Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, 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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 1 of 77
Found at i:82 original size:26 final size:24
Alignment explanation
Indices: 40--93 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
30 CTGGGAGTGA
*
40 GAAAAATTTTTTAGAAATTTTTGG
1 GAAAAATTTTTTAGAAATTTCTGG
* *
64 CGAAAATTTTTTCTGGAAATTTCTGG
1 -GAAAAATTTTT-TAGAAATTTCTGG
90 GAAA
1 GAAA
94 TTTCCAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.41
Consensus pattern (24 bp):
GAAAAATTTTTTAGAAATTTCTGG
Found at i:622 original size:27 final size:27
Alignment explanation
Indices: 583--657 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
573 CACTCCAGGT
* * *
583 TTTTTTTTTTTTTTCTTCTTTCTTTGAA
1 TTTTTTTATTTTAT-TTATTTCTTTGAA
611 TTTTTTTATTTTATTTATTTCTTTG--
1 TTTTTTTATTTTATTTATTTCTTTGAA
636 TTTATTTTAATTTTTATTTATT
1 TTT-TTTT-A-TTTTATTTATT
658 AGATTAGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 3 0.07
26 4 0.10
27 11 0.27
28 23 0.56
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (27 bp):
TTTTTTTATTTTATTTATTTCTTTGAA
Found at i:889 original size:60 final size:58
Alignment explanation
Indices: 736--1138 Score: 517
Period size: 59 Copynumber: 6.7 Consensus size: 58
726 AAATTCCAAA
* *
736 AAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-TTTC
796 --AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
*
852 AAAAAAAAAATATTTTTGGGGAAAAGTTGAAACTATCAATTTTCCTCAGAAATAAATTTC
1 --AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
* *
912 GAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 -AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC-T--CAG--AAATAAATTT-C
*
977 AAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 -AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-TTTC
*** * *
1037 AAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT-TGAAAATCGAAATTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAAT--AAATTTC
* *
1097 -CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1139 CTACAAAAAA
Statistics
Matches: 308, Mismatches: 21, Indels: 29
0.86 0.06 0.08
Matches are distributed among these distances:
56 4 0.01
57 45 0.15
58 6 0.02
59 121 0.39
60 68 0.22
61 6 0.02
62 4 0.01
64 11 0.04
65 43 0.14
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (58 bp):
AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
Found at i:1006 original size:124 final size:119
Alignment explanation
Indices: 735--1138 Score: 572
Period size: 124 Copynumber: 3.4 Consensus size: 119
725 AAAATTCCAA
735 AAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC--AA
1 AAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAA
* *
798 AAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAATAAATTTCA
65 AAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTCC
* * *
853 AAAAAAAAATATTTTTGGGGAAAAGTTGAAACTATCAATTTTCCTCAGAAATAAA-TTTCGAAAA
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC-AAAA
917 AAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
65 AAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTT---AG-AAAATAAATTTCC
*
977 AAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAA
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAA
***
1042 AAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTCC
66 AAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAAT--AAATTTCC
1098 ---AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1139 CTACAAAAAA
Statistics
Matches: 262, Mismatches: 12, Indels: 24
0.88 0.04 0.08
Matches are distributed among these distances:
116 4 0.02
117 44 0.17
118 48 0.18
119 46 0.18
120 1 0.00
121 8 0.03
122 2 0.01
123 1 0.00
124 104 0.40
125 4 0.02
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (119 bp):
AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAA
AAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTCC
Found at i:6319 original size:119 final size:116
Alignment explanation
Indices: 6130--6708 Score: 721
Period size: 119 Copynumber: 5.0 Consensus size: 116
6120 TCTTGTGCAT
* * *
6130 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTGATTTTTTTGAAAATTT-ATTTTTAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA---ACTTTTTTGAAACTTTGATTTTCAAGGAA
* **
6194 AATTGATACTTTCAACGTTTCCCCAAAAATATTTTTTTTTGAAAATTTTGATTTTCAA
63 AATTGATACTTTCAACTTTTCCCCAAAAA-A-CCTTTTTTG-AAATTTT-ATTTTCAA
* * * *
6252 GGAAAATTGATACTTTCAATTTTTCCTCAAAAACCTTTTTTGAAA-TTTTATTTTTAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAACTTTTTTGAAACTTTGATTTTCAAGGAAAAT
* *
6316 TGATACTTTCAACTTTTCCCCAAAAAA--ATTTTTGAAACTTTGATTTTCAA
66 TGATACTTTCAACTTTTCCCCAAAAAACCTTTTTTGAAA-TTTTATTTTCAA
* * *
6366 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAAC-TTGTGGAAACTTTGATTTTCAAGAAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAACTTTTTTGAAACTTTGATTTTCAAGGAAAAT
* *
6429 TGATACTTTCAACTTTTCCTC-AAAAACCTTTTTTGAAATTTTATTTTTAA
66 TGATACTTTCAACTTTTCCCCAAAAAACCTTTTTTGAAATTTTATTTTCAA
* *
6479 GGAAAATTGATACTTTCAACTTTTCC-CAAAAAAAATTTTTTTTTTTAAACTTTGATTTTCAAGG
1 GGAAAATTGATACTTTCAACTTTTCCTC--AAAAAA---CTTTTTTGAAACTTTGATTTTCAAGG
* * *
6543 AAAATTGATACTTTCAACTTTTCCTC-AAAAACCTTTTTTGAAATATTATTTTTAA
61 AAAATTGATACTTTCAACTTTTCCCCAAAAAACCTTTTTTGAAATTTTATTTTCAA
*
6598 GGAAAATTGATACTTTCAACTTTTCC-CAAAAAAAATTTTTTGAAACTTTGATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAAACTTTTTTGAAACTTTGATTTTCAAGGAAAA
** *
6662 TTGATACTTTCAACTTTTCCCCAAAAAATATTTTTTG-ATTTTTATTT
65 TTGATACTTTCAACTTTTCCCCAAAAAACCTTTTTTGAAATTTTATTT
6709 AAAGAAAATA
Statistics
Matches: 414, Mismatches: 30, Indels: 33
0.87 0.06 0.07
Matches are distributed among these distances:
112 13 0.03
113 77 0.19
114 47 0.11
115 71 0.17
116 12 0.03
118 11 0.03
119 151 0.36
122 32 0.08
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (116 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAAACTTTTTTGAAACTTTGATTTTCAAGGAAAAT
TGATACTTTCAACTTTTCCCCAAAAAACCTTTTTTGAAATTTTATTTTCAA
Found at i:6333 original size:57 final size:57
Alignment explanation
Indices: 6130--6688 Score: 660
Period size: 57 Copynumber: 9.6 Consensus size: 57
6120 TCTTGTGCAT
** * *
6130 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTGATTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA---CCTTTTTTGAAATTTTATTTTCAA
* * **
6190 GGAAAATTGATACTTTCAACGTTTCCCCAAAAATATTTTTTTTTGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAA-A-CCTTTTTTG-AAATTTT-ATTTTCAA
* *
6252 GGAAAATTGATACTTTCAATTTTTCCTCAAAAACCTTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAATTTTATTTTCAA
* ** *
6309 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-AATTTTTGAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAA-TTTTATTTTCAA
* * *
6366 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA-C-TTGTGGAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAA-TTTTATTTTCAA
* *
6422 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAATTTTATTTTCAA
** * *
6479 GGAAAATTGATACTTTCAACTTTTCC-CAAAAAAAATTTTTTTTTTTAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTC---AAAAA--CCTTTTTTGAAA-TTTTATTTTCAA
* *
6541 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAATATTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAATTTTATTTTCAA
** *
6598 GGAAAATTGATACTTTCAACTTTTCC-CAAAAAAAATTTTTTGAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAACCTTTTTTGAAA-TTTTATTTTCAA
*
6656 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA
6689 ATATTTTTTG
Statistics
Matches: 438, Mismatches: 44, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
56 63 0.14
57 166 0.38
58 63 0.14
59 13 0.03
60 40 0.09
61 23 0.05
62 69 0.16
63 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.42
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAATTTTATTTTCAA
Found at i:6436 original size:25 final size:25
Alignment explanation
Indices: 6347--6437 Score: 65
Period size: 25 Copynumber: 3.4 Consensus size: 25
6337 AAAAAAATTT
*
6347 TTGAAACTTTGATTTTCAAGGAAAA
1 TTGAAACTTTGATTTTCAAGAAAAA
* * ***
6372 TTGATACTTTCAACTTTTCCTCAAAAA
1 TTGAAACTTT-GA-TTTTCAAGAAAAA
6399 CTTGTGGAAACTTTGATTTTCAAGAAAAA
1 --T-T-GAAACTTTGATTTTCAAGAAAAA
*
6428 TTGATACTTT
1 TTGAAACTTT
6438 CAACTTTTCC
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
25 16 0.33
26 2 0.04
27 10 0.21
29 11 0.23
30 2 0.04
31 7 0.15
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (25 bp):
TTGAAACTTTGATTTTCAAGAAAAA
Found at i:6730 original size:12 final size:12
Alignment explanation
Indices: 6713--6737 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6703 TTATTTAAAG
6713 AAAATAAAATAA
1 AAAATAAAATAA
6725 AAAATAAAATAA
1 AAAATAAAATAA
6737 A
1 A
6738 GGTAAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:7167 original size:19 final size:20
Alignment explanation
Indices: 7131--7171 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
7121 GAATATTCAC
*
7131 CGGATTCTGGGATTTTTCGT
1 CGGAATCTGGGATTTTTCGT
7151 CGGAATCTGGG-TTTTTCGT
1 CGGAATCTGGGATTTTTCGT
7170 CG
1 CG
7172 AAAGTTCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.10, C:0.17, G:0.32, T:0.41
Consensus pattern (20 bp):
CGGAATCTGGGATTTTTCGT
Found at i:7699 original size:3 final size:3
Alignment explanation
Indices: 7693--7723 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
7683 AAGAGAAAAA
7693 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
7724 AGATATATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:7841 original size:19 final size:17
