Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, 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: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 50 of 402
Found at i:9596006 original size:55 final size:55
Alignment explanation
Indices: 9595940--9596043 Score: 165
Period size: 55 Copynumber: 1.9 Consensus size: 55
9595930 AAAACCATTT
* *
9595940 TTTATTAAAA-TTGTTGAAACCTTTTGATTTTTTAACATTTATATTTTGACCGTTA
1 TTTATTAAAATTTATTGAAACCTTTT-ATTTTCTAACATTTATATTTTGACCGTTA
*
9595995 TTTATTAAAATTTATTGAAGCCTTTTATTTTCTAACATTTATATTTTGA
1 TTTATTAAAATTTATTGAAACCTTTTATTTTCTAACATTTATATTTTGA
9596044 TTTTGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
55 32 0.71
56 13 0.29
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.54
Consensus pattern (55 bp):
TTTATTAAAATTTATTGAAACCTTTTATTTTCTAACATTTATATTTTGACCGTTA
Found at i:9597623 original size:22 final size:21
Alignment explanation
Indices: 9597583--9597644 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
9597573 ATTTTAATCT
*
9597583 TTTTAATTTTTTCAATGTTCAA
1 TTTTAATTTTTT-ATTGTTCAA
*
9597605 TTTTAAATTTTTTATTGTTTTAA
1 TTTT-AATTTTTTATTG-TTCAA
*
9597628 -TTTATTTTTTTATTGTT
1 TTTTAATTTTTTATTGTT
9597645 ATAATCTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 11 0.31
22 10 0.29
23 12 0.34
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTAATTTTTTATTGTTCAA
Found at i:9598133 original size:17 final size:17
Alignment explanation
Indices: 9598106--9598147 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
9598096 TTCCTATACA
9598106 ATTTA-TTTTTAATCTT
1 ATTTACTTTTTAATCTT
*
9598122 -TTTAACTTTTTAGTCTT
1 ATTT-ACTTTTTAATCTT
9598139 ATTTACTTT
1 ATTTACTTT
9598148 CTGTCATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 3 0.14
16 1 0.05
17 15 0.68
18 3 0.14
ACGTcount: A:0.21, C:0.10, G:0.02, T:0.67
Consensus pattern (17 bp):
ATTTACTTTTTAATCTT
Found at i:9598598 original size:17 final size:18
Alignment explanation
Indices: 9598568--9598601 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9598558 TTTAACATTA
*
9598568 AAAAAAATACAAAGAAAT
1 AAAAAAAGACAAAGAAAT
9598586 AAAAAAAGA-AAAGAAA
1 AAAAAAAGACAAAGAAA
9598602 AATGATCGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.82, C:0.03, G:0.09, T:0.06
Consensus pattern (18 bp):
AAAAAAAGACAAAGAAAT
Found at i:9598691 original size:57 final size:57
Alignment explanation
Indices: 9598621--9598953 Score: 384
Period size: 57 Copynumber: 5.7 Consensus size: 57
9598611 TTTTGTACAG
* * * *
9598621 GGAAAATTAATACTTTCAACTTCTCCCCAAAATATTTTTTAGAAACTTTAATTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTAGAAACTTTAATTTCAA
* * * * *
9598678 GGAAAATTGATACTTT-AACTTTTCCTCAAAAAAACTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAATA-TTTTTTAGAAACTTTAATTTCAA
* *
9598736 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAACTTTAATTTCAA
1 GGAAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTAGAAACTTTAATTTCAA
* * **
9598794 GGAAAATTGATACTTTCAACTTTTCCTC-AGAATATTTTTTAGAAACCTTAATTTTGA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTAGAAACTTTAATTTCAA
* *
9598851 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTAAAAAAAC-TTATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAATA--TTTTTT--AGAAACTTTAATTTCAA
* *
9598912 AGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTA
1 GGAAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTA
9598954 AATCTTTTTA
Statistics
Matches: 237, Mismatches: 28, Indels: 22
0.83 0.10 0.08
Matches are distributed among these distances:
56 8 0.03
57 79 0.33
58 79 0.33
59 16 0.07
60 11 0.05
61 34 0.14
62 10 0.04
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTAGAAACTTTAATTTCAA
Found at i:9598742 original size:58 final size:58
Alignment explanation
Indices: 9598621--9598953 Score: 422
Period size: 58 Copynumber: 5.7 Consensus size: 58
9598611 TTTTGTACAG
* * * *
9598621 GGAAAATTAATACTTTCAACTTCTCC-CCAAAATATTTTTTAGAAACTTTAATTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAACTTTAATTTCAA
* * * * *
9598678 GGAAAATTGATACTTT-AACTTTTCCTCAAAAAAACTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTAGAAACTTTAATTTCAA
* *
9598736 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAACTTTAATTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAACTTTAATTTCAA
* * **
9598794 GGAAAATTGATACTTTCAACTTTTCCTC-AGAATATTTTTTAGAAACCTTAATTTTGA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAACTTTAATTTCAA
* *
9598851 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTAAAAAAAC-TTATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTT--AGAAACTTTAATTTCAA
* *
9598912 AGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTA
9598954 AATCTTTTTA
Statistics
Matches: 240, Mismatches: 28, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
56 8 0.03
57 74 0.31
58 85 0.35
59 22 0.09
60 6 0.03
61 40 0.17
62 5 0.02
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAACTTTAATTTCAA
Found at i:9598775 original size:115 final size:116
Alignment explanation
Indices: 9598621--9598953 Score: 431
Period size: 115 Copynumber: 2.9 Consensus size: 116
9598611 TTTTGTACAG
* * * * *
9598621 GGAAAATTAATACTTTCAAC-TTCTCCCCAAAATATTTTTTAGAAACTTTAATTTCGAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAACTTTAATTTCAAGGAAAAT
* * * *
9598685 TGATACTTT-AACTTTTCCTCAAAAAAACTTTTTTTGAAAATTTATTTTTAA
66 TGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTAGAAAACTTAATTTTAA
*
9598736 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAACTTTAATTTCAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAACTTTAATTTCAAGGAAAAT
* * *
9598801 TGATACTTTCAACTTTTCCTC-AGAATATTTTTTAGAAACCTTAATTTTGA
66 TGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTAATTTTAA
* * * *
9598851 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTAAAAAAAC-TTATTTTCAAAGA
1 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATA--TTTTTT--AGAAACTTTAATTTCAAGGA
*
9598915 AAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTA
62 AAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTA
9598954 AATCTTTTTA
Statistics
Matches: 191, Mismatches: 20, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
115 71 0.37
116 52 0.27
117 17 0.09
118 35 0.18
119 16 0.08
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (116 bp):
GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAACTTTAATTTCAAGGAAAAT
TGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTAATTTTAA
Found at i:9601791 original size:109 final size:109
Alignment explanation
Indices: 9601650--9601937 Score: 409
Period size: 109 Copynumber: 2.6 Consensus size: 109
9601640 ACTGGATTTT
* * *
9601650 TTTTTATTTTTTTTGCTTTTTATTATTTGATCAAAGCTCCTCTAAGTAGAGGCTCAACGACTTTG
1 TTTTTGTTTTTTTT--TTTTTAAT-TTTGATCAAAGCTCCTCTAAGAAGAGGCTCAACGACTTTG
* *
9601715 AGAAACATAAACAAAGCTCCTCTAAATAGAGGTAAATTTTTTTGTTG
63 AGAAACATAAACAAAGCTCCTATAAACAGAGGTAAATTTTTTTGTTG
* * *
9601762 TTTTTGTTTTTTTTTTTTTAATTTTGATCAAAGCACCTCTAAGAAAAGGCTCAATGACTTTGAGA
1 TTTTTGTTTTTTTTTTTTTAATTTTGATCAAAGCTCCTCTAAGAAGAGGCTCAACGACTTTGAGA
