1 AATTTTAATATAAT
*
107175 AATTTATATTAT-AT
1 AATTT-TAATATAAT
107189 AAATTTTAATATAAT
1 -AATTTTAATATAAT
*
107204 TATTT
1 AATTT
107209 ATTCATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTTTAATATAAT
Found at i:107187 original size:15 final size:15
Alignment explanation
Indices: 107128--107210 Score: 50
Period size: 15 Copynumber: 5.6 Consensus size: 15
107118 AAGTTGTATT
*
107128 ATAATTGTAT-TTAAA
1 ATAATT-TATATTATA
*
107143 ATATTTTATATT-TA
1 ATAATTTATATTATA
*
107157 TATAAATTT-TAATATA
1 -AT-AATTTATATTATA
107173 ATAATTTATATTAT-
1 ATAATTTATATTATA
*
107187 ATAAATTT-TAATATA
1 AT-AATTTATATTATA
*
107202 ATTATTTAT
1 ATAATTTAT
107211 TCATATTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
14 20 0.38
15 27 0.51
16 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (15 bp):
ATAATTTATATTATA
Found at i:107191 original size:29 final size:30
Alignment explanation
Indices: 107142--107210 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
107132 TTGTATTTAA
*
107142 AATATTTTATATTTATATAAATTTTAATAT
1 AATAATTTATATTTATATAAATTTTAATAT
107172 AATAATTTATA-TTATATAAATTTTAATAT
1 AATAATTTATATTTATATAAATTTTAATAT
*
107201 AATTATTTAT
1 AATAATTTAT
107211 TCATATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
29 27 0.73
30 10 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
AATAATTTATATTTATATAAATTTTAATAT
Found at i:107200 original size:17 final size:16
Alignment explanation
Indices: 107145--107196 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 16
107135 TATTTAAAAT
107145 ATTTTATATTTATATAA
1 ATTTTATA-TTATATAA
107162 ATTTTA-A-TATA-ATA
1 ATTTTATATTATATA-A
107176 A-TTTATATTATATAA
1 ATTTTATATTATATAA
107191 ATTTTA
1 ATTTTA
107197 ATATAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
13 5 0.17
14 7 0.23
15 6 0.20
16 6 0.20
17 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:107249 original size:17 final size:17
Alignment explanation
Indices: 107215--107252 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
107205 ATTTATTCAT
*
107215 ATTA-TTTTAAATTTTA
1 ATTATTTTTAAATTATA
*
107231 ATTATTTTTATATTATA
1 ATTATTTTTAAATTATA
107248 ATTAT
1 ATTAT
107253 GTAACGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTATTTTTAAATTATA
Found at i:107436 original size:10 final size:11
Alignment explanation
Indices: 107393--107437 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
107383 GTTAACAAAT
107393 ATTTTATTATA
1 ATTTTATTATA
* *
107404 TTTTTATAATA
1 ATTTTATTATA
107415 ATTTTATT-TA
1 ATTTTATTATA
107425 ATTTT-TTATA
1 ATTTTATTATA
107435 ATT
1 ATT
107438 ACTTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 2 0.07
10 12 0.41
11 15 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTATTATA
Found at i:107620 original size:3 final size:3
Alignment explanation
Indices: 107603--107667 Score: 53
Period size: 3 Copynumber: 21.3 Consensus size: 3
107593 ATATAAAAAT
* * * *
107603 ATA A-A ATA TTA ATA ATA ACA ATA TTA ATA ATA ATTA ATA ATA AGAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA A-TA
107649 ATA A-A ATA ATA ATTA ATA A
1 ATA ATA ATA ATA A-TA ATA A
107668 AAAATTGACT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
2 4 0.08