Alignment explanation
Indices: 7801--7885 Score: 89
Period size: 19 Copynumber: 4.6 Consensus size: 17
7791 ATACATATAT
*
7801 AAAATAATAATAATAATA
1 AAAATAA-AATAAAAATA
7819 AAAATAAAATAAAAATGTA
1 AAAATAAAATAAAAA--TA
7838 AAAATACAAAATAAAAATA
1 AAAAT--AAAATAAAAATA
*
7857 AATTAAAAAAATAAAAATA
1 AA--AATAAAATAAAAATA
7876 AAAATAAAAT
1 AAAATAAAAT
7886 GAAGAAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
17 14 0.24
18 7 0.12
19 25 0.43
21 12 0.21
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (17 bp):
AAAATAAAATAAAAATA
Found at i:7848 original size:7 final size:6
Alignment explanation
Indices: 7801--7884 Score: 91
Period size: 6 Copynumber: 13.5 Consensus size: 6
7791 ATACATATAT
* *
7801 AAAATA ATAATA ATAATA AAAAT- AAAATA AAAATGTA AAAATA CAAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA--TA AAAATA -AAAATA
7851 AAAATA AATTAA-A AAAATA AAAATA AAAATA AAA
1 AAAATA AA--AATA AAAATA AAAATA AAAATA AAA
7885 TGAAGAAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
5 7 0.10
6 45 0.65
7 9 0.13
8 8 0.12
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:7856 original size:32 final size:31
Alignment explanation
Indices: 7801--7884 Score: 114
Period size: 32 Copynumber: 2.7 Consensus size: 31
7791 ATACATATAT
* *
7801 AAAATAATAATAATAATAAAAATAAAATAAA
1 AAAATAAAAATAAAAATAAAAATAAAATAAA
** *
7832 AATGTAAAAATACAAAATAAAAATAAATTAAA
1 AAAATAAAAATA-AAAATAAAAATAAAATAAA
7864 AAAATAAAAATAAAAATAAAA
1 AAAATAAAAATAAAAATAAAA
7885 TGAAGAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 18 0.40
32 27 0.60
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (31 bp):
AAAATAAAAATAAAAATAAAAATAAAATAAA
Found at i:7859 original size:25 final size:24
Alignment explanation
Indices: 7815--7883 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
7805 TAATAATAAT
*
7815 AATAAAAATAAAATAAAAATGT-AAA
1 AATAAAAATAAAA-ATAAAT-TAAAA
7840 AATACAAAATAAAAATAAATTAAAAA
1 AATA-AAAATAAAAATAAATT-AAAA
7866 AATAAAAATAAAAATAAA
1 AATAAAAATAAAAATAAA
7884 ATGAAGAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
24 1 0.03
25 23 0.57
26 16 0.40
ACGTcount: A:0.78, C:0.01, G:0.01, T:0.19
Consensus pattern (24 bp):
AATAAAAATAAAAATAAATTAAAA
Found at i:7900 original size:2 final size:2
Alignment explanation
Indices: 7895--7921 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7885 TGAAGAAAAA
7895 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 A
7922 CAGACTTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8426 original size:183 final size:181
Alignment explanation
Indices: 8037--9260 Score: 435
Period size: 181 Copynumber: 6.9 Consensus size: 181
8027 AAACGGAAAC
* ** *
8037 AATTGTTTTATGACAAAACAAAAAGGTCATAAGAATTTGAAATAAATAATTATTCAGATAGACAT
1 AATTATTTTATGACAAAAC-AAAAGGTCATAAGAATTCCAAATAAATAATTATTCAAATAGACAT
* * * * ***
8102 AACGATTTGAATTTGTTCGATAAATAGATTTATTTTTTAAATCTTTTACTTATTAATTGTCTTAA
65 AACGATTTAAACTTGTTCGATAAATAGATTTATTTTTTAAATCTCTTAATTATTAATTGTAAGAA
* * *
8167 TATTAATAAATTTGTATTATTTTATTTGAAATAAGCTTATATGAACAAATAA
130 TATTAATAAATTGGTATTATTTTATTTCAAATAACCTTATATGAACAAATAA
* * * * * * *
8219 AATTATTATATGACAAACCAAAAGGTTAT-AGCAATTCCAAATCAATAATTGTTCAAATGGCCAT
1 AATTATTTTATGACAAAACAAAAGGTCATAAG-AATTCCAAATAAATAATTATTCAAATAGACAT
** * * * *
8283 AATTATTTAAACTTGTTCGGTGAATAGATTTGTTTTTATAAATCTCTTAATTATTAATTTTAAGA
65 AACGATTTAAACTTGTTCGATAAATAGATTTATTTTT-TAAATCTCTTAATTATTAATTGTAAGA
* * *
8348 ATATTAATAACA-TGGTATTTTTTTTATTTCCAATAACCTTATATGAATTGAAAT-A
129 ATATTAATAA-ATTGGTA-TTATTTTATTTCAAATAACCTTATATGAA--CAAATAA
* ** * * * *
8403 AGTT-TTTTATGACAAAACAAAAGGTCATAACG-ATTTGAAATAGATAACTATTTAAATAGTCAT
1 AATTATTTTATGACAAAACAAAAGGTCATAA-GAATTCCAAATAAATAATTATTCAAATAGACAT
* * * * * **
8466 GAC-A-GTAAA------C-----AT--ATTTATTTCTAAAAT-TTTTCCCTTATTAATTGTCAA-
65 AACGATTTAAACTTGTTCGATAAATAGATTTATTTTTTAAATCTCTT-AATTATTAATTGT-AAG
* * * * * * *
8514 AATATTAATAGATTAGTATTATTTTA-ATCTAAATAAGCTTGTATGAATAGAA-AC
128 AATATTAATAAATTGGTATTATTTTATTTC-AAATAACCTTATATGAACA-AATAA
** * * * ** ** *
8568 AATTGCTTTATAACAGAACAAAATGTCATAA-AGATTTGAAATAAATAATTGCTCAAATAGTCAT
1 AATTATTTTATGACAAAACAAAAGGTCATAAGA-ATTCCAAATAAATAATTATTCAAATAGACAT
* * ** * * *
8632 AACTATTTGAACAAGTTTGATAAATAGATTTATTTTTTAAATCACCTT--TTAATT--TT-TGA-
65 AACGATTTAAACTTGTTCGATAAATAGATTTATTTTTTAAATC-TCTTAATT-ATTAATTGTAAG
* * * * *
8691 AATATTAATAGATTAGTATTACTTTATTTCGAATAAACTTATATGAACAAA-AA
128 AATATTAATAAATTGGTATTATTTTATTTCAAATAACCTTATATGAACAAATAA
* * * ** * * *
8744 CATT-TGTTGTATGACAAAACAAAAAGTAATAATG-ATTTGAAATATATAATTGTTCAAATAG-T
1 AATTAT-TT-TATGACAAAACAAAAGGTCATAA-GAATTCCAAATAAATAATTATTCAAATAGAC
*** * * * * * * * *
8806 ATAATTTTTTGAACTAGTT-AAGTAAACATAATTATTTTTTAAATCTCTT-ATTATT--TTTTGA
63 ATAACGATTTAAACTTGTTCGA-TAAATAGATTTATTTTTTAAATCTCTTAATTATTAATTGTAA
** * ** * *** *
8867 -AATATTAATAAATTCATTTTATTTTATTTTGAATAAGC-TAGTATGAATTGAGAA
127 GAATATTAATAAATTGGTATTATTTTATTTCAAATAACCTTA-TATGAACAAATAA
* * ** * * * * *
8921 AATTGTTTTATGACAAGACAAAAGGTCATAACG-ATTTGAAATAGATAATTGTTCATATAGTCTT
1 AATTATTTTATGACAAAACAAAAGGTCATAA-GAATTCCAAATAAATAATTATTCAAATAGACAT
* * ** * * * * * * **
8985 AACTATTTGAA-TTGATTCGGCAAACAAATATATTTTTTAAATCCCTTAGTTATTAATTTTTGGA
65 AACGATTTAAACTTG-TTCGATAAATAGATTTATTTTTTAAATCTCTTAATTATTAATTGTAAGA
** * * * * ** * * * *
9049 ATATTCTTAGATTAGTATTGTCTTATTTTGAATAAGCTTGTATGAATAGAA-AT
129 ATATTAATAAATTGGTATTATTTTATTTCAAATAACCTTATATGAACA-AATAA
* * * * ** * * * * * *
9102 AATTGTTTTAAGACATAACAAAAGGTTATAATG-ATTTGAAGTATAGAATTGTTCAAACAGTCAT
1 AATTATTTTATGACAAAACAAAAGGTCATAA-GAATTCCAAATAAATAATTATTCAAATAGACAT
** * * * * * *
9166 AATTATTTGAA-TTGGTTCGGTAAACAAATTCATTTTTTAAATCTCTT-ATTAATT--TT-TGA-
65 AACGATTTAAACTT-GTTCGATAAATAGATTTATTTTTTAAATCTCTTAATT-ATTAATTGTAAG
* **
9225 AAGATTAATAAATTATTATTATTTTATTTCAAATAA
128 AATATTAATAAATTGGTATTATTTTATTTCAAATAA
9261 TCATGTGTGA
Statistics
Matches: 808, Mismatches: 177, Indels: 119
0.73 0.16 0.11
Matches are distributed among these distances:
164 1 0.00
165 7 0.01
166 75 0.09
167 29 0.04
168 13 0.02
170 2 0.00
175 12 0.01
176 135 0.17
177 153 0.19
178 10 0.01
179 6 0.01
180 10 0.01
181 218 0.27
182 55 0.07
183 72 0.09
184 5 0.01
185 5 0.01
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (181 bp):
AATTATTTTATGACAAAACAAAAGGTCATAAGAATTCCAAATAAATAATTATTCAAATAGACATA
ACGATTTAAACTTGTTCGATAAATAGATTTATTTTTTAAATCTCTTAATTATTAATTGTAAGAAT
ATTAATAAATTGGTATTATTTTATTTCAAATAACCTTATATGAACAAATAA
Found at i:8461 original size:16 final size:17
Alignment explanation
Indices: 8429--8461 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8419 ACAAAAGGTC
8429 ATAACGATTTGAAATAG
1 ATAACGATTTGAAATAG
*
8446 ATAACTATTT-AAATAG
1 ATAACGATTTGAAATAG
8462 TCATGACAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (17 bp):
ATAACGATTTGAAATAG
Found at i:9094 original size:181 final size:180
Alignment explanation
Indices: 8513--9321 Score: 744
Period size: 177 Copynumber: 4.5 Consensus size: 180
8503 TTAATTGTCA
* * * * *
8513 AAATATTAATAGATTAGTATTATTTTAATCTAAATAAGCTTGTATGAATAGAAACAATTGCTTTA
1 AAATATTAATAGATTAGTATTATCTTATTTTGAATAAGCTTGTATGAATAGAAACAATTGTTTTA
* * * * *
8578 TAAC-AGAACAAAATGTCATAAAGATTTGAAATAAATAATTGCTCAAATAGTCATAACTATTTGA
66 TGACAAG-ACAAAAGGTCATAATGATTTGAAATATATAATTGTTCAAATAGTCATAACTATTTGA
** * * * *
8642 A-CAAGTTTGATAAATAGATTTATTTTTTAAATCACC---TT-TTAATTTTTG
130 ATTGAGTTCGGTAAACA-AATTATTTTTTAAATC-CCTTATTATTAATTTTTG
* * * * * * *
8690 AAATATTAATAGATTAGTATTA-CTTTATTTCGAATAAACTTATATGAACAAAAACATTTGTTGT
1 AAATATTAATAGATTAGTATTATC-TTATTTTGAATAAGCTTGTATGAATAGAAACAATTGTTTT
* * * * *
8754 ATGACAAAACAAAAAGTAATAATGATTTGAAATATATAATTGTTCAAATAGT-ATAATTTTTTGA
65 ATGACAAGACAAAAGGTCATAATGATTTGAAATATATAATTGTTCAAATAGTCATAACTATTTGA
* ** *
8818 ACT-AGTTAAGTAAACATAATTATTTTTTAAATCTCTTATTA-T--TTTTTG
130 ATTGAGTTCGGTAAACA-AATTATTTTTTAAATCCCTTATTATTAATTTTTG
* * * * *
8866 AAATATTAATAAATTCA-TTTTATTTTATTTTGAATAAGCTAGTATGAATTGAGAA-AATTGTTT
1 AAATATTAATAGATT-AGTATTATCTTATTTTGAATAAGCTTGTATGAATAGA-AACAATTGTTT
* * * *
8929 TATGACAAGACAAAAGGTCATAACGATTTGAAATAGATAATTGTTCATATAGTCTTAACTATTTG
64 TATGACAAGACAAAAGGTCATAATGATTTGAAATATATAATTGTTCAAATAGTCATAACTATTTG
*
8994 AATTGA-TTCGGCAAACAAATATATTTTTTAAATCCCTTAGTTATTAATTTTTG
129 AATTGAGTTCGGTAAACAAAT-TATTTTTTAAATCCCTTA-TTATTAATTTTTG
* ** * *
9047 GAATATTCTTAGATTAGTATTGTCTTATTTTGAATAAGCTTGTATGAATAGAAATAATTGTTTTA
1 AAATATTAATAGATTAGTATTATCTTATTTTGAATAAGCTTGTATGAATAGAAACAATTGTTTTA
* * * * * *
9112 AGACATA-ACAAAAGGTTATAATGATTTGAAGTATAGAATTGTTCAAACAGTCATAATTATTTGA
66 TGACA-AGACAAAAGGTCATAATGATTTGAAATATATAATTGTTCAAATAGTCATAACTATTTGA
*
9176 ATTG-GTTCGGTAAACAAATTCATTTTTTAAAT--C-TCTTATTAATTTTTG
130 ATTGAGTTCGGTAAACAAATT-ATTTTTTAAATCCCTTATTATTAATTTTTG
* * * * ** * * * * *
9224 AAAGATTAATAAATTATTATTATTTTATTTCAAATAATCATGTGTG-ATAAAAAACAATTGTTAT
1 AAATATTAATAGATTAGTATTATCTTATTTTGAATAAGCTTGTATGAAT-AGAAACAATTGTTTT
* *
9288 ATGACCAA-ACAAAAGGTGATAATGATTTAAAATA
65 ATGA-CAAGACAAAAGGTCATAATGATTTGAAATA
9322 ATATCTTATT
Statistics
Matches: 512, Mismatches: 96, Indels: 48
0.78 0.15 0.07
Matches are distributed among these distances:
175 1 0.00
176 138 0.27
177 218 0.43
178 11 0.02
179 2 0.00
180 4 0.01
181 137 0.27
182 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (180 bp):
AAATATTAATAGATTAGTATTATCTTATTTTGAATAAGCTTGTATGAATAGAAACAATTGTTTTA
TGACAAGACAAAAGGTCATAATGATTTGAAATATATAATTGTTCAAATAGTCATAACTATTTGAA
TTGAGTTCGGTAAACAAATTATTTTTTAAATCCCTTATTATTAATTTTTG
Found at i:9951 original size:21 final size:21
Alignment explanation