9601827 AACATAAACAAAGCTCCTATAAACAGAGGTAAATTTTTTTGTTG
66 AACATAAACAAAGCTCCTATAAACAGAGGTAAATTTTTTTGTTG
* * **
9601871 -TTTTGCTTTCTTTTTTAAAATTTTGATCAAAGCTCCTCTAA-ACAGGAGGCTCAACGACTTTGA
1 TTTTTGTTTTTTTTTTTTTAATTTTGATCAAAGCTCCTCTAAGA-A-GAGGCTCAACGACTTTGA
9601934 GAAA
64 GAAA
9601938 TAAATGGCTC
Statistics
Matches: 159, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
107 1 0.01
108 37 0.23
109 101 0.64
110 7 0.04
112 13 0.08
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (109 bp):
TTTTTGTTTTTTTTTTTTTAATTTTGATCAAAGCTCCTCTAAGAAGAGGCTCAACGACTTTGAGA
AACATAAACAAAGCTCCTATAAACAGAGGTAAATTTTTTTGTTG
Found at i:9602168 original size:41 final size:41
Alignment explanation
Indices: 9601902--9602197 Score: 276
Period size: 41 Copynumber: 7.1 Consensus size: 41
9601892 TTTGATCAAA
* * * *
9601902 GCTCCTCTAAACAGGAGGCTCAACGACTTTGAGAAATAAATG
1 GCTCCTCTAATCA-GAGGCTCAACAACTTTGAAAAATAAATT
* * *
9601944 GCTCCTCTAATCAGAGGCTCAACAGCTTTTAAAAATAAATA
1 GCTCCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAATT
* * * *
9601985 GCTCCTTTAATCAAAGGCTCAACGACTTTGAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAATT
9602026 GCTCCTCTAATCAGAGGCTCAACAACTTTGAAAATAGCTAAA--
1 GCTCCTCTAATCAGAGGCTCAACAACTTTGAAAA-A--TAAATT
* * *
9602068 GCT-CTCTAATCAGAGGCTCAACGACTTTTGGAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCAACAAC-TTTGAAAAATAAATT
* * * * *
9602109 ACTTCTCTAAAT-AGAGGCACCACAACTTTGAAAAGTAAATT
1 GCTCCTCT-AATCAGAGGCTCAACAACTTTGAAAAATAAATT
* * * ** *
9602150 ACTCCTCTAAACAGAGGCACCTCAACTTTTAAAAAATAAATT
1 GCTCCTCTAATCAGAGGCTCAACAAC-TTTGAAAAATAAATT
9602192 GCTCCT
1 GCTCCT
9602198 TGACAATCAT
Statistics
Matches: 215, Mismatches: 29, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
39 4 0.02
40 2 0.01
41 146 0.68
42 56 0.26
43 3 0.01
44 4 0.02
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.26
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAATT
Found at i:9603884 original size:7 final size:8
Alignment explanation
Indices: 9603865--9603944 Score: 56
Period size: 9 Copynumber: 9.1 Consensus size: 8
9603855 TTGAATCTTT
9603865 TTTTTTCA
1 TTTTTTCA
9603873 TTTTTTCA
1 TTTTTTCA
9603881 TTTTCTT-A
1 TTTT-TTCA
9603889 TTTTTTTCTTA
1 -TTTTTTC--A
*
9603900 TTTTTTCCT
1 TTTTTT-CA
9603909 TTTTTTCCCCA
1 TTTTTT---CA
9603920 TTTTTCTCA
1 TTTTT-TCA
9603929 TTTTTTC-
1 TTTTTTCA
9603936 TTTTTTCA
1 TTTTTTCA
9603944 T
1 T
9603945 CATCTTCTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
7 7 0.12
8 18 0.30
9 19 0.32
10 6 0.10
11 9 0.15
12 1 0.02
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:9603968 original size:21 final size:18
Alignment explanation
Indices: 9603863--9603971 Score: 71
Period size: 21 Copynumber: 5.8 Consensus size: 18
9603853 ATTTGAATCT
*
9603863 TTTTTTTTCA-TTTTTTC
1 TTTTTTCTCATTTTTTTC
* *
9603880 -ATTTTCTTATTTTTTTC
1 TTTTTTCTCATTTTTTTC
* *
9603897 TTATTTTTTCCTTTTTTTCCCC
1 TT-TTTTCTCATTTTTTT---C
*
9603919 ATTTTTCTCA-TTTTTTC
1 TTTTTTCTCATTTTTTTC
9603936 TTTTTTCATCATCTTCTTTTC
1 TTTTTTC-TCAT-TT-TTTTC
9603957 TTTTTTTCTCATTTT
1 -TTTTTTCTCATTTT
9603972 CATCCATTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
16 6 0.09
17 14 0.20
18 3 0.04
19 13 0.19
20 10 0.14
21 15 0.21
22 9 0.13
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTCTCATTTTTTTC
Found at i:9608902 original size:60 final size:58
Alignment explanation
Indices: 9608753--9609383 Score: 750
Period size: 60 Copynumber: 10.7 Consensus size: 58
9608743 TTTTGTACAG
* * * ** *
9608753 GGAAAATTGATACTTTCAACTTCTCC-CCAAAATATTTTTTAGAAATTTTAATTTT-GA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTT-ATTTTCAA
* * * *
9608810 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTTGAAAACTTATTTTCAA
* * *
9608869 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTTTGAAAACTTATTTTCAA
* *
9608929 GAAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTGGAAAGCTTATTTTCAA
1 GGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTT-GAAAACTTATTTTCAA
* * * * * *
9608988 AGAAAATTGATACTTTCAACTTTTTCTC-AAAATATTTTTTAGAAACCTTAATTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTCAA
* * * *
9609045 GGAAAATTGATACTTTCAACTTTTCCTCAAAGATTTTTTTTTTTGAAAGCTTATTTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAA-A-ATATTTTTTTGAAAACTTATTTTCAA
* * * *
9609105 GGAAAATTGATACTTTTAACTTTTCCTCAAAAATAGTTTTTAGAAAAAATTATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTG-AAAACTTATTTTCAA
* * *
9609164 GGAAAATTGATACTTTCCACTTTTCCTCAAAAATATTTTTTAGAAAAAATTATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTG-AAAACTTATTTTCAA
*
9609223 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTGAAAAAAACTTCTTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTG---AAAACTTATTTTCAA
* * * *
9609283 AGAAAATTGATACTTTAAACTTTTTCTCAAAAATATTTTTTTAAAAAAACTTATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT--GAAAACTTATTTTCAA
*
9609343 AGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
9609384 AAATCTTTTT
Statistics
Matches: 509, Mismatches: 49, Indels: 29
0.87 0.08 0.05
Matches are distributed among these distances:
57 63 0.12
58 50 0.10
59 184 0.36
60 200 0.39
61 12 0.02
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTCAA
Found at i:9608942 original size:119 final size:116
Alignment explanation
Indices: 9608753--9609384 Score: 770
Period size: 119 Copynumber: 5.4 Consensus size: 116
9608743 TTTTGTACAG
* * ** *
9608753 GGAAAATTGATACTTTCAACTTCTCC-CCAAAATATTTTTTAGAAATTTTAATTTT-GAGAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTT-ATTTTCAAGAAAAA
* * *
9608816 TTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTTGAAAATTTATTTTTAA
65 TTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTTGAAAACTTATTTTCAA
* * * *
9608869 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTTGAAAATTTATTTTTAAGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTTAGAAAACTTATTTTCAAGAAAA
*
9608934 ATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTGGAAAGCTTATTTTCAA
64 ATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTT-GAAAACTTATTTTCAA
* * * * * *
9608988 AGAAAATTGATACTTTCAACTTTTTCTC-AAAATATTTTTTAGAAACCTTAATTTCGAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATTTTCAAGAAAAAT
* * * *
9609052 TGATACTTTCAACTTTTCCTCAAAGATTTTTTTTTTTGAAAGCTTATTTTCGA
66 TGATACTTTCAACTTTTCCTCAAA-A-ATATTTTTTTGAAAACTTATTTTCAA
* * * *
9609105 GGAAAATTGATACTTTTAACTTTTCCTCAAAAATAGTTTTTAGAAAAAATTATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAG-AAAACTTATTTTCAAGAAAAA
* * *
9609170 TTGATACTTTCCACTTTTCCTCAAAAATATTTTTTAGAAAAAATTATTTTCAA
65 TTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTG-AAAACTTATTTTCAA
* *
9609223 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAAAAACTTCTTTTCAA-AGAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT--AGAAAACTTATTTTCAAGA-AA
* * *
9609287 AATTGATACTTTAAACTTTTTCTCAAAAATATTTTTTTAAAAAAACTTATTTTCAA
63 AATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT--GAAAACTTATTTTCAA
*
9609343 AGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTA
9609385 AATCTTTTTA