3 37 0.76
4 8 0.16
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:107620 original size:22 final size:22
Alignment explanation
Indices: 107595--107670 Score: 82
Period size: 22 Copynumber: 3.3 Consensus size: 22
107585 TTTTTAACAT
107595 ATAAAAATATAAAATATTAATA
1 ATAAAAATATAAAATATTAATA
*
107617 ATAACAATATTAATAATAATTAATA
1 ATAAAAATA-TAA-AAT-ATTAATA
* *
107642 ATAAGAA-ATAAAATAATAATTA
1 ATAAAAATATAAAATATTAA-TA
107664 ATAAAAA
1 ATAAAAA
107671 ATTGACTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.09
22 19 0.41
23 6 0.13
24 4 0.09
25 13 0.28
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (22 bp):
ATAAAAATATAAAATATTAATA
Found at i:107625 original size:15 final size:14
Alignment explanation
Indices: 107603--107669 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 14
107593 ATATAAAAAT
107603 ATAAAATATTAATA
1 ATAAAATATTAATA
107617 ATAACAATATTAATA
1 ATAA-AATATTAATA
* *
107632 ATAATTAATAATAAGAA
1 ATAA--AATATTAA-TA
*
107649 ATAAAATAATAATTA
1 ATAAAATATTAA-TA
107664 ATAAAA
1 ATAAAA
107670 AATTGACTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.09
15 29 0.64
16 7 0.16
17 5 0.11
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (14 bp):
ATAAAATATTAATA
Found at i:107656 original size:25 final size:24
Alignment explanation
Indices: 107595--107671 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 24
107585 TTTTTAACAT
107595 ATAAAAATATAA-AAT-ATTAATA
1 ATAAAAATATAATAATAATTAATA
*
107617 ATAACAATATTAATAATAATTAATA
1 ATAAAAATA-TAATAATAATTAATA
*
107642 ATAAGAAATAAAATAATAATTAATA
1 ATAA-AAATATAATAATAATTAATA
107667 A-AAAA
1 ATAAAA
107672 TTGACTAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
22 8 0.17
23 5 0.10
24 5 0.10
25 26 0.54
26 4 0.08
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (24 bp):
ATAAAAATATAATAATAATTAATA
Found at i:111249 original size:43 final size:41
Alignment explanation
Indices: 111179--111336 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 41
111169 ATTTACCGTA
* * *
111179 TAAACGTCGCGAAATATTAAAATTTAGTGGCATTTTAAGCGTG
1 TAAA-GTCGCTAAAT-TTCAAATTTAGTGGCATTTTAAGTGTG
*
111222 TAAATGTTGCTAAATTTCAAATTTTAGTGGCATTTTAAGTGTGG
1 TAAA-GTCGCTAAATTTCAAA-TTTAGTGGCATTTTAAGTGT-G
* * * * *
111266 GAAAGCCACTAAA-TTCAAAATTTAGTGGCCTTTT--GTGTA
1 TAAAGTCGCTAAATTTC-AAATTTAGTGGCATTTTAAGTGTG
111305 TAAACGTCGCTAAATTTCAACATTTAGTGGCA
1 TAAA-GTCGCTAAATTTCAA-ATTTAGTGGCA
111337 CTTATCTATA
Statistics
Matches: 94, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
39 3 0.03
40 13 0.14
41 13 0.14
42 21 0.22
43 40 0.43
44 4 0.04
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (41 bp):
TAAAGTCGCTAAATTTCAAATTTAGTGGCATTTTAAGTGTG
Found at i:116042 original size:252 final size:252
Alignment explanation
Indices: 115580--116086 Score: 883
Period size: 252 Copynumber: 2.0 Consensus size: 252
115570 GCTTCATTTG
* *
115580 GATCATCTTCTTCGTCTTCATCCTCATCACTTTGATTATCAAAATCATCACCTTCATACACCTCC
1 GATCATCTTCTTCGTCTTCATCCTCATCACTCTAATTATCAAAATCATCACCTTCATACACCTCC
* *
115645 CATAACTGCTTTAACTCTTAAATAAGCGGTTGAGTATAAATGTCAATATCATTCCCTGGACCTTT
66 CATAACTGCTTTAACTCTTAAATAAGAGGTTAAGTATAAATGTCAATATCATTCCCTGGACCTTT
*