Indices: 9908--9952 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9898 ATTATTAAAA
* *
9908 TTAAATTAAATAAAATAATAT
1 TTAAAATAAATAAAATAAGAT
* *
9929 TTAAAATAAATACAATTAGAT
1 TTAAAATAAATAAAATAAGAT
9950 TTA
1 TTA
9953 TAACTCAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TTAAAATAAATAAAATAAGAT
Found at i:10698 original size:12 final size:12
Alignment explanation
Indices: 10664--10698 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
10654 AATATTATTA
*
10664 TTAATTAGTAGT
1 TTAATTAATAGT
10676 TTAATTAAATAGT
1 TTAATT-AATAGT
10689 TTAATTAATA
1 TTAATTAATA
10699 TTCTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (12 bp):
TTAATTAATAGT
Found at i:10775 original size:15 final size:15
Alignment explanation
Indices: 10732--10779 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
10722 AATTGTTATT
10732 ATTAAGATAATAATA
1 ATTAAGATAATAATA
10747 ATGTTATA-ATTAATAATA
1 A--TTA-AGA-TAATAATA
10765 ATTAAGATAATAATA
1 ATTAAGATAATAATA
10780 TAGTTTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 10 0.36
16 4 0.14
17 4 0.14
18 10 0.36
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (15 bp):
ATTAAGATAATAATA
Found at i:11086 original size:3 final size:3
Alignment explanation
Indices: 11080--11104 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11070 AATAATAATA
11080 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
11105 AATAATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:11305 original size:21 final size:22
Alignment explanation
Indices: 11261--11306 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
11251 AAATTGACTA
*
11261 TTAAAATTAAATAAAATAATAT
1 TTAAAATTAAATAAAATAAGAT
* *
11283 TTAAAA-TAAATACAATTAGAT
1 TTAAAATTAAATAAAATAAGAT
11304 TTA
1 TTA
11307 TAACTAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
TTAAAATTAAATAAAATAAGAT
Found at i:11918 original size:17 final size:18
Alignment explanation
Indices: 11861--11936 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 18
11851 TATATAATTA
11861 AATTATTAATTATTTTATT
1 AATT-TTAATTATTTTATT
* * *
11880 AATAATTAATAATAATTAATT
1 AAT-TTTAAT--TATTTTATT
11901 -ATTTTAATTATTTTATT
1 AATTTTAATTATTTTATT
* *
11918 AATTTAAACTATTTTATT
1 AATTTTAATTATTTTATT
11936 A
1 A
11937 TTATTTTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
17 7 0.16
18 16 0.36
19 13 0.29
20 2 0.04
21 7 0.16
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTTAATTATTTTATT
Found at i:12226 original size:31 final size:30
Alignment explanation
Indices: 12172--12232 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
12162 AATCAATATT
*
12172 ATATTATTAAATATTAATATAATAATTAATA
1 ATATTATTAAATAGTAATATAATAA-TAATA
* * *
12203 ATATTATTAATTAGTAGTTTAATAATAATA
1 ATATTATTAAATAGTAATATAATAATAATA
12233 TAATAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (30 bp):
ATATTATTAAATAGTAATATAATAATAATA
Found at i:12303 original size:10 final size:10
Alignment explanation
Indices: 12270--12312 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
12260 TTAAATGATA
12270 ATAATTAAAT
1 ATAATTAAAT
* *
12280 ATAGTT-TAT
1 ATAATTAAAT
*
12289 ATAATTAATT
1 ATAATTAAAT
12299 ATAATTAAAT
1 ATAATTAAAT
12309 ATAA
1 ATAA
12313 AACTAATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (10 bp):
ATAATTAAAT
Found at i:13032 original size:11 final size:11
Alignment explanation
Indices: 13018--13043 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13008 TAATAATCTA
13018 TTATATTAAAT
1 TTATATTAAAT
13029 TTATATTAAAT
1 TTATATTAAAT
13040 TTAT
1 TTAT
13044 GATTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTATATTAAAT
Found at i:15092 original size:24 final size:26
Alignment explanation
Indices: 15065--15117 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
15055 ATATTAATTA
**
15065 TTAAAT-AATTATTTTTAAA-ATAAT
1 TTAAATAAATTATTAATAAATATAAT
15089 TTAAATAAATTATTAATAAATATAAT
1 TTAAATAAATTATTAATAAATATAAT
15115 TTA
1 TTA
15118 TTATTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.24
25 11 0.44
26 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAAATAAATTATTAATAAATATAAT
Found at i:15533 original size:65 final size:63
Alignment explanation
Indices: 15453--15579 Score: 141
Period size: 65 Copynumber: 2.0 Consensus size: 63
15443 TATAATTATT
* * *
15453 ATATTAAATAGATTAAATAATTATA-GTTAAATACATAA-TATATATTAATTATATATATTTATT
1 ATATTAAATAGATT-AAT-ATTATATATTAAATAAATAACTATAAATTAA-TA-ATATATTTATT
15516 AG
62 AG
** **
15518 ATATTAAATCTATTAATATTATATATTATTTAAATAACTATAAATTAATAATATATTTATTA
1 ATATTAAATAGATTAATATTATATATTAAATAAATAACTATAAATTAATAATATATTTATTA
15580 AATAAAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
63 18 0.34
64 14 0.26
65 21 0.40
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (63 bp):
ATATTAAATAGATTAATATTATATATTAAATAAATAACTATAAATTAATAATATATTTATTAG
Found at i:15579 original size:15 final size:15
Alignment explanation
Indices: 15487--15580 Score: 52
Period size: 15 Copynumber: 6.1 Consensus size: 15
15477 AGTTAAATAC
15487 ATAATATA--TATTA
1 ATAATATATTTATTA
15500 ATTATATATATTTATTA
1 A-TA-ATATATTTATTA
* * *
15517 GATATTAAATCTATTA
1 -ATAATATATTTATTA
*
15533 ATATTATATATTATTTAA
1 ATAATATAT-TTA-TT-A
*
15551 ATAACTATA--AATTA
1 ATAA-TATATTTATTA
15565 ATAATATATTTATTA
1 ATAATATATTTATTA
15580 A
1 A
15581 ATAAAATTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
13 5 0.08
14 7 0.11
15 20 0.32
16 12 0.19
17 9 0.15
18 5 0.08
19 4 0.06
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (15 bp):
ATAATATATTTATTA
Found at i:16318 original size:29 final size:25
Alignment explanation
Indices: 16251--16320 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 25
16241 AACAATACTA
16251 ATATGATTATAATATAAAATAATATT
1 ATAT-ATTATAATATAAAATAATATT
*
16277 ATATACTATAATATATAAATAATATT
1 ATATATTATAATATA-AAATAATATT
16303 AT-TATT-T-AT-TAAAATAAT
1 ATATATTATAATATAAAATAAT
16321 TATAATTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 7 0.17
22 2 0.05
23 2 0.05
24 1 0.02
25 13 0.32
26 16 0.39
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (25 bp):
ATATATTATAATATAAAATAATATT
Found at i:16888 original size:11 final size:10
Alignment explanation
Indices: 16850--17013 Score: 111
Period size: 10 Copynumber: 15.8 Consensus size: 10
16840 GTAAATGTTA
16850 TTAATTATTATT
1 TTAA-TATTA-T
*
16862 TTAATAATAT
1 TTAATATTAT
*
16872 TCAATATTAAT
1 TTAATATT-AT
16883 TTAATATTA-
1 TTAATATTAT
16892 TTAACTATTAT
1 TTAA-TATTAT
*
16903 TTAATAATAT
1 TTAATATTAT
* *
16913 TAAATATGAT
1 TTAATATTAT
* *
16923 TTAACAATAT
1 TTAATATTAT
16933 TTAATATTAAT
1 TTAATATT-AT
16944 TTAATCA-TA-
1 TTAAT-ATTAT
16953 TTAAGTATTAAT
1 TTAA-TATT-AT
16965 TTAATATTAAT
1 TTAATATT-AT
*
16976 TCAATATTAT
1 TTAATATTAT
* *
16986 TAAATAATAT
1 TTAATATTAT
*
16996 TCAATATT-T
1 TTAATATTAT
17005 TGTAATATT
1 T-TAATATT
17014 GAGACTAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 22
0.74 0.12 0.13
Matches are distributed among these distances:
9 11 0.09
10 62 0.51
11 40 0.33
12 9 0.07
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (10 bp):
TTAATATTAT
Found at i:17011 original size:20 final size:20
Alignment explanation
Indices: 16855--17003 Score: 149
Period size: 21 Copynumber: 7.2 Consensus size: 20
16845 TGTTATTAAT
16855 TATTATTTTAATAATATTCAA
1 TATTA-TTTAATAATATTCAA
*
16876 TATTAATTTAATATTATT-AA
1 TATT-ATTTAATAATATTCAA
*
16896 CTATTATTTAATAATATTAAA
1 -TATTATTTAATAATATTCAA
* * *
16917 TATGATTTAACAATATTTAA
1 TATTATTTAATAATATTCAA
*
16937 TATTAATTTAATCATATT-AA
1 TATT-ATTTAATAATATTCAA
*
16957 GTATTAATTTAATATTAATTCAA
1 -TATT-ATTTAATAAT-ATTCAA
*
16980 TATTATTAAATAATATTCAA
1 TATTATTTAATAATATTCAA
17000 TATT
1 TATT
17004 TTGTAATATT
Statistics
Matches: 109, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
20 46 0.42
21 53 0.49
22 8 0.07
23 2 0.02
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (20 bp):
TATTATTTAATAATATTCAA
Found at i:17066 original size:29 final size:29
Alignment explanation
Indices: 17019--17097 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
17009 ATATTGAGAC
17019 TAAATATTAATTTAA-AATATTTTGATAT-T
1 TAAATATTAATTTAATAATATTTT-A-ATGT
17048 TAAA-ATT-ATTCTAATAATATTTTAATGT
1 TAAATATTAATT-TAATAATATTTTAATGT
17076 TAAATATTAATTTAATAATATT
1 TAAATATTAATTTAATAATATT
17098 ATTTTTAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
27 5 0.11
28 12 0.27
29 25 0.56
30 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (29 bp):
TAAATATTAATTTAATAATATTTTAATGT
Found at i:17263 original size:39 final size:39
Alignment explanation
Indices: 17213--17314 Score: 102
Period size: 39 Copynumber: 2.7 Consensus size: 39
17203 TTTTAAAATC
* * *
17213 TTAATATTATTTGAATAATATTTTAATA-TAAACATTATT
1 TTAATAATATTTTAATAATATTTT-ATACTAAACATTAAT
* * * *
17252 TTAATAATATTTTCATATTCTTTTATACTAAATATTAAT
1 TTAATAATATTTTAATAATATTTTATACTAAACATTAAT
*
17291 TTAGTAATATTTTAAT-AT-TTTTAT
1 TTAATAATATTTTAATAATATTTTAT
17315 TTAATATTGT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
37 6 0.12
38 4 0.08
39 42 0.81
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (39 bp):
TTAATAATATTTTAATAATATTTTATACTAAACATTAAT
Found at i:17264 original size:11 final size:11
Alignment explanation
Indices: 17248--17418 Score: 51
Period size: 11 Copynumber: 15.9 Consensus size: 11
17238 ATATAAACAT
17248 TATTTTAATAA
1 TATTTTAATAA
* *
17259 TATTTTCATAT
1 TATTTTAATAA
*
17270 TCTTTTATACTAAA
1 TATTTTA-A-T-AA
*
17284 TATTAATTTAGTAA
1 TA-T--TTTAATAA
17298 TATTTTAAT-A
1 TATTTTAATAA
*
17308 T-TTTTATTTAA
1 TATTTTA-ATAA
* **
17319 TATTGTCTTAA