Statistics
Matches: 448, Mismatches: 51, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
115 6 0.01
116 65 0.15
117 55 0.12
118 91 0.20
119 170 0.38
120 61 0.14
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (116 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATTTTCAAGAAAAAT
TGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTCAA
Found at i:9609283 original size:30 final size:28
Alignment explanation
Indices: 9609240--9609343 Score: 66
Period size: 30 Copynumber: 3.5 Consensus size: 28
9609230 TGATACTTTC
*
9609240 AACTTTTCCTCAAAAATATTTTTTGAAAAA
1 AACTTTT-TTCAAAAATATTTTTT-AAAAA
* ** ***
9609270 AACTTCTTTTCAAAGAA-AATTGATACTTTA
1 AACTT-TTTTCAAA-AATATTTTTTA-AAAA
9609300 AACTTTTTCTCAAAAATATTTTTTTAAAAA
1 AACTTTTT-TCAAAAATA-TTTTTTAAAAA
9609330 AACTTATTTTCAAA
1 AACTT-TTTTCAAA
9609344 GAAAATTGAT
Statistics
Matches: 54, Mismatches: 13, Indels: 14
0.67 0.16 0.17
Matches are distributed among these distances:
29 6 0.11
30 37 0.69
31 11 0.20
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (28 bp):
AACTTTTTTCAAAAATATTTTTTAAAAA
Found at i:9609386 original size:59 final size:59
Alignment explanation
Indices: 9608754--9609385 Score: 710
Period size: 59 Copynumber: 10.7 Consensus size: 59
9608744 TTTGTACAGG
* * ** * *
9608754 GAAAATTGATACTTTCAACTTCTCC-CCAAAATATTTTTT-AGAAATTTTAATTTTGAGA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAGAAAACTT-ATTTTCAAA
* * * * *
9608812 -AAAATTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTT-TGAAAATTTATTTTTAAG
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTAAGAAAACTTATTTTCAAA
* * * *
9608870 GAAAATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTT-TGAAAATTTATTTT-TAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTTAAGAAAACTTATTTTCAAA
** *
9608929 GAAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTGGAAAGCTTATTTTCAAA
1 G-AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTAAGAAAACTTATTTTCAAA
* * * * *
9608989 GAAAATTGATACTTTCAACTTTTTCTC-AAAATATTTTTT-AGAAACCTTAATTTCGAG
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAGAAAACTTATTTTCAAA
* * ** * * *
9609046 GAAAATTGATACTTTCAACTTTTCCTCAAAGATTTTTTTTTTTGAAAGCTTATTTTCGAG
1 GAAAATTGATACTTTCAACTTTTCCTCAAA-AATATTTTTTAAGAAAACTTATTTTCAAA
* * * *
9609106 GAAAATTGATACTTTTAACTTTTCCTCAAAAATAGTTTTT-AGAAAAAATTATTTTCAAG
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAG-AAAACTTATTTTCAAA
* * *
9609165 GAAAATTGATACTTTCCACTTTTCCTCAAAAATATTTTTT-AGAAAAAATTATTTTCAAG
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAG-AAAACTTATTTTCAAA
* *
9609224 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAAAAACTTCTTTTCAAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-AAGAAAACTTATTTTCAAA
* * *
9609284 GAAAATTGATACTTTAAACTTTTTCTCAAAAATATTTTTTTAAAAAAACTTATTTTCAAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTAAGAAAACTTATTTTCAAA
9609344 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAA
9609386 ATCTTTTTAT
Statistics
Matches: 510, Mismatches: 48, Indels: 31
0.87 0.08 0.05
Matches are distributed among these distances:
57 62 0.12
58 38 0.07
59 209 0.41
60 188 0.37
61 13 0.03
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.43
Consensus pattern (59 bp):
GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAGAAAACTTATTTTCAAA
Found at i:9611911 original size:13 final size:13
Alignment explanation
Indices: 9611890--9611919 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9611880 AAAAAATGAT
9611890 AAATATGAAATAA
1 AAATATGAAATAA
*
9611903 AAATCTGAAATAA
1 AAATATGAAATAA
9611916 AAAT
1 AAAT
9611920 GAAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (13 bp):
AAATATGAAATAA
Found at i:9611922 original size:11 final size:11
Alignment explanation
Indices: 9611888--9611929 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
9611878 TTAAAAAATG
*
9611888 ATAAATATGAA
1 ATAAAAATGAA
9611899 ATAAAAATCTGAA
1 ATAAAAA--TGAA
9611912 ATAAAAATGAA
1 ATAAAAATGAA
9611923 A-AAAAAT
1 ATAAAAAT
9611930 TTTTACAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 6 0.21
11 11 0.39
13 11 0.39
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.21
Consensus pattern (11 bp):
ATAAAAATGAA
Found at i:9620221 original size:74 final size:75
Alignment explanation
Indices: 9620086--9620255 Score: 254
Period size: 74 Copynumber: 2.3 Consensus size: 75
9620076 CACCTAAGGT
* * *
9620086 AAGGGATCGATCCCCTCTT-AAAGGGATCAATCGGTTGCTCAGACAGAATGTTTCCCAAGTTCGA
1 AAGGGATCGATCCCCTCTTAAAAGAGATCAATCGATTGCTCAGACAGAATGTTTCCCAAGTTCAA
*
9620150 AAACCCAGAA
66 AAACCAAGAA
* * *
9620160 AAGGGATCGATCACTTCTTAAAAGAGATCAATCGATTGCTCAGACAGAATG-TTCCCCAGTTCAA
1 AAGGGATCGATCCCCTCTTAAAAGAGATCAATCGATTGCTCAGACAGAATGTTTCCCAAGTTCAA
9620224 AAACCAAGAA
66 AAACCAAGAA
*
9620234 AATGGATCGATCCCCTCTTAAA
1 AAGGGATCGATCCCCTCTTAAA
9620256 GGAATCGATC
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 56 0.66
75 29 0.34
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (75 bp):
AAGGGATCGATCCCCTCTTAAAAGAGATCAATCGATTGCTCAGACAGAATGTTTCCCAAGTTCAA
AAACCAAGAA
Found at i:9621463 original size:27 final size:29
Alignment explanation
Indices: 9621433--9621486 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
9621423 GAATAATGTG
*
9621433 GATATACATGAAT-AA-ACGACTAACATA
1 GATATACACGAATAAATACGACTAACATA
*
9621460 GATATATACGAATAAATACGACTAACA
1 GATATACACGAATAAATACGACTAACA
9621487 CAAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 2 0.09
29 10 0.43
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (29 bp):
GATATACACGAATAAATACGACTAACATA
Found at i:9621648 original size:24 final size:23
Alignment explanation
Indices: 9621619--9621690 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 23
9621609 TTTAATACTC
* *
9621619 ATTTAATATGTAATTAATATATAT
1 ATTTAAAATTTAATT-ATATATAT
9621643 ATTTAAAATTTAATT-TATATAT
1 ATTTAAAATTTAATTATATATAT
9621665 ATTTAAAATTTAATTTATATTATAT
1 ATTTAAAATTTAA-TTATA-TATAT
9621690 A
1 A
9621691 ACTATATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
22 20 0.47
23 2 0.05
24 15 0.35
25 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
ATTTAAAATTTAATTATATATAT
Found at i:9621664 original size:22 final size:22
Alignment explanation
Indices: 9621636--9621689 Score: 99
Period size: 22 Copynumber: 2.4 Consensus size: 22
9621626 ATGTAATTAA
9621636 TATATATATTTAAAATTTAATT
1 TATATATATTTAAAATTTAATT
9621658 TATATATATTTAAAATTTAATT
1 TATATATATTTAAAATTTAATT
9621680 TATATTATAT
1 TATA-TATAT
9621690 AACTATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATATATTTAAAATTTAATT
Found at i:9624835 original size:14 final size:14
Alignment explanation
Indices: 9624815--9624849 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
9624805 TTTTATTTCT
*
9624815 AAAATATAAAGATA
1 AAAATATAAAAATA
*
9624829 CAAATATAAAAATA
1 AAAATATAAAAATA
9624843 AAAATAT
1 AAAATAT
9624850 TTCTACTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAATATAAAAATA
Found at i:9626275 original size:24 final size:24
Alignment explanation
Indices: 9626248--9626316 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