115710 CTCTTTGGGAATAATCATAAACAAGGATAAAGAAAAGATTGTTTCATTCAAATCCATGAGGGCAA
131 CTCTTCGGGAATAATCATAAACAAGGATAAAGAAAAGATTGTTTCATTCAAATCCATGAGGGCAA
115775 ATTATAAAGATTAAGATAATTGTCCAAATACTATAAAAAGTACTTATCATTTTAAAT
196 ATTATAAAGATTAAGATAATTGTCCAAATACTATAAAAAGTACTTATCATTTTAAAT
115832 GATCATCTTCTTCGTCTTCATCCTCATCACTCTAATTATCAAAATCATCACCTTCATACACCTCC
1 GATCATCTTCTTCGTCTTCATCCTCATCACTCTAATTATCAAAATCATCACCTTCATACACCTCC
*
115897 CATAACTGCTTTAACTCTTCAATAAGAGGTTAAGTATAAATGTCAATATCATTCCCTGGGACCTT
66 CATAACTGCTTTAACTCTTAAATAAGAGGTTAAGTATAAATGTCAATATCATTCCCT-GGACCTT
* *
115962 TCTCTTCGGGAATAATCATAAACAA-GATAAAG-AAAGATTGTTTCATTCAAATCCATGGGGGGA
130 TCTCTTCGGGAATAATCATAAACAAGGATAAAGAAAAGATTGTTTCATTCAAATCCATGAGGGCA
* * *
116025 AATTATAAAGAATTAAGATAATTGTCCAAGTACTATAAGAAGTATTTATCATTTTAAAT
195 AATTATAAAG-ATTAAGATAATTGTCCAAATACTATAAAAAGTACTTATCATTTTAAAT
116084 GAT
1 GAT
116087 TAAAACCATC
Statistics
Matches: 242, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
251 39 0.16
252 172 0.71
253 31 0.13
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (252 bp):
GATCATCTTCTTCGTCTTCATCCTCATCACTCTAATTATCAAAATCATCACCTTCATACACCTCC
CATAACTGCTTTAACTCTTAAATAAGAGGTTAAGTATAAATGTCAATATCATTCCCTGGACCTTT
CTCTTCGGGAATAATCATAAACAAGGATAAAGAAAAGATTGTTTCATTCAAATCCATGAGGGCAA
ATTATAAAGATTAAGATAATTGTCCAAATACTATAAAAAGTACTTATCATTTTAAAT
Found at i:117495 original size:2 final size:2
Alignment explanation
Indices: 117436--117475 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
117426 CGTAATCCTT
117436 TA TA TA TA T- TA TA TA -A 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 TA TA TA TA TA TA
117476 CACACGTCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:117621 original size:25 final size:26
Alignment explanation
Indices: 117588--117645 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
117578 ATAAATCATT
* *
117588 TATTAAATT-TTAAATTAATTAAAAA
1 TATTTAATTATTAAATTAATAAAAAA
* *
117613 TATTTAATTATTTACTTAATAAAAAA
1 TATTTAATTATTAAATTAATAAAAAA
117639 T-TTTAAT
1 TATTTAAT
117646 CGTTACATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTTAATTATTAAATTAATAAAAAA
Found at i:119477 original size:41 final size:41
Alignment explanation
Indices: 119400--119520 Score: 134
Period size: 41 Copynumber: 3.0 Consensus size: 41
119390 CGTTTTTAGT
* * **
119400 AAAACGCCACTAAAATTAATTTAATAATGGTGTTTTAAAGC
1 AAAACGCCGCTAAAATTAATTTAATAGTGGCATTTTAAAGC
* * * * * *
119441 CAAACGCCGTTGAAATTAATTTAATAGTGACATTTTATAGT
1 AAAACGCCGCTAAAATTAATTTAATAGTGGCATTTTAAAGC
**
119482 AAAACGTTGCTAAAATTAATTTAATAGTGGCATTTTAAA
1 AAAACGCCGCTAAAATTAATTTAATAGTGGCATTTTAAA
119521 TAATCAAACG
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (41 bp):
AAAACGCCGCTAAAATTAATTTAATAGTGGCATTTTAAAGC
Found at i:123138 original size:34 final size:34
Alignment explanation
Indices: 123075--123139 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
123065 TGTCAACCTA
* *
123075 CTCCTCGTCAACTAGATAATTCACGTGTCAATTG
1 CTCCTCGTCAACTAGATAATACACATGTCAATTG
* * *
123109 CTCCTTGTCAACTAGATACTACATATGTCAA
1 CTCCTCGTCAACTAGATAATACACATGTCAA
123140 CCTATTCCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (34 bp):
CTCCTCGTCAACTAGATAATACACATGTCAATTG
Done.