1 TATTTTAATAA
17330 TA-TTTAAT-A
1 TATTTTAATAA
17339 TATTTTAAT-A
1 TATTTTAATAA
*
17349 -ATTTT--GAA
1 TATTTTAATAA
* *
17357 TA-TTTCATAT
1 TATTTTAATAA
*
17367 TATTTTAATAG
1 TATTTTAATAA
* *
17378 TATTTAAAT-T
1 TATTTTAATAA
17388 TA-TTTAAT-A
1 TATTTTAATAA
*
17397 TGAATTTAATAA
1 T-ATTTTAATAA
17409 TATTTTAATA
1 TATTTTAATA
17419 TTACTTCACC
Statistics
Matches: 118, Mismatches: 24, Indels: 36
0.66 0.13 0.20
Matches are distributed among these distances:
8 4 0.03
9 20 0.17
10 19 0.16
11 55 0.47
12 6 0.05
13 2 0.02
14 6 0.05
15 2 0.02
17 4 0.03
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (11 bp):
TATTTTAATAA
Found at i:17347 original size:10 final size:10
Alignment explanation
Indices: 17332--17419 Score: 67
Period size: 11 Copynumber: 8.8 Consensus size: 10
17322 TGTCTTAATA
17332 TTTAATATAT
1 TTTAATATAT
17342 TTTAATA-AT
1 TTTAATATAT
*
17351 TTTGA-ATA-
1 TTTAATATAT
*
17359 TTTCATATTAT
1 TTTAATA-TAT
17370 TTTAATAGTAT
1 TTTAATA-TAT
* *
17381 TTAAATTTA-
1 TTTAATATAT
*
17390 TTTAATATGAA
1 TTTAATAT-AT
17401 TTTAATAATAT
1 TTTAAT-ATAT
17412 TTTAATAT
1 TTTAATAT
17420 TACTTCACCA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
8 5 0.08
9 14 0.23
10 14 0.23
11 27 0.44
12 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (10 bp):
TTTAATATAT
Found at i:17350 original size:20 final size:20
Alignment explanation
Indices: 17327--17419 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
17317 AATATTGTCT
17327 TAATATTTAATATATTTTAA
1 TAATATTTAATATATTTTAA
* *
17347 TAAT-TTTGA-ATA-TTTCA
1 TAATATTTAATATATTTTAA
* *
17364 TATTATTTTAATAGTATTTAAA
1 TAATA-TTTAATA-TATTTTAA
* *
17386 T-TTATTTAATATGAATTTAA
1 TAATATTTAATAT-ATTTTAA
17406 TAATATTTTAATAT
1 TAATA-TTTAATAT
17420 TACTTCACCA
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
17 7 0.12
18 3 0.05
19 9 0.16
20 18 0.32
21 7 0.12
22 12 0.21
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (20 bp):
TAATATTTAATATATTTTAA
Found at i:17547 original size:29 final size:28
Alignment explanation
Indices: 17515--17615 Score: 84
Period size: 29 Copynumber: 3.5 Consensus size: 28
17505 TGTTAAGTTA
17515 ATAATATTTTAATAGTAAATATTAATTTT
1 ATAATATTTTAATA-TAAATATTAATTTT
* *
17544 ATAATATTATAATATGATAATATT-ATATT
1 ATAATATTTTAATAT-A-AATATTAATTTT
*
17573 AT--TGATTTGT-ATAATAAATATTAATTTA
1 ATAAT-ATTT-TAAT-ATAAATATTAATTTT
*
17601 ATAATATTTGAATAT
1 ATAATATTTTAATAT
17616 TAATTAATTA
Statistics
Matches: 57, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
27 7 0.12
28 14 0.25
29 29 0.51
30 7 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.50
Consensus pattern (28 bp):
ATAATATTTTAATATAAATATTAATTTT
Found at i:17553 original size:8 final size:8
Alignment explanation
Indices: 17515--17575 Score: 56
Period size: 8 Copynumber: 8.0 Consensus size: 8
17505 TGTTAAGTTA
17515 ATAATATT
1 ATAATATT
* *
17523 TTAATAGT
1 ATAATATT
17531 A-AATA-T
1 ATAATATT
*
17537 -TAATTTT
1 ATAATATT
17544 ATAATATT
1 ATAATATT
*
17552 ATAATATG
1 ATAATATT
17560 ATAATATT
1 ATAATATT
*
17568 ATATTATT
1 ATAATATT
17576 GATTTGTATA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
6 4 0.10
7 5 0.12
8 33 0.79
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (8 bp):
ATAATATT
Found at i:22028 original size:2 final size:2
Alignment explanation
Indices: 22021--22105 Score: 52
Period size: 2 Copynumber: 43.5 Consensus size: 2
22011 TAAGTATTCC
* * * * * *
22021 TA TA TA TA AA TA TA AA TA TA AA TA TA TT TA TA TT TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
22063 TA TA TA GGA -A TA CT- TA TA -A T- TT 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
22103 TA T
1 TA T
22106 CAAGCATACT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
1 4 0.06
2 57 0.90
3 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22224 original size:2 final size:2
Alignment explanation
Indices: 22217--22283 Score: 57
Period size: 2 Copynumber: 34.5 Consensus size: 2
22207 ACCAATATTT
* * * * *
22217 TA TA TA TA TA TA TA TA TA TG TA TA TA TA CA -A TA TT TC T- TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
22257 TG TG 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 T
22284 GAATAGGGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22788 original size:1 final size:1
Alignment explanation
Indices: 22782--22815 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
22772 TTGAAAACTT
22782 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22816 CTTAAACTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:36295 original size:13 final size:12
Alignment explanation
Indices: 36273--36303 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
36263 CCTTAATCTG
36273 AAAAAAAAAAAT
1 AAAAAAAAAAAT
36285 AAAAAATAAAAAT
1 AAAAAA-AAAAAT
36298 AAAAAA
1 AAAAAA
36304 CCATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAAAAAAAT
Found at i:37951 original size:18 final size:17
Alignment explanation
Indices: 37919--37952 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
37909 GAAGTCCCTT
*
37919 TCAGATGGAAAAATGAA
1 TCAGAAGGAAAAATGAA
37936 TCAGAAGGACAAAATGA
1 TCAGAAGGA-AAAATGA
37953 TAAATGAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.09, G:0.24, T:0.15
Consensus pattern (17 bp):
TCAGAAGGAAAAATGAA
Found at i:40671 original size:2 final size:2
Alignment explanation
Indices: 40664--40690 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40654 TCATATAATA
40664 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
40691 AAGTAAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41679 original size:19 final size:19
Alignment explanation
Indices: 41642--41686 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
41632 CAAAATATAT
*
41642 AAAATATAAATAGTATAATC
1 AAAATATAAATA-TATAATA
41662 AAAATATCAAAT-TATAATA
1 AAAATAT-AAATATATAATA
41681 AAAATA
1 AAAATA
41687 AAAGTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 12 0.52
20 7 0.30
21 4 0.17
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATATAAATATATAATA
Found at i:49739 original size:4 final size:4
Alignment explanation
Indices: 49724--49764 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
49714 TATATATCAC
*
49724 TCTA TCTG TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
49765 TAGTTTACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.51
Consensus pattern (4 bp):
TCTA
Found at i:52413 original size:15 final size:15
Alignment explanation
Indices: 52393--52424 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
52383 AAAAGATAAG
*
52393 ATATATATTTAAATT
1 ATATATATGTAAATT
52408 ATATATATGTAAATT
1 ATATATATGTAAATT
52423 AT
1 AT
52425 TAGAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATATATATGTAAATT
Found at i:52464 original size:127 final size:132
Alignment explanation
Indices: 52234--52476 Score: 347
Period size: 127 Copynumber: 1.8 Consensus size: 132
52224 AATAAGTAGA
52234 AAATTAATTTTAAAAGATAAAAGATATATATTTAAATTATATATATATATATATCTAAATTATTA
1 AAATTAATTTTAAAAGAT-AAAGATATATA-TT--ATTATATATATATATATATCTAAATTATTA
*
52299 GAAAAAATAATTTTGGATAACTAATAATGTTTAAATACTTTTATTTATTTGATAAATACCATAAA
62 GAAAAAATAATTTTGGATAACTAATAATGTTTAAATAC--TCATTTATTTGATAAATACCATAAA
52364 ATTATTAG
125 ATTATTAG
*
52372 AAATTAATTTTAAAAGAT-AAGATATATA-T-TTA-A-AT-TATATATATGTAAATTATTAG-AA
1 AAATTAATTTTAAAAGATAAAGATATATATTATTATATATATATATATATCTAAATTATTAGAAA
* *
52430 AATTAATTTTGGATAACTAATAATTTTTAAATACTCATTTATTTGAT
66 AAATAATTTTGGATAACTAATAATGTTTAAATACTCATTTATTTGAT
52477 TAATTTTACA
Statistics
Matches: 101, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
125 12 0.12
127 34 0.34
128 20 0.20
129 2 0.02
130 1 0.01
131 3 0.03
134 1 0.01
136 10 0.10
138 18 0.18
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.43
Consensus pattern (132 bp):
AAATTAATTTTAAAAGATAAAGATATATATTATTATATATATATATATATCTAAATTATTAGAAA
AAATAATTTTGGATAACTAATAATGTTTAAATACTCATTTATTTGATAAATACCATAAAATTATT
AG
Found at i:55091 original size:22 final size:21
Alignment explanation
Indices: 55037--55091 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
55027 AAAATTACAT
*
55037 TTATTTTTAAATTTTAAAAGA
1 TTATTTTTAAATTTTAAAAAA
* *
55058 TATATATCTAAATTATTAAAAAA
1 T-TATTTTTAAATT-TTAAAAAA
55081 TTATTTTTAAA
1 TTATTTTTAAA
55092 AAATATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.04
22 18 0.67
23 8 0.30
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TTATTTTTAAATTTTAAAAAA
Found at i:56822 original size:23 final size:22
Alignment explanation
Indices: 56796--56844 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
56786 TAAAAAATGG
* *
56796 AAAAATGAAAGATAGAAAACAAA
1 AAAAATGAAAAAAAGAAAA-AAA
56819 AAAAATGAAAAAAAGAAAAAAA
1 AAAAATGAAAAAAAGAAAAAAA
56841 AAAA
1 AAAA
56845 GGAAGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.82, C:0.02, G:0.10, T:0.06
Consensus pattern (22 bp):
AAAAATGAAAAAAAGAAAAAAA
Found at i:56853 original size:25 final size:23
Alignment explanation
Indices: 56809--56857 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
56799 AATGAAAGAT
* *
56809 AGAAAACAAAAAAAATGAAAAAA
1 AGAAAAAAAAAAAAAGGAAAAAA
56832 AGAAAAAAAAAAAGGAAGGAAAAAA
1 AGAAAAAAAAAAA--AAGGAAAAAA
56857 A
1 A
56858 CTTATTAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
25 10 0.45
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (23 bp):
AGAAAAAAAAAAAAAGGAAAAAA
Found at i:57368 original size:13 final size:14
Alignment explanation
Indices: 57350--57391 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
57340 GTTATCTAAT
57350 TAAAAAAGA-AAAA