9626238 ATTTATTATT
9626248 ATTTGATTTCATATATTAAAAATA
1 ATTTGATTTCATATATTAAAAATA
** *
9626272 ATTT-A----ATAT-TT-ATTATT
1 ATTTGATTTCATATATTAAAAATA
9626289 ATTTGATTTCATATATTAAAAATA
1 ATTTGATTTCATATATTAAAAATA
9626313 ATTT
1 ATTT
9626317 ACTCTCCACT
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
17 7 0.22
18 3 0.09
19 4 0.12
22 4 0.12
23 3 0.09
24 11 0.34
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (24 bp):
ATTTGATTTCATATATTAAAAATA
Found at i:9626281 original size:41 final size:41
Alignment explanation
Indices: 9626235--9626317 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
9626225 TAAAGTACAA
9626235 AATATTTATTATTATTTGATTTCATATATTAAAAATAATTT
1 AATATTTATTATTATTTGATTTCATATATTAAAAATAATTT
9626276 AATATTTATTATTATTTGATTTCATATATTAAAAATAATTT
1 AATATTTATTATTATTTGATTTCATATATTAAAAATAATTT
9626317 A
1 A
9626318 CTCTCCACTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (41 bp):
AATATTTATTATTATTTGATTTCATATATTAAAAATAATTT
Found at i:9626682 original size:14 final size:14
Alignment explanation
Indices: 9626649--9626696 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
9626639 ATTTTTATAT
* *
9626649 TTTAATAATTAATGA
1 TTTAAAAATAAAT-A
9626664 TTTAAAAATAAATA
1 TTTAAAAATAAATA
9626678 TTT-AAAATAAATA
1 TTTAAAAATAAATA
*
9626691 TATAAA
1 TTTAAA
9626697 TTAACTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.41
14 6 0.21
15 11 0.38
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
TTTAAAAATAAATA
Found at i:9626801 original size:42 final size:42
Alignment explanation
Indices: 9626740--9626821 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
9626730 ATTATAATGA
9626740 TAGGATAAACAAAAATCTATAAAATATAGTCATATTAATTGT
1 TAGGATAAACAAAAATCTATAAAATATAGTCATATTAATTGT
* *
9626782 TAGGATAAAGAAAATTCTATAAAATATAGTCATATTAATT
1 TAGGATAAACAAAAATCTATAAAATATAGTCATATTAATT
9626822 TCAATCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (42 bp):
TAGGATAAACAAAAATCTATAAAATATAGTCATATTAATTGT
Found at i:9627221 original size:4 final size:4
Alignment explanation
Indices: 9627207--9627262 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
9627197 AAGGATTTGG
* *
9627207 TTTA ATTA TTTA TTTA TTTA -TTA TGTCA TTTA TTT- TGTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA T-TTA TTTA TTTA
*
9627255 TTTT TTTA
1 TTTA TTTA
9627263 GATTTTACCT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
3 4 0.10
4 34 0.81
5 4 0.10
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:9639090 original size:18 final size:17
Alignment explanation
Indices: 9639058--9639091 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9639048 ACTATGCTTG
9639058 AAAAGAAAAAAAATGAA
1 AAAAGAAAAAAAATGAA
*
9639075 AAAATAAAAAAGAATGA
1 AAAAGAAAAAA-AATGA
9639092 CTCAAGTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (17 bp):
AAAAGAAAAAAAATGAA
Found at i:9640185 original size:44 final size:44
Alignment explanation
Indices: 9640112--9640538 Score: 509
Period size: 44 Copynumber: 9.8 Consensus size: 44
9640102 CGATGAGCCT
* *
9640112 TTTATTTTTC-AAAGTTGTTGAGCCTCTGCTTAGATGAGCTTTA
1 TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * *
9640155 TTTATTTTTCAAATGTCATTGAGCCTCTGCTTAGAAGAGCTTTA
1 TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTA
* *
9640199 TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGAAGCTTTG
1 TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTA
* **
9640243 TTTATTTTTTAAAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTA
1 TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * *
9640287 TTTATTTTTCAAAAGTAGTTGAG-CTCTGCCTAAAGGAGCTTTA
1 TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTA
** *
9640330 TTTATTTTTCAAAAGTCGTTGAGCCTCTATTTAGAGGAACTTTA
1 TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * * *
9640374 TATATTTTTCAAAAGTCGTTAAGCCTTTGCTTAGAGGAGCTTTG
1 TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * * ** * *
9640418 TTTATTTTCCAAAAGTCATTGAACCTCTATTTAGAAGAGCTTTG
1 TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTA
** * *
9640462 TTTATTTTTCAAAAGTCGTTGAGCCTCTATTTAGAGGAGTTTTG
1 TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * * * *
9640506 TTTATTCTCCAAAAGTTG-TAAACCTCTGCTTAG
1 TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAG
9640539 GGGAATTTTG
Statistics
Matches: 328, Mismatches: 54, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
43 59 0.18
44 269 0.82
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.43
Consensus pattern (44 bp):
TTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTA
Found at i:9640407 original size:175 final size:175
Alignment explanation
Indices: 9640112--9640485 Score: 543
Period size: 175 Copynumber: 2.1 Consensus size: 175
9640102 CGATGAGCCT
* * * * *
9640112 TTTATTTTTC-AAAGTTGTTGAGCCTCTGCTTAGATGAGCTTTATTTATTTTTCAAATGTCATTG
1 TTTATTTTTCAAAAGTAGTTGAG-CTCTGCCTAAAGGAGCTTTATTTATTTTTCAAAAGTCATTG
* * * *
9640176 AGCCTCTGCTTAGAAGAGCTTTATTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAGAAGCTT
65 AGCCTCTACTTAGAAGAACTTTATATATTTTTCAAAAGTCGTTAAGCCTCTGCTTAGAGAAGCTT
** * * *
9640241 TGTTTATTTTTTAAAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTA
130 TGTTTATTTTCCAAAAGTCATTGAACCTCTATTTAGAAGAGCTTTA
*
9640287 TTTATTTTTCAAAAGTAGTTGAGCTCTGCCTAAAGGAGCTTTATTTATTTTTCAAAAGTCGTTGA
1 TTTATTTTTCAAAAGTAGTTGAGCTCTGCCTAAAGGAGCTTTATTTATTTTTCAAAAGTCATTGA
* * * *
9640352 GCCTCTATTTAGAGGAACTTTATATATTTTTCAAAAGTCGTTAAGCCTTTGCTTAGAGGAGCTTT
66 GCCTCTACTTAGAAGAACTTTATATATTTTTCAAAAGTCGTTAAGCCTCTGCTTAGAGAAGCTTT
*
9640417 GTTTATTTTCCAAAAGTCATTGAACCTCTATTTAGAAGAGCTTTG
131 GTTTATTTTCCAAAAGTCATTGAACCTCTATTTAGAAGAGCTTTA
*
9640462 TTTATTTTTCAAAAGTCGTTGAGC
1 TTTATTTTTCAAAAGTAGTTGAGC
9640486 CTCTATTTAG
Statistics
Matches: 177, Mismatches: 21, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
175 166 0.94
176 11 0.06
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (175 bp):
TTTATTTTTCAAAAGTAGTTGAGCTCTGCCTAAAGGAGCTTTATTTATTTTTCAAAAGTCATTGA
GCCTCTACTTAGAAGAACTTTATATATTTTTCAAAAGTCGTTAAGCCTCTGCTTAGAGAAGCTTT
GTTTATTTTCCAAAAGTCATTGAACCTCTATTTAGAAGAGCTTTA
Found at i:9640754 original size:4 final size:4
Alignment explanation
Indices: 9640745--9640790 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
9640735 GGTTTAATTA
*
9640745 TTAT TTAT TTAT TTA- TTAT GTCAT TTAT TT-T GTTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT -TTAT TTAT TTAT TT
9640791 TTCTAGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
3 4 0.11
4 28 0.78
5 4 0.11
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:9641634 original size:4 final size:4
Alignment explanation
Indices: 9641595--9641622 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
9641585 CATTTTTTTG
9641595 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
9641623 ACTTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:9644510 original size:19 final size:18
Alignment explanation
Indices: 9644479--9644540 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 18
9644469 GTTCTAAGAT
*