1 TAAAAAAGACAAAA
57363 TAAAAAAGACAAAA
1 TAAAAAAGACAAAA
* *
57377 AACAAAAAAACAAAA
1 TA-AAAAAGACAAAA
57392 AGATTTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 9 0.36
14 5 0.20
15 11 0.44
ACGTcount: A:0.83, C:0.07, G:0.05, T:0.05
Consensus pattern (14 bp):
TAAAAAAGACAAAA
Found at i:57369 original size:15 final size:15
Alignment explanation
Indices: 57358--57392 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
57348 ATTAAAAAAG
*
57358 AAAAATAAAAAAGACA
1 AAAAACAAAAAA-ACA
57374 AAAAACAAAAAAACA
1 AAAAACAAAAAAACA
57389 AAAA
1 AAAA
57393 GATTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.03
Consensus pattern (15 bp):
AAAAACAAAAAAACA
Found at i:57393 original size:23 final size:22
Alignment explanation
Indices: 57351--57394 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
57341 TTATCTAATT
* *
57351 AAAAAAGAAAAATAAAAAAGAC
1 AAAAAACAAAAAAAAAAAAGAC
57373 AAAAAACAAAAAAACAAAAAGA
1 AAAAAACAAAAAAA-AAAAAGA
57395 TTTGAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.84, C:0.07, G:0.07, T:0.02
Consensus pattern (22 bp):
AAAAAACAAAAAAAAAAAAGAC
Found at i:57553 original size:15 final size:15
Alignment explanation
Indices: 57521--57554 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
57511 GATTTATATT
*
57521 AAAAAAAAACTAAAA
1 AAAAAAAAACCAAAA
*
57536 AAAAAAAAACCAAGA
1 AAAAAAAAACCAAAA
57551 AAAA
1 AAAA
57555 CAGAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.03
Consensus pattern (15 bp):
AAAAAAAAACCAAAA
Found at i:59016 original size:23 final size:23
Alignment explanation
Indices: 58966--59009 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
58956 ATCTAATTAA
58966 AAAAATAAAAAAAACAAAAAACC
1 AAAAATAAAAAAAACAAAAAACC
58989 AAAAATAAAAACAAA-AAAAAA
1 AAAAATAAAAA-AAACAAAAAA
59010 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.05
Consensus pattern (23 bp):
AAAAATAAAAAAAACAAAAAACC
Found at i:59151 original size:21 final size:21
Alignment explanation
Indices: 59121--59175 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
59111 TATTAAAGAA
*
59121 TAAA-ATATAAAAAAATTTAT
1 TAAATATATAAAAAAATTCAT
*
59141 TAAATATATAAAAATATTCAT
1 TAAATATATAAAAAAATTCAT
59162 TAAATAT-TAAAAAA
1 TAAATATATAAAAAA
59176 GTAAGTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATATATAAAAAAATTCAT
Found at i:59666 original size:34 final size:32
Alignment explanation
Indices: 59627--59716 Score: 81
Period size: 34 Copynumber: 2.7 Consensus size: 32
59617 TTATAACATT
*
59627 TTTTTTTATAAAATAACATATAATATATAAATA
1 TTTTTTTATAAAATAACATAT-ATAAATAAATA
* * *
59660 TATTTTTATATTAACTAACTTATATAAATAAATA
1 T-TTTTT-TATAAAATAACATATATAAATAAATA
**
59694 TTTTTAAATAAAATTAAGCATAT
1 TTTTTTTATAAAA-TAA-CATAT
59717 TTAATACGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
32 4 0.09
33 8 0.18
34 20 0.45
35 12 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (32 bp):
TTTTTTTATAAAATAACATATATAAATAAATA
Found at i:59771 original size:12 final size:12
Alignment explanation
Indices: 59746--59788 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
59736 TAATTAGTTA
*
59746 TTAA-TTTATTT
1 TTAATTTTATAT
59757 TTAATTTTATAT
1 TTAATTTTATAT
*
59769 TTAATTTAATATT
1 TTAATTTTATA-T
59782 TTAATTT
1 TTAATTT
59789 ATTTTGACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 4 0.14
12 16 0.57
13 8 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTAATTTTATAT
Found at i:59788 original size:18 final size:17
Alignment explanation
Indices: 59746--59789 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
59736 TAATTAGTTA
* *
59746 TTAATTTATTTTTAATT
1 TTAATTTAATTTAAATT
59763 TTATATTTAATTTAATATT
1 TTA-ATTTAATTTAA-ATT
59782 TTAATTTA
1 TTAATTTA
59790 TTTTGACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTTAATTTAAATT
Found at i:59805 original size:21 final size:21
Alignment explanation
Indices: 59776--59815 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
59766 TATTTAATTT
*
59776 AATATTTTAATTTATTTTGAC
1 AATAATTTAATTTATTTTGAC
59797 AATAATTTAATTTATTTTG
1 AATAATTTAATTTATTTTG
59816 TTGTTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (21 bp):
AATAATTTAATTTATTTTGAC
Found at i:60011 original size:17 final size:19
Alignment explanation
Indices: 59986--60034 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 19
59976 ACTTTTTCTC
*
59986 AAATTAAAATATTAA-A-A
1 AAATAAAAATATTAAGAGA
60003 AAATAAAAAT-TATAAGAGA
1 AAATAAAAATAT-TAAGAGA
*
60022 AACTAAAAATATT
1 AAATAAAAATATT
60035 GAACTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.04
17 12 0.46
18 1 0.04
19 11 0.42
20 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (19 bp):
AAATAAAAATATTAAGAGA
Found at i:64379 original size:115 final size:114
Alignment explanation
Indices: 64178--64402 Score: 405
Period size: 115 Copynumber: 2.0 Consensus size: 114
64168 AGTTGATAAG
*
64178 TTTATATTTTATTTTGGTTTGACATTAGAGGTCTCAAATATATACTTCTTATGATAGGAGATAGT
1 TTTATATTTTATTTTGGTTTGACATTAGAGGTCTCAAATATATACTTCTTATGATAGGAGACAGT
64243 ATGGAAATTTGATATTTTTGGGAAGATATTGAATGTAGGAAGAGGTATT
66 ATGGAAATTTGATATTTTTGGGAAGATATTGAATGTAGGAAGAGGTATT
*
64292 TTTATTTTTTATTTTGGTTTGACATTAGAGTGTCTCAAATATATACTTCTTATGATAGGAGACAG
1 TTTATATTTTATTTTGGTTTGACATTAGAG-GTCTCAAATATATACTTCTTATGATAGGAGACAG
* *
64357 TGTGGAAATTTGATATTTTTGGGATGATATTGAATGTAGGAAGAGG
65 TATGGAAATTTGATATTTTTGGGAAGATATTGAATGTAGGAAGAGG
64403 CTTTAATACG
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
114 29 0.27
115 77 0.73
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (114 bp):
TTTATATTTTATTTTGGTTTGACATTAGAGGTCTCAAATATATACTTCTTATGATAGGAGACAGT
ATGGAAATTTGATATTTTTGGGAAGATATTGAATGTAGGAAGAGGTATT
Found at i:69572 original size:39 final size:39
Alignment explanation
Indices: 69529--69605 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
69519 CTTATCAGAT
* * *
69529 TCCCTTTCATGTCCAAAACATCAAACCGGATCCTCCAAC
1 TCCCTTGCAAGTCCAAAACATCAAACCAGATCCTCCAAC
*
69568 TCCCTTGCAAGTCCAAAACATCCAACCAGATCCTCCAA
1 TCCCTTGCAAGTCCAAAACATCAAACCAGATCCTCCAA
69606 GCCCGAAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.32, C:0.39, G:0.08, T:0.21
Consensus pattern (39 bp):
TCCCTTGCAAGTCCAAAACATCAAACCAGATCCTCCAAC
Found at i:80465 original size:39 final size:40
Alignment explanation
Indices: 80404--80509 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 40
80394 ATGAGTTTTA
** * *
80404 AAATTTTAAGGTTGTGTACCTTCATTTTAAAAAAG-CCTT
1 AAATTTTAAAATTGTATGCCTTCATTTTAAAAAAGTCCTT
** * **
80443 AAATTTTAAAATTGTATGCCTTCATTTTGGAGAAGTTTTT
1 AAATTTTAAAATTGTATGCCTTCATTTTAAAAAAGTCCTT
*
80483 AAATTTTAAAATTGTATGCCTCCATTT
1 AAATTTTAAAATTGTATGCCTTCATTT
80510 GGGAGGAGTC
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 28 0.50
40 28 0.50
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (40 bp):
AAATTTTAAAATTGTATGCCTTCATTTTAAAAAAGTCCTT
Found at i:80490 original size:40 final size:40
Alignment explanation
Indices: 80441--80529 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
80431 TAAAAAAGCC
* * *
80441 TTAAATTTTAAAATTGTATGCCTTCATTTTGGAGAAGTTT
1 TTAAATTTTAAAATTGTATGCCTCCATTTGGGAGAAGTCT
*
80481 TTAAATTTTAAAATTGTATGCCTCCATTTGGGAGGAGTCT
1 TTAAATTTTAAAATTGTATGCCTCCATTTGGGAGAAGTCT
80521 TTAAATTTT
1 TTAAATTTT
80530 GAAAGTTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (40 bp):
TTAAATTTTAAAATTGTATGCCTCCATTTGGGAGAAGTCT
Found at i:80579 original size:12 final size:12
Alignment explanation
Indices: 80564--80588 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
80554 AGGATCTTTT
80564 AAAAAAAGAAAA
1 AAAAAAAGAAAA
80576 AAAAAAAGAAAA
1 AAAAAAAGAAAA
80588 A
1 A
80589 TCTTCTGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:80837 original size:29 final size:30
Alignment explanation
Indices: 80763--80839 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
80753 TTTTTTGTGT
* *
80763 TTATCTTTATTTTTATTTTATTATTTCTATA
1 TTATATTTATTTTTA-TTTATTATTTATATA
* * *
80794 TTGTGTTAATTTTTATTT-TTATTTATATA
1 TTATATTTATTTTTATTTATTATTTATATA
*
80823 TTATATTTATCTTTATT
1 TTATATTTATTTTTATT
80840 GTTCCTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 23 0.61
30 3 0.08
31 12 0.32
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (30 bp):
TTATATTTATTTTTATTTATTATTTATATA
Found at i:82150 original size:96 final size:99
Alignment explanation
Indices: 82040--82267 Score: 257
Period size: 96 Copynumber: 2.3 Consensus size: 99
82030 ATGAAAATGC
* * *
82040 TTTTTAAATTAATCTTATCAAATTATTAGAAGATTTAAATGTCAAAACTAAATCTTATCAAA-GA
1 TTTTGAAATTAATCTTACCAAATTATTAGAAGATTTAAATCT-AAAACTAAATCTTATCAAATGA
* *
82104 TTGGAA-ATTT-TAAT-TTTTTTAAGAAAATAAAA
65 TTGGAAGATTTATAATCTTTTTAAAAAAAATAAAA
* * * * * *
82136 TTTTGAAATTAATCTTACCAAATTGTTAAAAGATTTAAATCTTAAATTAAATTTTATCAAATTAT
1 TTTTGAAATTAATCTTACCAAATTATTAGAAGATTTAAATCTAAAACTAAATCTTATCAAATGAT
*
82201 TGGAAGGTTTAATAATCTTTTTAAAAAAAATAAAA
66 TGGAAGATTT-ATAATCTTTTTAAAAAAAATAAAA
** * *
82236 AATTGAAATTAATCCTACCAAACTATTGAGAA
1 TTTTGAAATTAATCTTACCAAATTATT-AGAA
82268 ATTCAATTCT
Statistics
Matches: 108, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
95 16 0.15
96 44 0.41
97 3 0.03
99 4 0.04
100 38 0.35
101 3 0.03
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (99 bp):
TTTTGAAATTAATCTTACCAAATTATTAGAAGATTTAAATCTAAAACTAAATCTTATCAAATGAT
TGGAAGATTTATAATCTTTTTAAAAAAAATAAAA
Found at i:83034 original size:63 final size:63
Alignment explanation
Indices: 82966--83173 Score: 249
Period size: 63 Copynumber: 3.3 Consensus size: 63
82956 TTGTGAGGGG
* * * * *
82966 ATTATTGAAGATATTTTTGGCTAGAAACGTCTTGAATAACCTTCATTAAATTTTTTGTAAGGA
1 ATTATTGAAGGTGTTTTTGGCCAGAAACGCCTTGAATAACCTTCATTAAATTTTTTATAAGGA
* * * * * ** *
83029 ATTATTGAAGGTGTTTTTGACCAAAAACGCCTTGAATAATC-TGA-AAAAAATTTTAAAAGGAA
1 ATTATTGAAGGTGTTTTTGGCCAGAAACGCCTTGAATAACCTTCATTAAATTTTTTATAAGG-A
* *
83091 ATTATTGAAGGTGTTTTTTGCCAGAAAGGCCTTGAATAACCTTCATTAAATTTTTTATAAGGA
1 ATTATTGAAGGTGTTTTTGGCCAGAAACGCCTTGAATAACCTTCATTAAATTTTTTATAAGGA
*
83154 ATTATTGAAGGTTTTTTTGG
1 ATTATTGAAGGTGTTTTTGG
83174 TCAAAAATGC
Statistics
Matches: 117, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
61 11 0.09
62 39 0.33
63 55 0.47
64 12 0.10
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (63 bp):
ATTATTGAAGGTGTTTTTGGCCAGAAACGCCTTGAATAACCTTCATTAAATTTTTTATAAGGA
Found at i:83123 original size:62 final size:64
Alignment explanation
Indices: 82990--83172 Score: 196
Period size: 62 Copynumber: 2.9 Consensus size: 64
82980 TTTTGGCTAG
* * ** **
82990 AAACGTCTTGAATAACCTTCATTAAATTTTTTGTAAGGAATTATTGAAGGTG-TTTTTGACCAA
1 AAACGCCTTGAATAACCTTCATAAAAAATTTTAAAAGGAATTATTGAAGGTGTTTTTTGACCAA
* * *
83053 AAACGCCTTGAATAATC-TGA-AAAAAATTTTAAAAGGAAATTATTGAAGGTGTTTTTTG-CCAG
1 AAACGCCTTGAATAACCTTCATAAAAAATTTTAAAAGG-AATTATTGAAGGTGTTTTTTGACCAA
* * ** *
83115 AAAGGCCTTGAATAACCTTCATTAAATTTTTTATAAGGAATTATTGAAGGT-TTTTTTG
1 AAACGCCTTGAATAACCTTCATAAAAAATTTTAAAAGGAATTATTGAAGGTGTTTTTTG
83173 GTCAAAAATG
Statistics
Matches: 100, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
61 11 0.11
62 41 0.41
63 36 0.36
64 12 0.12
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (64 bp):
AAACGCCTTGAATAACCTTCATAAAAAATTTTAAAAGGAATTATTGAAGGTGTTTTTTGACCAA
Found at i:85286 original size:3 final size:3
Alignment explanation
Indices: 85278--85354 Score: 100
Period size: 3 Copynumber: 25.7 Consensus size: 3
85268 CACATATGGT
* * * * *
85278 AGA AGA AGA AGT AGA AGA AAA AAA AGA AGA AGA AAA ATA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
85326 AGA ATA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
85355 TAAAAGAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:85293 original size:12 final size:12
Alignment explanation
Indices: 85276--85362 Score: 71
Period size: 12 Copynumber: 7.8 Consensus size: 12
85266 GGCACATATG
85276 GTAGAAGAAGAA
1 GTAGAAGAAGAA
85288 GTAGAAGAA-AA
1 GTAGAAGAAGAA
*
85299 --AAAAGAAGAA
1 GTAGAAGAAGAA
*
85309 G-A-AA-AATAA
1 GTAGAAGAAGAA
*
85318 GAAGAAGAAGAA
1 GTAGAAGAAGAA
85330 -TAAGAAGAAGAA
1 GT-AGAAGAAGAA
*
85342 GAAGAAGAAGAA
1 GTAGAAGAAGAA
*
85354 GTAAAAGAA
1 GTAGAAGAA
85363 AAAAAAAAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
9 11 0.18
10 5 0.08
11 5 0.08
12 40 0.66
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (12 bp):
GTAGAAGAAGAA
Found at i:85308 original size:15 final size:15
Alignment explanation
Indices: 85290--85376 Score: 93
Period size: 15 Copynumber: 5.7 Consensus size: 15
85280 AAGAAGAAGT
85290 AGAAGAAAAAAAAGA
1 AGAAGAAAAAAAAGA
*
85305 AGAAGAAAAATAAGA
1 AGAAGAAAAAAAAGA
* *
85320 AGAAGAAGAATAAGA
1 AGAAGAAAAAAAAGA
* *
85335 AGAAGAAGAAGAAGA
1 AGAAGAAAAAAAAGA
*
85350 AGAAGTAAAAGAAAAAA
1 AGAAG-AAAA-AAAAGA
*
85367 AAAAGAAAAA
1 AGAAGAAAAA
85377 TTGATAAGAC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
15 48 0.76
16 7 0.11
17 8 0.13
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (15 bp):
AGAAGAAAAAAAAGA
Found at i:85365 original size:6 final size:6
Alignment explanation
Indices: 85298--85376 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
85288 GTAGAAGAAA
* * * * * *
85298 AAAAAG AAGAAG AAAAAT AAGAAG AAGAAG AATAAGAAG AAGAAG AAGAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -A-AA-AAG AAAAAG AAAAAG
* *
85349 AAGAAG TAAAAG AAAAA- AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
85377 TTGATAAGAC
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
5 5 0.08
6 47 0.80
7 2 0.03
8 2 0.03
9 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:85368 original size:9 final size:9
Alignment explanation
Indices: 85278--85376 Score: 78
Period size: 9 Copynumber: 11.1 Consensus size: 9
85268 CACATATGGT
*
85278 AGAAGAAGA
1 AGAAGAAAA
*
85287 AGTAGAAGAA
1 AGAAGAA-AA
85297 A-AA-AAAGA
1 AGAAGAAA-A
85305 AGAAGAAAA
1 AGAAGAAAA
* *
85314 ATAAGAAGA
1 AGAAGAAAA
*
85323 AGAAGAATA
1 AGAAGAAAA
*
85332 AGAAGAAGA
1 AGAAGAAAA
*
85341 AGAAGAAGA
1 AGAAGAAAA
*
85350 AGAAGTAAA
1 AGAAGAAAA
85359 AGAA-AAAA
1 AGAAGAAAA
*
85367 AAAAGAAAA
1 AGAAGAAAA
85376 A
1 A
85377 TTGATAAGAC
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
7 1 0.01
8 10 0.14
9 57 0.78
10 5 0.07
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (9 bp):
AGAAGAAAA
Found at i:92073 original size:37 final size:35
Alignment explanation
Indices: 92003--92083 Score: 126
Period size: 37 Copynumber: 2.3 Consensus size: 35
91993 TGATTATATA
*
92003 TTATTGTTTACATATGTTAGATTATATATAATTGT
1 TTATTGTTTACATATGTTAAATTATATATAATTGT
*
92038 TTATTGTTTATATATTGTTTAAATTATATATAATTGT
1 TTATTGTTTACATA-TG-TTAAATTATATATAATTGT
92075 TTATTGTTT
1 TTATTGTTT
92084 GGCTTTTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 13 0.31
36 2 0.05
37 27 0.64
ACGTcount: A:0.30, C:0.01, G:0.10, T:0.59
Consensus pattern (35 bp):
TTATTGTTTACATATGTTAAATTATATATAATTGT
Found at i:92409 original size:66 final size:67
Alignment explanation
Indices: 92300--92434 Score: 245
Period size: 66 Copynumber: 2.0 Consensus size: 67
92290 GTGCTTCTCC
*
92300 TGAAAATATATAAGTGTAATTCTAAAGGTATGTCTGAAATATTATTCTTAATGAAAATGTGACAT
1 TGAAAATATATAAGTGTAATTATAAAGGTATGTCTGAAATATTATTCTTAATGAAAATGTGACAT
92365 TA
66 TA
*
92367 TGAAAATATATAAGTTTAATTAT-AAGGTATGTCTGAAATATTATTCTTAATGAAAATGTGACAT
1 TGAAAATATATAAGTGTAATTATAAAGGTATGTCTGAAATATTATTCTTAATGAAAATGTGACAT
92431 TA
66 TA
92433 TG
1 TG
92435 CTTACATAGT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 45 0.68
67 21 0.32
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (67 bp):
TGAAAATATATAAGTGTAATTATAAAGGTATGTCTGAAATATTATTCTTAATGAAAATGTGACAT
TA
Found at i:92771 original size:3 final size:3
Alignment explanation
Indices: 92759--92796 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
92749 TTTATTTTTT
*
92759 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
92797 GCTCTTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:95008 original size:15 final size:15
Alignment explanation
Indices: 94988--95023 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
94978 GGTGTAACTC
*
94988 TTTATCTATATTTGT
1 TTTATCGATATTTGT
95003 TTTATCGATATTTGT
1 TTTATCGATATTTGT
95018 TTTATC
1 TTTATC
95024 AGACTTGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.64
Consensus pattern (15 bp):
TTTATCGATATTTGT
Found at i:95659 original size:49 final size:49
Alignment explanation
Indices: 95597--95696 Score: 112
Period size: 49 Copynumber: 2.0 Consensus size: 49
95587 AATTAAAACA
* * * * *
95597 TACAAATCTATACTTATAGGCTTTAAGCGTT-AGTATAGATAAAAAAAAT
1 TACAAATCCATACTAATAGGCATCAACCGTTGA-TATAGATAAAAAAAAT
* * *
95646 TACAAGTCCATACTAATGGGCATCAACCGTTGATATAGGTAAAAAAAAT
1 TACAAATCCATACTAATAGGCATCAACCGTTGATATAGATAAAAAAAAT
95695 TA
1 TA
95697 AAACATATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
49 41 0.98
50 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (49 bp):
TACAAATCCATACTAATAGGCATCAACCGTTGATATAGATAAAAAAAAT
Found at i:102737 original size:6 final size:6
Alignment explanation
Indices: 102726--102750 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
102716 GAATCCACTG
102726 CCCTTA CCCTTA CCCTTA CCCTTA C
1 CCCTTA CCCTTA CCCTTA CCCTTA C
102751 ACTCGAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCTTA
Found at i:112742 original size:12 final size:12
Alignment explanation
Indices: 112725--112758 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
112715 TTATTCAATC
112725 TAAAATTTAAAA
1 TAAAATTTAAAA
112737 TAAAA-TTAAAA
1 TAAAATTTAAAA
*
112748 TAAAATGTAAA
1 TAAAATTTAAA
112759 CAGGAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
TAAAATTTAAAA
Found at i:119329 original size:8 final size:8
Alignment explanation
Indices: 119316--119341 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
119306 AGGGATCGAT
119316 AGTGTGAG
1 AGTGTGAG
119324 AGTGTGAG
1 AGTGTGAG
119332 AGTGTGAG
1 AGTGTGAG
119340 AG
1 AG
119342 ACTAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.50, T:0.23
Consensus pattern (8 bp):
AGTGTGAG
Found at i:120452 original size:5 final size:5
Alignment explanation
Indices: 120444--120476 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
120434 ATTTTGGTAT
120444 TTTTA TTTTA TTTTA TTTTA TTTT- TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
120477 TTAATTACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTA
Found at i:120457 original size:24 final size:24
Alignment explanation
Indices: 120430--120476 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
120420 TTTCTTTGTT
*
120430 TTTTATTTTGGTATTTTTATTTTA
1 TTTTATTTTAGTATTTTTATTTTA
* *
120454 TTTTATTTTATTTTTTTTATTTT
1 TTTTATTTTAGTATTTTTATTTT
120477 TTAATTACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (24 bp):
TTTTATTTTAGTATTTTTATTTTA
Found at i:120477 original size:10 final size:10
Alignment explanation
Indices: 120441--120478 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
120431 TTTATTTTGG
120441 TATTTTTATTT
1 TATTTTT-TTT
*
120452 TATTTTATTT
1 TATTTTTTTT
120462 TA-TTTTTTT
1 TATTTTTTTT
120471 TATTTTTT
1 TATTTTTT
120479 AATTACTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.33
10 10 0.42
11 6 0.25
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TATTTTTTTT