9644479 AAAACATTATTTTTATTG
1 AAAAAATTATTTTTATTG
9644497 AAAAAATTACTTTTT-TTAG
1 AAAAAATTA-TTTTTATT-G
9644516 ATAAAAATGTAGTTTTTATTG
1 A-AAAAAT-TA-TTTTTATTG
9644537 AAAA
1 AAAA
9644541 TATGAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 10 0.27
19 7 0.19
20 9 0.24
21 9 0.24
22 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (18 bp):
AAAAAATTATTTTTATTG
Found at i:9644531 original size:21 final size:20
Alignment explanation
Indices: 9644475--9644535 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 20
9644465 TGATGTTCTA
9644475 AGATAAAACATTATTTTTATT
1 AGATAAAA-ATTATTTTTATT
9644496 -GA-AAAAATTACTTTTT-TT
1 AGATAAAAATTA-TTTTTATT
9644514 AGATAAAAATGTAGTTTTTATT
1 AGATAAAAAT-TA-TTTTTATT
9644536 GAAAATATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
18 6 0.18
19 11 0.32
20 8 0.24
21 7 0.21
22 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (20 bp):
AGATAAAAATTATTTTTATT
Found at i:9644593 original size:37 final size:37
Alignment explanation
Indices: 9644552--9644632 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
9644542 ATGAAAAAAA
* *
9644552 ATAAAA-CATAAAATATTTTTATTTAATATTATTACAT
1 ATAAAATC-TAAAATATATTTACTTAATATTATTACAT
9644589 ATAAAATCTAAAATATATTTACTTAATATTATTACAT
1 ATAAAATCTAAAATATATTTACTTAATATTATTACAT
9644626 ATAAAAT
1 ATAAAAT
9644633 TTGTTTTCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 40 0.98
38 1 0.02
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (37 bp):
ATAAAATCTAAAATATATTTACTTAATATTATTACAT
Found at i:9644779 original size:18 final size:18
Alignment explanation
Indices: 9644748--9644810 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
9644738 CAAAAATAAC
*
9644748 TGTTATTCACATATTACG
1 TGTTATTCATATATTACG
*
9644766 TGTTACTCATATATTA-G
1 TGTTATTCATATATTACG
* * *
9644783 TATTA-TGA-ATATTACA
1 TGTTATTCATATATTACG
9644799 TGTTATTCATAT
1 TGTTATTCATAT
9644811 TTTATTAAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 6 0.17
16 6 0.17
17 7 0.20
18 16 0.46
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.48
Consensus pattern (18 bp):
TGTTATTCATATATTACG
Found at i:9645247 original size:19 final size:19
Alignment explanation
Indices: 9645209--9645249 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
9645199 AATTTTTTAT
*
9645209 ATATTTATTTTGTAAATAA
1 ATATTTATTTTATAAATAA
9645228 ATATTTA-TTTATAAATTAA
1 ATATTTATTTTATAAA-TAA
9645247 ATA
1 ATA
9645250 AAATTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATATTTATTTTATAAATAA
Found at i:9650751 original size:18 final size:19
Alignment explanation
Indices: 9650700--9650753 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
9650690 AAACCCTAAA
*
9650700 AAACCCTAAAACGAGACTCT
1 AAACCCT-AAACGAAACTCT
* **
9650720 AAAACCTATGCGAAACT-T
1 AAACCCTAAACGAAACTCT
9650738 AAACCCTAAACGAAAC
1 AAACCCTAAACGAAAC
9650754 CTTGAAGTCT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 14 0.52
19 7 0.26
20 6 0.22
ACGTcount: A:0.48, C:0.28, G:0.09, T:0.15
Consensus pattern (19 bp):
AAACCCTAAACGAAACTCT
Found at i:9652256 original size:19 final size:21
Alignment explanation
Indices: 9652232--9652295 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 21
9652222 TAATTATTGA
*
9652232 AAAATTCAATA-TCAAA-GTC
1 AAAATTCAAAACTCAAAGGTC
9652251 AAAATT-AAAACTCAAAGGTC
1 AAAATTCAAAACTCAAAGGTC
* * *
9652271 AAAAGTCAAAAATCATAAAGTC
1 AAAATTCAAAACTCA-AAGGTC
9652293 AAA
1 AAA
9652296 GGGGTATAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.08
19 11 0.30
20 8 0.22
21 7 0.19
22 8 0.22
ACGTcount: A:0.58, C:0.14, G:0.08, T:0.20
Consensus pattern (21 bp):
AAAATTCAAAACTCAAAGGTC
Found at i:9652278 original size:7 final size:7
Alignment explanation
Indices: 9652245--9652295 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
9652235 ATTCAATATC
9652245 AAAGTCA
1 AAAGTCA
*
9652252 AAA-TTA
1 AAAGTCA
*
9652258 AAACTCA
1 AAAGTCA
*
9652265 AAGGTCA
1 AAAGTCA
9652272 AAAGTCA
1 AAAGTCA
*
9652279 AAAATCA
1 AAAGTCA
9652286 TAAAGTCA
1 -AAAGTCA
9652294 AA
1 AA
9652296 GGGGTATAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
6 5 0.14
7 24 0.69
8 6 0.17
ACGTcount: A:0.59, C:0.14, G:0.10, T:0.18
Consensus pattern (7 bp):
AAAGTCA
Found at i:9660525 original size:27 final size:27
Alignment explanation
Indices: 9660471--9660525 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
9660461 AAAACTGAAA
* * *
9660471 GCAGAGAAGAACCGGCAGTAGAAGAAC
1 GCAGAAAAGAACAGGCAGAAGAAGAAC
9660498 GCAGAAAAGAAACAGGCAGAAGAA-AAC
1 GCAGAAAAG-AACAGGCAGAAGAAGAAC
9660525 G
1 G
9660526 TGAGGCAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.51, C:0.16, G:0.31, T:0.02
Consensus pattern (27 bp):
GCAGAAAAGAACAGGCAGAAGAAGAAC
Found at i:9660547 original size:1 final size:1
Alignment explanation
Indices: 9660541--9660567 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
9660531 CAGAAAACGC
9660541 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
9660568 GAGGGCTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9665338 original size:2 final size:2
Alignment explanation
Indices: 9665331--9665381 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
9665321 CTTAAACCTT
* * *
9665331 TA TA TA TA TA TA AA TA AA TA TA TA AA 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
9665373 TA TA TA TA T
1 TA TA TA TA T
9665382 TCTTCCGGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:9665707 original size:30 final size:31
Alignment explanation
Indices: 9665671--9665745 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 31
9665661 TATAATTTTG
* **
9665671 TAGGCTCCATAATTTTTTCTTTTGTC-AATA
1 TAGGCTCAATAATTTTTTCTTTTAACTAATA
*
9665701 TAGGCTCAATACTTTTTTCTTTTAACTAATA
1 TAGGCTCAATAATTTTTTCTTTTAACTAATA
9665732 TAGGCTCAATAATT
1 TAGGCTCAATAATT
9665746 AGATATTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 22 0.56
31 17 0.44
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (31 bp):
TAGGCTCAATAATTTTTTCTTTTAACTAATA
Found at i:9673602 original size:87 final size:88
Alignment explanation
Indices: 9673446--9673607 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 88
9673436 TTGTTGTATT
* *
9673446 GAGGGTAAAAATGAAATTTTAAAATATTGTAATTTTATTTTTTGATAAAGTACTAAACTGAGAGG
1 GAGGGTAAAAATGAAATTTTAAAATATTCTAATTTTATTTTTTGATAAAGTACTAAACTGAGAGA
9673511 TAAGAAGTAGCGGCAGTATTGGA
66 TAAGAAGTAGCGGCAGTATTGGA
* * *
9673534 GAGGGTAAAAATGAAA-TTTACAATATTCTAATTTTGTTTTTTGATAAAGTACTAAACTTAGAGA
1 GAGGGTAAAAATGAAATTTTAAAATATTCTAATTTTATTTTTTGATAAAGTACTAAACTGAGAGA
9673598 TAAGAAGTAG
66 TAAGAAGTAG
9673608 TAGCGATATT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
87 53 0.77
88 16 0.23
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (88 bp):
GAGGGTAAAAATGAAATTTTAAAATATTCTAATTTTATTTTTTGATAAAGTACTAAACTGAGAGA
TAAGAAGTAGCGGCAGTATTGGA
Found at i:9673631 original size:87 final size:88
Alignment explanation
Indices: 9673452--9673631 Score: 222
Period size: 87 Copynumber: 2.1 Consensus size: 88
9673442 TATTGAGGGT
* *
9673452 AAAAATGAAATTTTAAAATATTGTAATTTTATTTTTTGATAAAGTACTAAACTGAGAGGTAAGAA
1 AAAAATGAAATTTTAAAATATTCTAATTTTATTTTTTGATAAAGTACTAAACTGAGAGATAAGAA
* ****
9673517 GTAGCGGCAGTATTGGAGAGGGT
66 GTAGCAGCAGTATTGGAGAAAAA
* * *
9673540 AAAAATGAAA-TTTACAATATTCTAATTTTGTTTTTTGATAAAGTACTAAACTTAGAGATAAGAA
1 AAAAATGAAATTTTAAAATATTCTAATTTTATTTTTTGATAAAGTACTAAACTGAGAGATAAGAA
*
9673604 GTAGTAGC-GATATTGGTA-AAAAA
66 GTAGCAGCAG-TATTGG-AGAAAAA
9673627 AAAAA
1 AAAAA
9673632 GTGGCAGCGG
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
86 1 0.01
87 67 0.85
88 11 0.14
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (88 bp):
AAAAATGAAATTTTAAAATATTCTAATTTTATTTTTTGATAAAGTACTAAACTGAGAGATAAGAA
GTAGCAGCAGTATTGGAGAAAAA
Found at i:9684437 original size:41 final size:41
Alignment explanation
Indices: 9684392--9684469 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
9684382 TGTATGGTGA
9684392 CAGCTGAAGCTTTAACTGCACTGAGTATATGAAACAAGTTG
1 CAGCTGAAGCTTTAACTGCACTGAGTATATGAAACAAGTTG
9684433 CAGCTGAAGCTTTAACTGCACTGAGTATATGAAACAA
1 CAGCTGAAGCTTTAACTGCACTGAGTATATGAAACAA
9684470 AGAGAAAAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (41 bp):
CAGCTGAAGCTTTAACTGCACTGAGTATATGAAACAAGTTG
Found at i:9693220 original size:22 final size:24
Alignment explanation
Indices: 9693177--9693220 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
9693167 TGATAGTAAC
*
9693177 TTATCAACAAAGGGTGTCCAATTA
1 TTATCAACAAAAGGTGTCCAATTA
9693201 TTAT-AACAAAAGG-GTCCAAT
1 TTATCAACAAAAGGTGTCCAAT
9693221 ATAAGAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (24 bp):
TTATCAACAAAAGGTGTCCAATTA
Found at i:9693931 original size:13 final size:14
Alignment explanation
Indices: 9693913--9693944 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
9693903 AAAAATTTAC
9693913 AAAAAGTTAAAAA-
1 AAAAAGTTAAAAAG
9693926 AAAAAGTTAAAAAG
1 AAAAAGTTAAAAAG
9693940 AAAAA
1 AAAAA
9693945 AGAGCTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (14 bp):
AAAAAGTTAAAAAG
Found at i:9703825 original size:12 final size:12
Alignment explanation
Indices: 9703794--9703831 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
9703784 TATTTTTTTT
9703794 TAATTTTT-ATA
1 TAATTTTTAATA
*
9703805 TATTATTTTAATA
1 TAAT-TTTTAATA
9703818 TAATTTTTAATA
1 TAATTTTTAATA
9703830 TA
1 TA
9703832 TTTAAATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 3 0.13
12 14 0.61
13 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TAATTTTTAATA
Found at i:9703833 original size:22 final size:24
Alignment explanation
Indices: 9703794--9703839 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
9703784 TATTTTTTTT
*
9703794 TAATTTTTATATATTATTTTAATA
1 TAATTTTTATATATTATTTAAATA
9703818 TAATTTTTA-ATA-TATTTAAATA
1 TAATTTTTATATATTATTTAAATA
9703840 GATTTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 3 0.14
24 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TAATTTTTATATATTATTTAAATA
Found at i:9706494 original size:22 final size:21
Alignment explanation
Indices: 9706462--9706503 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
9706452 GTGGCTCTGG
9706462 TTTTTTGAAAGAA-GATGAAT
1 TTTTTTGAAAGAAGGATGAAT
9706482 TTTTTTAGAAAAGAAGGATGAA
1 TTTTTT-G-AAAGAAGGATGAA
9706504 ATAAAGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 6 0.32
23 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (21 bp):
TTTTTTGAAAGAAGGATGAAT
Found at i:9732461 original size:3 final size:3
Alignment explanation
Indices: 9732455--9732486 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
9732445 AATAATAATA
*
9732455 ATG ATG ATA ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
9732487 AACAACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:9743947 original size:25 final size:20
Alignment explanation
Indices: 9743901--9743938 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
9743891 GATTGCATCC
9743901 ATTGCATTCATGAATTACAT
1 ATTGCATTCATGAATTACAT
9743921 ATTGCATTCATGAATTAC
1 ATTGCATTCATGAATTAC
9743939 GTTTAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (20 bp):
ATTGCATTCATGAATTACAT
Found at i:9744494 original size:35 final size:35
Alignment explanation
Indices: 9744415--9744785 Score: 117
Period size: 35 Copynumber: 10.6 Consensus size: 35
9744405 TGATTAGCAA
* * * *
9744415 TCATCTTTATTTTCTAATTTGGA-TTTTGT-CTCAG
1 TCATCTTTATTTTCTAACTTGTAGCTTTATCCT-AG
** *
9744449 TCATAATTATTTTCTAACTTGTAGCTTTATCCTGG
1 TCATCTTTATTTTCTAACTTGTAGCTTTATCCTAG
* * *
9744484 TCATCTTTATTTTTTGATTTGT-GACTTTGA-CCTAG
1 TCATCTTTATTTTCTAACTTGTAG-CTTT-ATCCTAG
* * * * *
9744519 TCATCTATATTTTCTAACTCGT-GCCGTCATCTTAG
1 TCATCTTTATTTTCTAACTTGTAG-CTTTATCCTAG
* * * * * *
9744554 TCATCTTTA-TTTCTGATTTGCAACTTTA-ACTTG
1 TCATCTTTATTTTCTAACTTGTAGCTTTATCCTAG
** * * * *
9744587 ATCATCTTTATTCCCTGACTTG-CGATTTCATCTTAG
1 -TCATCTTTATTTTCTAACTTGTAGCTTT-ATCCTAG
* *
9744623 TCATCTTTATTTTTTAACTTGCT-GCTTTGAT-CTGG
1 TCATCTTTATTTTCTAACTTG-TAGCTTT-ATCCTAG
* ** * * *
9744658 TCA---TTCTTTT-TAACTTACAACTTCATCCCAG
1 TCATCTTTATTTTCTAACTTGTAGCTTTATCCTAG
* * *
9744689 TCATCTTTATTTT-TTACTTGTGATTGCAGCTTCATTCCGA-
1 TCATCTTTATTTTCTAAC-T-TG--T--AGCTTTA-TCCTAG
* *
9744729 TCATCTTTATTTTCTAACTTGTGGCTTCATCCTAG
1 TCATCTTTATTTTCTAACTTGTAGCTTTATCCTAG
* *
9744764 TCAACTTTATTTCCTAACTTGT
1 TCATCTTTATTTTCTAACTTGT
9744786 GATTTAATCC
Statistics
Matches: 243, Mismatches: 68, Indels: 51
0.67 0.19 0.14
Matches are distributed among these distances:
30 2 0.01
31 14 0.06
32 6 0.02
33 2 0.01
34 57 0.23
35 120 0.49
36 12 0.05
37 1 0.00
39 2 0.01
40 20 0.08
41 7 0.03
ACGTcount: A:0.19, C:0.20, G:0.11, T:0.49
Consensus pattern (35 bp):
TCATCTTTATTTTCTAACTTGTAGCTTTATCCTAG
Found at i:9745980 original size:17 final size:17
Alignment explanation
Indices: 9745949--9745986 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
9745939 CTTGGGAAAG
*
9745949 AAGAAAAAGAGAAAACA
1 AAGAAAAAGAGAAAAAA
9745966 AAGAAAAAGCA-AAAAAA
1 AAGAAAAAG-AGAAAAAA
9745983 AAGA
1 AAGA
9745987 GGAGTAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAGAAAAAA
Found at i:9749757 original size:8 final size:8
Alignment explanation
Indices: 9749744--9749795 Score: 59
Period size: 9 Copynumber: 6.1 Consensus size: 8
9749734 ATTTATTTTC
9749744 AAATAAAA
1 AAATAAAA
9749752 AAATAAAA
1 AAATAAAA
9749760 AATATAAAA
1 AA-ATAAAA
*
9749769 AGCATAAAA
1 A-AATAAAA
9749778 AACATAAAA
1 AA-ATAAAA
*
9749787 ATATAAAA
1 AAATAAAA
9749795 A
1 A
9749796 TTTTGGAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
8 17 0.45
9 21 0.55
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (8 bp):
AAATAAAA
Found at i:9749786 original size:26 final size:26
Alignment explanation
Indices: 9749746--9749795 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
9749736 TTATTTTCAA
9749746 ATAAAAAAATAAAAAATATAAAAAGC
1 ATAAAAAAATAAAAAATATAAAAAGC
9749772 ATAAAAAACAT-AAAAATATAAAAA
1 ATAAAAAA-ATAAAAAATATAAAAA
9749796 TTTTGGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (26 bp):
ATAAAAAAATAAAAAATATAAAAAGC
Found at i:9749796 original size:8 final size:8
Alignment explanation
Indices: 9749744--9749796 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
9749734 ATTTATTTTC
*
9749744 AAATAAAA