Found at i:120641 original size:12 final size:12
Alignment explanation
Indices: 120614--120653 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
120604 AGACAAATAA
120614 ATTTATAAATTT
1 ATTTATAAATTT
120626 -TTTATAAATTT
1 ATTTATAAATTT
**
120637 ATTTATTTATTT
1 ATTTATAAATTT
120649 ATTTA
1 ATTTA
120654 AATCATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTATAAATTT
Found at i:120644 original size:19 final size:20
Alignment explanation
Indices: 120610--120650 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
120600 CATTAGACAA
120610 ATAAATTTATAAATTT-TTT
1 ATAAATTTATAAATTTATTT
**
120629 ATAAATTTATTTATTTATTT
1 ATAAATTTATAAATTTATTT
120649 AT
1 AT
120651 TTAAATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATAAATTTATAAATTTATTT
Found at i:133694 original size:266 final size:270
Alignment explanation
Indices: 133210--133751 Score: 860
Period size: 266 Copynumber: 2.0 Consensus size: 270
133200 AAAAATTTTG
* *
133210 AATGAGATATCTTATATATACATGGAGGATTAAAAAATTTAATAGTTTAAGCTTTTTGACTCAAG
1 AATGAGATATCTTATATATACATGGAGGACTAAAAAATTTAATAGTTTAAGCTTTTGGACTCAAG
* *
133275 TACTGTCTAATATATATTTATGGACTCTCTGGTGTACTCTCATGGGCTTTAAATGTGACAAATTT
66 TACTGTCTAATATATATATATGGACTCTCTAGTGTA--C-CAT--GC-TTAAATGTGACAAATTT
* *
133340 TTCAACAACTGAAAATAAGGTTTTTTGAAATTAAATCACCTTTATTTTTATTAAATTCAACCAAT
125 TTCAACAACTGAAAAGAAGGTTTTCTGAAATTAAATCACCTTTATTTTTATTAAATTCAACCAAT
* *
133405 CTTTTAATAGGCTTATAAGATAACCAACACGAATAGAAAACTTAACTAATTAGAGAATGTGAAGC
190 CTTTTAATAGGCTTATAAGATAACCAACACGAATAGAAAACTCAACTAATCAGAGAATGTGAAGC
133470 ATAAAAATAAAACAGT
255 ATAAAAATAAAACAGT
* *
133486 AATGAGATATCTTATATATATATGGAGGACTAAAAAATTTAATAGTTTAAGCTTTTGGGCTCAAG
1 AATGAGATATCTTATATATACATGGAGGACTAAAAAATTTAATAGTTTAAGCTTTTGGACTCAAG
* * *
133551 TACTGTCTCATATATATATATAGG-CTCTTTAGTGTA-C-T-C-TAATTGTGACAAATTTTTCAA
66 TACTGTCTAATATATATATAT-GGACTCTCTAGTGTACCATGCTTAAATGTGACAAATTTTTCAA
*
133611 CAACTGGAAAGAAGGTTTTCTGAAATTAAATCACCTTTATTTTTATTAAATTCAACCAATCTTTT
130 CAACTGAAAAGAAGGTTTTCTGAAATTAAATCACCTTTATTTTTATTAAATTCAACCAATCTTTT
133676 AATAGGCTTATAAGATAACCAACACGAATAGAAAACTCAACTAATCAGAGAATGTGAAGCATAAA
195 AATAGGCTTATAAGATAACCAACACGAATAGAAAACTCAACTAATCAGAGAATGTGAAGCATAAA
133741 AATAAAACAGT
260 AATAAAACAGT
133752 TAACAGATAA
Statistics
Matches: 251, Mismatches: 14, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
266 156 0.62
268 1 0.00
271 1 0.00
272 1 0.00
276 90 0.36
277 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (270 bp):
AATGAGATATCTTATATATACATGGAGGACTAAAAAATTTAATAGTTTAAGCTTTTGGACTCAAG
TACTGTCTAATATATATATATGGACTCTCTAGTGTACCATGCTTAAATGTGACAAATTTTTCAAC
AACTGAAAAGAAGGTTTTCTGAAATTAAATCACCTTTATTTTTATTAAATTCAACCAATCTTTTA
ATAGGCTTATAAGATAACCAACACGAATAGAAAACTCAACTAATCAGAGAATGTGAAGCATAAAA
ATAAAACAGT
Found at i:141592 original size:24 final size:26
Alignment explanation
Indices: 141558--141618 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 26
141548 ATGTTAAATT
*
141558 TATTAAGTAATTT-AT-TTTTTAGCA
1 TATTAATTAATTTAATATTTTTAGCA
*
141582 TATTAATTAATTTAATATTTTTATCA
1 TATTAATTAATTTAATATTTTTAGCA
141608 TA--AATTAATTT
1 TATTAATTAATTT
141619 TAATTTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 21 0.64
25 2 0.06
26 10 0.30
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (26 bp):
TATTAATTAATTTAATATTTTTAGCA
Found at i:143441 original size:55 final size:56
Alignment explanation
Indices: 143382--143521 Score: 167
Period size: 55 Copynumber: 2.5 Consensus size: 56
143372 CGCTTAGCAT
* * *
143382 CTGTCAGTATAAACTTATATTTTTTAATTTC-TTTACCTATACCAACAGTTAGAGA
1 CTGTCAGTATAAAATTATATGTTTTAATTTCTTTTACATATACCAACAGTTAGAGA
* * * * *
143437 CTGTCAGTATAAAATTGTATGCTTTAA-TTCTTTTACATATATCGACGGTTAGAGA
1 CTGTCAGTATAAAATTATATGTTTTAATTTCTTTTACATATACCAACAGTTAGAGA
* * *
143492 TTGTCAGTATAGATTTATATGTTTTAATTT
1 CTGTCAGTATAAAATTATATGTTTTAATTT
143522 TTATGATATT
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
54 3 0.04
55 65 0.93
56 2 0.03
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (56 bp):
CTGTCAGTATAAAATTATATGTTTTAATTTCTTTTACATATACCAACAGTTAGAGA
Found at i:143647 original size:24 final size:24
Alignment explanation
Indices: 143615--143661 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
143605 ATATTTTAAA
* *
143615 AATTATATTTTTAATTATTAATATT
1 AATTATATTTATAATCA-TAATATT
143640 AATT-TATTTATAATCATAATAT
1 AATTATATTTATAATCATAATAT
143662 GATATGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTATATTTATAATCATAATATT
Found at i:144667 original size:68 final size:68
Alignment explanation
Indices: 144593--144719 Score: 218
Period size: 68 Copynumber: 1.9 Consensus size: 68
144583 ACATAAGGTA
* *
144593 AAAAGATAATCATCCATTTATATACCAGTAGAAATAATTTTATAAACATCTTATTCATTCATATA
1 AAAAGATAATCATCCATTTATATACCAGCAAAAATAATTTTATAAACATCTTATTCATTCATATA
144658 TAC
66 TAC
* *
144661 AAAAGATAATCATCTATTTATATACCAGCAAAAATAATTTTATAAATATCTTATTCATT
1 AAAAGATAATCATCCATTTATATACCAGCAAAAATAATTTTATAAACATCTTATTCATT
144720 AATGTAATGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (68 bp):
AAAAGATAATCATCCATTTATATACCAGCAAAAATAATTTTATAAACATCTTATTCATTCATATA
TAC
Found at i:147676 original size:25 final size:25
Alignment explanation
Indices: 147648--147723 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
147638 TAAATAACAC
147648 AACTTTTATTCTACCAATATAATTT
1 AACTTTTATTCTACCAATATAATTT
* *
147673 AACTATCATATT-TA--AATA-ACA--C
1 AACT-T-TTATTCTACCAATATA-ATTT
147695 AACTTTTATTCTACCAATATAATTT
1 AACTTTTATTCTACCAATATAATTT
147720 AACT
1 AACT
147724 GAATGATGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 18
0.63 0.07 0.30
Matches are distributed among these distances:
20 4 0.11
21 3 0.08
22 4 0.11
23 6 0.16
24 6 0.16
25 8 0.21
26 3 0.08
27 4 0.11
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.42
Consensus pattern (25 bp):
AACTTTTATTCTACCAATATAATTT
Found at i:147699 original size:47 final size:47
Alignment explanation
Indices: 147630--147723 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
147620 TATTGATCCA
147630 ATCATATTTAAATAACACAACTTTTATTCTACCAATATAATTTAACT
1 ATCATATTTAAATAACACAACTTTTATTCTACCAATATAATTTAACT
147677 ATCATATTTAAATAACACAACTTTTATTCTACCAATATAATTTAACT
1 ATCATATTTAAATAACACAACTTTTATTCTACCAATATAATTTAACT
147724 GAATGATGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (47 bp):
ATCATATTTAAATAACACAACTTTTATTCTACCAATATAATTTAACT
Found at i:152158 original size:125 final size:125
Alignment explanation
Indices: 151969--152199 Score: 292
Period size: 125 Copynumber: 1.8 Consensus size: 125
151959 TTATAAGGGA
*
151969 TTATTAAAGGCATTTTCTACCAAAAACGCCTTTAATAATCCCTTTCATTTTTTATGAGGGGATTA
1 TTATTAAAGGCATTTTCTACCAAAAACGCCTTTAATAATCCCTTTCATTTTTTATGAGAGGATTA
* * *
152034 ATCAAGGTGTTTTGGCCT-AAAAAATATCTTGAATAATCCCTTACAAAAAATTGAATAAGG
66 ATCAAGATGTTTTGG-ATAAAAAAATACCTTGAATAATCCCTTACAAAAAATTGAATAAGG
* * *
152094 TTATTGAAGGCA-TTTCTAGCCAAAAATG-CTTTGAATAATCTCCTTAT-ATTTTTTATGA-ATG
1 TTATTAAAGGCATTTTCTA-CCAAAAACGCCTTT-AATAATC-CCTT-TCATTTTTTATGAGAGG
* *
152155 ATTATTCAAGATGTTTTTGATAAAAAAAATACCTTGAATAATCCC
62 ATTAATCAAGATGTTTTGGAT-AAAAAAATACCTTGAATAATCCC
152200 CTTCAATTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
124 11 0.12
125 43 0.47
126 36 0.40
127 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (125 bp):
TTATTAAAGGCATTTTCTACCAAAAACGCCTTTAATAATCCCTTTCATTTTTTATGAGAGGATTA
ATCAAGATGTTTTGGATAAAAAAATACCTTGAATAATCCCTTACAAAAAATTGAATAAGG
Found at i:154497 original size:21 final size:21
Alignment explanation
Indices: 154471--154524 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
154461 GAGCAACAAC
*
154471 AGCAAAGACTTTATGATCAAG
1 AGCAAAGACTTAATGATCAAG
* * *
154492 AGCAAAGCCTGAATGATCAAT
1 AGCAAAGACTTAATGATCAAG
*
154513 AGCAATGACTTA
1 AGCAAAGACTTA
154525 CAGCTTTTGA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.22
Consensus pattern (21 bp):
AGCAAAGACTTAATGATCAAG
Found at i:156389 original size:62 final size:61
Alignment explanation
Indices: 156281--156414 Score: 146
Period size: 62 Copynumber: 2.2 Consensus size: 61
156271 GAGAAAGTAT
* *
156281 CTTGAATAATCTCTTAGAAAAAATTGAATAGAATTAGTCAAGGCGTTTATAGCCAAAA-AC
1 CTTGAATAATCTCTTACAAAAAATTGAATAGAATTAGTCAAAGCGTTTATAGCCAAAATAC
* * * * * * *
156341 GCTTTGAATAATCAT-TTACAAAATATTGAATTGAGTTATTGAAAGCGTTTCTGGCCAAAATAC
1 -C-TTGAATAATC-TCTTACAAAAAATTGAATAGAATTAGTCAAAGCGTTTATAGCCAAAATAC
156404 CTTGAATAATC
1 CTTGAATAATC
156415 CCCTTAAATT
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
61 11 0.18
62 47 0.77
63 3 0.05
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (61 bp):
CTTGAATAATCTCTTACAAAAAATTGAATAGAATTAGTCAAAGCGTTTATAGCCAAAATAC
Found at i:158073 original size:26 final size:27
Alignment explanation
Indices: 158022--158073 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
158012 TAGGTTAAAT
*
158022 TTAGAGAAATTTATCACTAGAGATTTC
1 TTAGAGAAATTTATCACTAGAAATTTC
* *
158049 TTAGA-AAATTTATCATTTGAAATTT
1 TTAGAGAAATTTATCACTAGAAATTT
158074 TTAATAATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (27 bp):
TTAGAGAAATTTATCACTAGAAATTTC
Found at i:160215 original size:18 final size:18
Alignment explanation
Indices: 160134--160215 Score: 60
Period size: 18 Copynumber: 4.6 Consensus size: 18
160124 TTTAGATTCG
*
160134 CAAGAATTTTT-TATTTCA
1 CAAGAATTTTTAAATTT-A
* * * *
160152 CAAAAATTTTCAAGTTCA
1 CAAGAATTTTTAAATTTA
160170 CAAG-ATTTGTTAAATTTA
1 CAAGAATTT-TTAAATTTA
* * *
160188 CAAGATTTTTTAGATTTG
1 CAAGAATTTTTAAATTTA
160206 CAAGAATTTT
1 CAAGAATTTT
160216 ATATTCTTAA