1 AAATATAA
9749752 AAATA-AA
1 AAATATAA
9749759 AAATATAA
1 AAATATAA
*
9749767 AAAGCATAAA
1 AAA-TAT-AA
*
9749777 AAACATAA
1 AAATATAA
9749785 AAATATAA
1 AAATATAA
9749793 AAAT
1 AAAT
9749797 TTTGGAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
7 7 0.17
8 23 0.57
9 5 0.12
10 5 0.12
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (8 bp):
AAATATAA
Found at i:9753119 original size:16 final size:17
Alignment explanation
Indices: 9753086--9753119 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9753076 GGTCTCAAAG
*
9753086 ATAGAAAAAAAAGTGAA
1 ATAGAAAAAAAAGAGAA
9753103 ATAGAAAAAAAA-AGAA
1 ATAGAAAAAAAAGAGAA
9753119 A
1 A
9753120 GAAAGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (17 bp):
ATAGAAAAAAAAGAGAA
Found at i:9753495 original size:8 final size:8
Alignment explanation
Indices: 9753467--9753606 Score: 71
Period size: 8 Copynumber: 17.8 Consensus size: 8
9753457 ATCATTAATG
9753467 AATG-AAA
1 AATGAAAA
9753474 AA-GAAAA
1 AATGAAAA
**
9753481 AGGGAAAA
1 AATGAAAA
9753489 AATGAAAA
1 AATGAAAA
9753497 AA-G--AA
1 AATGAAAA
*
9753502 AAGGAAAA
1 AATGAAAA
9753510 AATG--AA
1 AATGAAAA
*
9753516 AAGGAAAA
1 AATGAAAA
9753524 AATGAAAAAAA
1 AATG---AAAA
9753535 AATGAAAGA
1 AATGAAA-A
9753544 AA-GAAAA
1 AATGAAAA
**
9753551 AGAAAAAAA
1 A-ATGAAAA
*
9753560 AATGAAAG
1 AATGAAAA
*
9753568 AATGGAAA
1 AATGAAAA
*
9753576 AATGGAAA
1 AATGAAAA
9753584 AATGTAAAA
1 AATG-AAAA
* *
9753593 AAAGATAA
1 AATGAAAA
9753601 AATGAA
1 AATGAA
9753607 GACTTAAATT
Statistics
Matches: 102, Mismatches: 17, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
5 4 0.04
6 7 0.07
7 9 0.09
8 60 0.59
9 14 0.14
11 8 0.08
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.09
Consensus pattern (8 bp):
AATGAAAA
Found at i:9753495 original size:22 final size:21
Alignment explanation
Indices: 9753467--9753533 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 21
9753457 ATCATTAATG
9753467 AATGAAAAAGAAAAAGGGAAAA
1 AATGAAAAAGAAAAA-GGAAAA
9753489 AATGAAAAA-AGAAAAGGAAAA
1 AATGAAAAAGA-AAAAGGAAAA
* *
9753510 AATGAAAAGGAAAAAATGAAAA
1 AATGAAAAAG-AAAAAGGAAAA
9753532 AA
1 AA
9753534 AAATGAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
21 15 0.38
22 24 0.60
23 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (21 bp):
AATGAAAAAGAAAAAGGAAAA
Found at i:9753503 original size:14 final size:13
Alignment explanation
Indices: 9753486--9753585 Score: 57
Period size: 14 Copynumber: 7.4 Consensus size: 13
9753476 GAAAAAGGGA
*
9753486 AAAAATGAAAAAAG
1 AAAAA-GAAAAATG
*
9753500 AAAAGGAAAAAATG
1 AAAAAG-AAAAATG
*
9753514 AAAAGGAAAAAATG
1 AAAAAG-AAAAATG
9753528 -AAAA-AAAAATG
1 AAAAAGAAAAATG
9753539 AAAGAAAGAAAAA-G
1 -AA-AAAGAAAAATG
9753553 -AAAA-AAAAATG
1 AAAAAGAAAAATG
9753564 AAAGAATGGAAAAATGG
1 AAA-AA--GAAAAAT-G
9753581 AAAAA
1 AAAAA
9753586 TGTAAAAAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
10 5 0.07
11 11 0.15
12 3 0.04
13 7 0.10
14 28 0.39
15 5 0.07
16 8 0.11
17 4 0.06
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (13 bp):
AAAAAGAAAAATG
Found at i:9753509 original size:35 final size:34
Alignment explanation
Indices: 9753470--9753566 Score: 99
Period size: 35 Copynumber: 2.8 Consensus size: 34
9753460 ATTAATGAAT
9753470 GAAAAAGAAAAAGGGAAAAAATGAAAAAAGAAAAG
1 GAAAAAGAAAAAGGGAAAAAATGAAAAAA-AAAAG
*
9753505 GAAAAA-ATGAAAA-GGAAAAAATGAAAAAAAAATG
1 GAAAAAGA--AAAAGGGAAAAAATGAAAAAAAAAAG
* **
9753539 AAAGAAAGAAAAAGAAAAAAAAATGAAA
1 GAA-AAAGAAAAAG-GGAAAAAATGAAA
9753567 GAATGGAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
34 11 0.21
35 25 0.48
36 16 0.31
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (34 bp):
GAAAAAGAAAAAGGGAAAAAATGAAAAAAAAAAG
Found at i:9753535 original size:10 final size:11
Alignment explanation
Indices: 9753485--9753566 Score: 60
Period size: 11 Copynumber: 7.0 Consensus size: 11
9753475 AGAAAAAGGG
9753485 AAAAAATGAAA
1 AAAAAATGAAA
**
9753496 AAAGAAA--AGG
1 AAA-AAATGAAA
9753506 AAAAAATGAAAA
1 AAAAAATG-AAA
9753518 GGAAAAAATGAAA
1 --AAAAAATGAAA
9753531 AAAAAATGAAAGA
1 AAAAAATG-AA-A
*
9753544 AAGAAAAAGAAA
1 AA-AAAATGAAA
9753556 AAAAAATGAAA
1 AAAAAATGAAA
9753567 GAATGGAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
9 3 0.05
10 4 0.07
11 19 0.34
12 9 0.16
13 8 0.14
14 13 0.23
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:9753567 original size:25 final size:24
Alignment explanation
Indices: 9753485--9753569 Score: 95
Period size: 25 Copynumber: 3.6 Consensus size: 24
9753475 AGAAAAAGGG
* *
9753485 AAAAAATGAAA-AAAGAAAAG--G
1 AAAAAATGAAAGAAAAAAAAGAAA
* *
9753506 AAAAAATGAAAAGGAAAAAATGAAA
1 AAAAAATG-AAAGAAAAAAAAGAAA
9753531 AAAAAATGAAAGAAAGAAAAAGAAA
1 AAAAAATGAAAGAAA-AAAAAGAAA
9753556 AAAAAATGAAAGAA
1 AAAAAATGAAAGAA
9753570 TGGAAAAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.15
22 3 0.06
23 6 0.11
24 6 0.11
25 30 0.57
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (24 bp):
AAAAAATGAAAGAAAAAAAAGAAA
Found at i:9753576 original size:25 final size:26
Alignment explanation
Indices: 9753521--9753585 Score: 96
Period size: 25 Copynumber: 2.5 Consensus size: 26
9753511 ATGAAAAGGA
9753521 AAAAATGAAAAAAAAATGAAAGAAAG
1 AAAAATGAAAAAAAAATGAAAGAAAG
*
9753547 AAAAA-GAAAAAAAAATGAAAGAATGG
1 AAAAATGAAAAAAAAATGAAAGAA-AG
*
9753573 AAAAATGGAAAAA
1 AAAAATGAAAAAA
9753586 TGTAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 18 0.51
26 11 0.31
27 6 0.17
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (26 bp):
AAAAATGAAAAAAAAATGAAAGAAAG
Found at i:9753895 original size:16 final size:16
Alignment explanation
Indices: 9753874--9753904 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9753864 TATGCTTTGA
9753874 ATTTGTTCTTATACCC
1 ATTTGTTCTTATACCC
*
9753890 ATTTGTTTTTATACC
1 ATTTGTTCTTATACC
9753905 AGACTCATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (16 bp):
ATTTGTTCTTATACCC
Found at i:9755048 original size:43 final size:43
Alignment explanation
Indices: 9754983--9755108 Score: 168
Period size: 43 Copynumber: 2.9 Consensus size: 43
9754973 GTGAATCCTA
* * *
9754983 AAATGAGAATCTTTGAATTTCAAATAAGAATCTTTGA-ATTTC
1 AAATAAGAATCTTTGATTTTCAAATGAGAATCTTTGAGATTTC
*
9755025 AAATAAGAATCTTTGAGTTTTCAAATGAGAATCTTTGAGTTTTC
1 AAATAAGAATCTTTGA-TTTTCAAATGAGAATCTTTGAGATTTC
9755069 AAATGAA-AATCTTTGACTTTT-AAATGAGAATCTTTGAGAT
1 AAAT-AAGAATCTTTGA-TTTTCAAATGAGAATCTTTGAGAT
9755109 GTGAAACCCT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
42 15 0.20
43 37 0.49
44 21 0.28
45 2 0.03
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (43 bp):
AAATAAGAATCTTTGATTTTCAAATGAGAATCTTTGAGATTTC
Found at i:9755049 original size:22 final size:22
Alignment explanation
Indices: 9754983--9755106 Score: 157
Period size: 21 Copynumber: 5.8 Consensus size: 22
9754973 GTGAATCCTA
* *
9754983 AAATGAGAATCTTTGA-ATTTC
1 AAATAAGAATCTTTGAGTTTTC
*
9755004 AAATAAGAATCTTTGA-ATTTC
1 AAATAAGAATCTTTGAGTTTTC
9755025 AAATAAGAATCTTTGAGTTTTC
1 AAATAAGAATCTTTGAGTTTTC
*
9755047 AAATGAGAATCTTTGAGTTTTC
1 AAATAAGAATCTTTGAGTTTTC
*
9755069 AAATGAA-AATCTTTGACTTTT-