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
17 4 0.08
18 39 0.81
19 5 0.10
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (18 bp):
CAAGAATTTTTAAATTTA
Found at i:160279 original size:17 final size:18
Alignment explanation
Indices: 160259--160292 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
160249 AAATTTGCAA
*
160259 GAATTT-AAGGTTCGTAT
1 GAATTTCAAGATTCGTAT
160276 GAATTTCAAGATTCGTA
1 GAATTTCAAGATTCGTA
160293 ATAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (18 bp):
GAATTTCAAGATTCGTAT
Found at i:160377 original size:21 final size:21
Alignment explanation
Indices: 160348--160388 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
160338 TAATTTGTAG
**
160348 AAATCCACATCCAAAATTTCT
1 AAATCCACATAAAAAATTTCT
*
160369 AAATTCACATAAAAAATTTC
1 AAATCCACATAAAAAATTTC
160389 AAGATTTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATCCACATAAAAAATTTCT
Found at i:160561 original size:24 final size:23
Alignment explanation
Indices: 160533--160599 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 23
160523 GTATTTCACA
160533 CCAAAAATTTCAAAGGTTCTCATT
1 CCAAAAATTTCAAAGGTTCTCA-T
* * * *
160557 CCAAAAACTTTTATAGTTTTTCAT
1 CCAAAAA-TTTCAAAGGTTCTCAT
*
160581 -CTAAAATTTCAAAGGTTCT
1 CCAAAAATTTCAAAGGTTCT
160600 TACTCAAAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
22 9 0.27
23 5 0.15
24 8 0.24
25 11 0.33
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (23 bp):
CCAAAAATTTCAAAGGTTCTCAT
Found at i:160593 original size:47 final size:46
Alignment explanation
Indices: 160493--160639 Score: 165
Period size: 46 Copynumber: 3.2 Consensus size: 46
160483 CACGTTCAAG
* * *
160493 ATTTCAAAGATTCTTACTCGAAAAACTTTA-GTATTTCACA-CCAAAA
1 ATTTCAAAGGTTCTCACTCAAAAAACTTTATGT-TTTCACATCC-AAA
* * * *
160539 ATTTCAAAGGTTCTCATTCCAAAAACTTTTATAGTTTT-TCATCTAAA
1 ATTTCAAAGGTTCTCACTCAAAAAAC-TTTAT-GTTTTCACATCCAAA
*
160586 ATTTCAAAGGTTCTTACTCAAAAAACTTTATGTTTTCACATCCAAA
1 ATTTCAAAGGTTCTCACTCAAAAAACTTTATGTTTTCACATCCAAA
160632 ATTTCAAA
1 ATTTCAAA
160640 AATTCTTATT
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
45 5 0.06
46 42 0.49
47 32 0.38
48 4 0.05
49 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.37
Consensus pattern (46 bp):
ATTTCAAAGGTTCTCACTCAAAAAACTTTATGTTTTCACATCCAAA
Found at i:160687 original size:20 final size:20
Alignment explanation
Indices: 160662--160699 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
160652 AACAACCAAA
160662 ATTTCAAAGATTCACATTTT
1 ATTTCAAAGATTCACATTTT
*
160682 ATTTCAAATATTCACATT
1 ATTTCAAAGATTCACATT
160700 CAAGAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.45
Consensus pattern (20 bp):
ATTTCAAAGATTCACATTTT
Found at i:160718 original size:24 final size:24
Alignment explanation
Indices: 160682--160746 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
160672 TTCACATTTT
* *
160682 ATTTCAAATATTCACATTCAAGAA
1 ATTTTAAAGATTCACATTCAAGAA
*
160706 ATTTTAAAGATTCACATTCAATAA
1 ATTTTAAAGATTCACATTCAAGAA
*
160730 ATTTTAGAGATTCACAT
1 ATTTTAAAGATTCACAT
160747 ATAAATTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTTTAAAGATTCACATTCAAGAA
Found at i:160752 original size:21 final size:23
Alignment explanation
Indices: 160660--160766 Score: 82
Period size: 24 Copynumber: 4.8 Consensus size: 23
160650 CGAACAACCA
*
160660 AAATTTCAAAGATTCACATT--T
1 AAATTTTAAAGATTCACATTAAT
* * * *
160681 -TATTTCAAATATTCACATTCAAG
1 AAATTTTAAAGATTCACATT-AAT
160704 AAATTTTAAAGATTCACATTCAAT
1 AAATTTTAAAGATTCACATT-AAT
*
160728 AAATTTTAGAGATTCACA-T-AT
1 AAATTTTAAAGATTCACATTAAT
* *
160749 AAA-TTCAAAGGTTCACAT
1 AAATTTTAAAGATTCACAT
160767 AAAAAAAATT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
20 28 0.40
21 5 0.07
23 1 0.01
24 36 0.51
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (23 bp):
AAATTTTAAAGATTCACATTAAT
Found at i:164422 original size:67 final size:67
Alignment explanation
Indices: 164342--164511 Score: 241
Period size: 67 Copynumber: 2.5 Consensus size: 67
164332 GACCTAGATT
** * *
164342 GAGCCAAGGTAAAAAACAAGTGATTGAGATTGAACCACGAGTTGAAAATTTCAAGATGACTTAGA
1 GAGCCAAGGTAAAAAATGAGTGATTGGGATTGAACCACGAGTTGAAAAATTCAAGATGACTTAGA
164407 CC
66 CC
* * *
164409 GAGCCAAGATAAAAAATGAGTGATTGGGATTGAACCATGAGTTGAAAAATTCAAGATGACTTGGA
1 GAGCCAAGGTAAAAAATGAGTGATTGGGATTGAACCACGAGTTGAAAAATTCAAGATGACTTAGA
*
164474 TC
66 CC
** *
164476 GAGCTGAGGTAAAAAATGAGTGATCGGGATTGAACC
1 GAGCCAAGGTAAAAAATGAGTGATTGGGATTGAACC
164512 GTAAATCAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 91 1.00
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (67 bp):
GAGCCAAGGTAAAAAATGAGTGATTGGGATTGAACCACGAGTTGAAAAATTCAAGATGACTTAGA
CC
Found at i:164524 original size:67 final size:67
Alignment explanation
Indices: 164386--164535 Score: 183
Period size: 67 Copynumber: 2.2 Consensus size: 67
164376 CCACGAGTTG
* * * *
164386 AAAATTTCAAGATGACTTAGACCGAGCCAAGATAAAAAATGAGTGATTGGGATTGAACCATGAGT
1 AAAAATTCAAGATGACTTAGACCGAGCCAAGATAAAAAATGAGTGATCGGGATTGAACCATAAAT
**
164451 TG
66 CA
* * ** * *
164453 AAAAATTCAAGATGACTTGGATCGAGCTGAGGTAAAAAATGAGTGATCGGGATTGAACCGTAAAT
1 AAAAATTCAAGATGACTTAGACCGAGCCAAGATAAAAAATGAGTGATCGGGATTGAACCATAAAT
164518 CA
66 CA
*
164520 AAAAATTCAAAATGAC
1 AAAAATTCAAGATGAC
164536 ATGTACTAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.23
Consensus pattern (67 bp):
AAAAATTCAAGATGACTTAGACCGAGCCAAGATAAAAAATGAGTGATCGGGATTGAACCATAAAT
CA
Found at i:164552 original size:67 final size:67
Alignment explanation
Indices: 164418--164565 Score: 172
Period size: 67 Copynumber: 2.2 Consensus size: 67
164408 CGAGCCAAGA
* * * ** * * **
164418 TAAAAAATGAGTGATTGGGATTGAACCATGAGTTGAAAAATTCAAGATGACTTGGATCGAGCTGA
1 TAAAAAATGAGTGATCGGGATTGAACCATAAATCAAAAAATTCAAAATGACATGGATAAAGCTGA
164483 GG
66 GG
* * *
164485 TAAAAAATGAGTGATCGGGATTGAACCGTAAATCAAAAAATTCAAAATGACATGTACTAAATC-G
1 TAAAAAATGAGTGATCGGGATTGAACCATAAATCAAAAAATTCAAAATGACATGGA-TAAAGCTG
164549 AGG
65 AGG
164552 TAAAAAATGAGTGA
1 TAAAAAATGAGTGA
164566 CCAAGATTGA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
67 65 0.96
68 3 0.04
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (67 bp):
TAAAAAATGAGTGATCGGGATTGAACCATAAATCAAAAAATTCAAAATGACATGGATAAAGCTGA
GG
Found at i:165255 original size:8 final size:8
Alignment explanation
Indices: 165244--165269 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
165234 CATCCCAACA
165244 CAAATAAT
1 CAAATAAT
165252 CAAATAAT
1 CAAATAAT
165260 CAAATAAT
1 CAAATAAT
165268 CA
1 CA
165270 TAACAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (8 bp):
CAAATAAT
Found at i:168346 original size:36 final size:36
Alignment explanation
Indices: 168306--168383 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
168296 GACTATGAAC
* *
168306 TGAAATAAATTTAGTCCTAGGGCCTACAGATCCTAA
1 TGAAATAAATTTAGTCCTAGGGCCTAAAGATCCCAA
168342 TGAAATAAATTTAGTCCTAGGGCCTAAAGATCCCAA
1 TGAAATAAATTTAGTCCTAGGGCCTAAAGATCCCAA
168378 TGAAAT
1 TGAAAT
168384 TCACAATTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (36 bp):
TGAAATAAATTTAGTCCTAGGGCCTAAAGATCCCAA
Found at i:168646 original size:23 final size:25
Alignment explanation
Indices: 168615--168678 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 25
168605 TACTTACCAA
*
168615 TCATGTTTTTTATCTTTTT-GTT-T
1 TCATTTTTTTTATCTTTTTGGTTCT
*
168638 TCATTTTTTTCA-CTTTTTGGTTCT
1 TCATTTTTTTTATCTTTTTGGTTCT
*
168662 T-ATTTATTTTTTTCTTT
1 TCATTT-TTTTTATCTTT
168679 CTTTTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 6 0.18
23 17 0.52
24 6 0.18
25 4 0.12
ACGTcount: A:0.09, C:0.11, G:0.06, T:0.73
Consensus pattern (25 bp):
TCATTTTTTTTATCTTTTTGGTTCT
Found at i:168698 original size:19 final size:19
Alignment explanation
Indices: 168629--168713 Score: 57
Period size: 19 Copynumber: 4.4 Consensus size: 19
168619 GTTTTTTATC
*
168629 TTTTTGTTTTCATTTTTTTCAC
1 TTTTTGTTTTC-TTTTTTT--T
* *
168651 TTTTTG-GTTCTTATTTATT
1 TTTTTGTTTTCTT-TTTTTT
*
168670 TTTTT-CTTTCTTTTTTTT
1 TTTTTGTTTTCTTTTTTTT
**
168688 TTTTTGTTTTCAGTTTTTT
1 TTTTTGTTTTCTTTTTTTT
*
168707 TTCTTGT
1 TTTTTGT
168714 ATACTTTCAT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
18 10 0.20
19 26 0.51
20 2 0.04
21 7 0.14
22 6 0.12
ACGTcount: A:0.06, C:0.09, G:0.07, T:0.78
Consensus pattern (19 bp):
TTTTTGTTTTCTTTTTTTT
Found at i:170518 original size:17 final size:17
Alignment explanation
Indices: 170477--170509 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
170467 TTTAAACTAC
*
170477 AAAATTATATCAACAAA
1 AAAAATATATCAACAAA
170494 AAAAATATATCAACAA
1 AAAAATATATCAACAA
170510 CTACAATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATATATCAACAAA
Found at i:172562 original size:14 final size:14
Alignment explanation
Indices: 172543--172588 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
172533 ATAAATAAAC
172543 AATAAAAATAAGAA
1 AATAAAAATAAGAA
172557 AAT--AAA-AAGCAA
1 AATAAAAATAAG-AA
172569 AATAAAAATAAGAA
1 AATAAAAATAAGAA
172583 AATAAA
1 AATAAA
172589 GCACCAAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 3 0.11
12 8 0.29
14 14 0.50
15 3 0.11
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (14 bp):
AATAAAAATAAGAA
Found at i:178298 original size:11 final size:11
Alignment explanation
Indices: 178282--178324 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
178272 ACATTTTAAA
178282 TTATATTATTT
1 TTATATTATTT
*
178293 TTATATTTTTAT
1 TTATATTATT-T
178305 TTATATTATTT
1 TTATATTATTT
178316 TTATATTAT
1 TTATATTAT
178325 ATTAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATATTATTT
Done.