1 AAAT-AAGAATCTTTGAGTTTTC
*
9755090 AAATGAGAATCTTTGAG
1 AAATAAGAATCTTTGAG
9755107 ATGTGAAACC
Statistics
Matches: 93, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
20 1 0.01
21 49 0.53
22 42 0.45
23 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (22 bp):
AAATAAGAATCTTTGAGTTTTC
Found at i:9755316 original size:108 final size:111
Alignment explanation
Indices: 9755101--9755302 Score: 320
Period size: 108 Copynumber: 1.8 Consensus size: 111
9755091 AATGAGAATC
* *
9755101 TTTGAGATGTGAAACCCTAAAATTTATCATATATGAATCTTGGAACTCGAATGAGAAGCTTTGAA
1 TTTGAGATGTGAAACCCTAAAATTTATCAAATATGAACCTTGGAACTCGAATGAGAAGCTTTGAA
9755166 ATTTTGGATGTGAATCTCCAAAATTCAAACGAAAAAGCTTAAACTT
66 ATTTTGGATGTGAATCTCCAAAATTCAAACGAAAAAGCTTAAACTT
* * * *
9755212 TTTG-GATGTG-AA-CCTCAAATTTATCAAATGTGAACCTTTGAACTTGAATGAGAAGCTTTGAA
1 TTTGAGATGTGAAACCCTAAAATTTATCAAATATGAACCTTGGAACTCGAATGAGAAGCTTTGAA
*
9755274 TTTTTGGATGTGAATCTCCAAAATTCAAA
66 ATTTTGGATGTGAATCTCCAAAATTCAAA
9755303 TGAGAATCTT
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
108 72 0.86
109 2 0.02
110 6 0.07
111 4 0.05
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (111 bp):
TTTGAGATGTGAAACCCTAAAATTTATCAAATATGAACCTTGGAACTCGAATGAGAAGCTTTGAA
ATTTTGGATGTGAATCTCCAAAATTCAAACGAAAAAGCTTAAACTT
Found at i:9755656 original size:43 final size:42
Alignment explanation
Indices: 9755578--9755874 Score: 366
Period size: 43 Copynumber: 7.0 Consensus size: 42
9755568 ATGATTGTCA
*
9755578 AGGAGCATTTTATTTTTTCAAAGTTGTGGTACCTCTGTTTAG
1 AGGAGCATTTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAG
* *
9755620 AGGAGCATTTTATTTTTTCAAAAGTTGTGGTGCCTCTATTTAA
1 AGGAGCATTTTATTTTTTC-AAAGTTGTGGTGCCTCTGTTTAG
** * *
9755663 AGGAGCATTTTATTTTTTTCAAAGTTGTGGTGTGTTTATTTAG
1 AGGAGCATTTTA-TTTTTTCAAAGTTGTGGTGCCTCTGTTTAG
* * * *
9755706 AGGAGCAATTTATTTTTTGCAAAGTTATGGTGCCTTTATTTAG
1 AGGAGCATTTTATTTTTT-CAAAGTTGTGGTGCCTCTGTTTAG
*
9755749 AGGAGCA-TTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAA
1 AGGAGCATTTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAG
* *
9755790 AGGAGTAATTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCATTTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAG
* * ***
9755831 AGGAACA-TTTATTTTTCTCAAAGTCGTTAAGCCTCTGTTTAG
1 AGGAGCATTTTATTTTT-TCAAAGTTGTGGTGCCTCTGTTTAG
9755873 AG
1 AG
9755875 AAGCTTTGTT
Statistics
Matches: 226, Mismatches: 23, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
40 4 0.02
41 63 0.28
42 62 0.27
43 90 0.40
44 7 0.03
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (42 bp):
AGGAGCATTTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAG
Found at i:9757043 original size:9 final size:9
Alignment explanation
Indices: 9756993--9757043 Score: 52
Period size: 8 Copynumber: 5.8 Consensus size: 9
9756983 AAAAAAAGGG
*
9756993 AAAAAATAA
1 AAAAAATAT
*
9757002 AAAAAAGCAT
1 AAAAAA-TAT
*
9757012 AAAAAACAT
1 AAAAAATAT
9757021 -AAAAATAT
1 AAAAAATAT
9757029 -AAAAATAT
1 AAAAAATAT
9757037 AAAAAAT
1 AAAAAAT
9757044 TTGGAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 15 0.41
9 15 0.41
10 7 0.19
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (9 bp):
AAAAAATAT
Found at i:9759298 original size:168 final size:168
Alignment explanation
Indices: 9759016--9759347 Score: 456
Period size: 168 Copynumber: 2.0 Consensus size: 168
9759006 GGACTATCTA
* * * * ** * *
9759016 TTCTTTTGATATGTGGATAATCTTAGATAATTCCCACATGTTTTGTGTTTAATAAATATATATTC
1 TTCTTTTCACATGTGGATAATCTTAGACAATCCCCACATGTTTTGCATTTAATAAATACACATTC
* * *
9759081 TTAATTTAACAAAATATTTTTTGAAAAAATTAATTAGAATTATTCACTTATAAATAACTAATATT
66 TTAATTCAACAAAATATTTTTTGAAAAAATTAATTACAATTAATCACTTATAAATAACTAATATT
*
9759146 TTTACTTTCAATAAATAAATTACT-ATTGATAGTGTGAT
131 CTTACTTTCAATAAATAAATTA-TGATTGATAGTGTGAT
* *
9759184 TTCTTTTCACATGTGGATAATCTTAGGCAATCCCCACGTGTTTTGCATTTAATAAATACACACTT
1 TTCTTTTCACATGTGGATAATCTTAGACAATCCCCACATGTTTTGCATTTAATAAATACACA-TT
*
9759249 -TTAATTCAAC-AAATAATTTTTT-AAAATAATTAATTACAATTAATCACTTATAAATATCTAAT
65 CTTAATTCAACAAAAT-ATTTTTTGAAAA-AATTAATTACAATTAATCACTTATAAATAACTAAT
*
9759311 ATTCTTGCTTTCAATAAATAAATTATGATTGATAGTG
128 ATTCTTACTTTCAATAAATAAATTATGATTGATAGTG
9759348 ATTTGCATTT
Statistics
Matches: 144, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
167 9 0.06
168 133 0.92
169 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (168 bp):
TTCTTTTCACATGTGGATAATCTTAGACAATCCCCACATGTTTTGCATTTAATAAATACACATTC
TTAATTCAACAAAATATTTTTTGAAAAAATTAATTACAATTAATCACTTATAAATAACTAATATT
CTTACTTTCAATAAATAAATTATGATTGATAGTGTGAT
Found at i:9759445 original size:124 final size:124
Alignment explanation
Indices: 9759225--9759475 Score: 389
Period size: 124 Copynumber: 2.0 Consensus size: 124
9759215 CCCCACGTGT
*
9759225 TTTGCATTTAATAAATACACACTTTTAATTCAACAAATAATTTTTTAAAATAATTAATTACAATT
1 TTTGCATTTAATAAATACACACTTTTAATTCAAAAAATAATTTTTTAAAATAATTAATTACAATT
*
9759290 AATCACTTATAAATATCTAATATTCTTGCTTTCAATAAATAAATTAT-GATTGATAGTGA
66 AATCACTTATAAATAACTAATATTCTTGCTTTCAATAAATAAATT-TCGATTGATAGTGA
* * *
9759349 TTTGCATTTAATAAATATACAGTTTTAATTTAAAAAATAATTTTTTGAAAA-AATTAATTACAAT
1 TTTGCATTTAATAAATACACACTTTTAATTCAAAAAATAATTTTTT-AAAATAATTAATTACAAT
* * * *
9759413 TATTCATTTATAAATAACTAATATTCTTGCTTTCAATAAATAAATTTCTATTGATGGTGA
65 TAATCACTTATAAATAACTAATATTCTTGCTTTCAATAAATAAATTTCGATTGATAGTGA
9759473 TTT
1 TTT
9759476 AGTGTATTTA
Statistics
Matches: 116, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
123 1 0.01
124 111 0.96
125 4 0.03
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.44
Consensus pattern (124 bp):
TTTGCATTTAATAAATACACACTTTTAATTCAAAAAATAATTTTTTAAAATAATTAATTACAATT
AATCACTTATAAATAACTAATATTCTTGCTTTCAATAAATAAATTTCGATTGATAGTGA
Found at i:9759788 original size:22 final size:22
Alignment explanation
Indices: 9759760--9759812 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
9759750 TAAAGTACAT
9759760 TACACACACGCGCACAAACGCA
1 TACACACACGCGCACAAACGCA
* *
9759782 TACACACACGCGCATACACGCA
1 TACACACACGCGCACAAACGCA
9759804 TACACACAC
1 TACACACAC
9759813 ACATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.42, G:0.11, T:0.08
Consensus pattern (22 bp):
TACACACACGCGCACAAACGCA
Found at i:9761848 original size:15 final size:16
Alignment explanation
Indices: 9761807--9761848 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
9761797 TAAATTAAGG
* *
9761807 TATTAAATAATATATT
1 TATTAAATAATACATA
9761823 TATTAATATAATACATA
1 TATTAA-ATAATACATA
9761840 TA-TAAATAA
1 TATTAAATAA
9761849 ATTAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 9 0.39
17 10 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTAAATAATACATA
Found at i:9762284 original size:18 final size:18
Alignment explanation
Indices: 9762249--9762285 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
9762239 CGATGCATAA
*
9762249 TATCCAGAACTTTATTTT
1 TATCCAGAACTCTATTTT
9762267 TATCC-GAACTCTATTTT
1 TATCCAGAACTCTATTTT
9762284 TA
1 TA
9762286 AAAAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (18 bp):
TATCCAGAACTCTATTTT
Found at i:9762434 original size:9 final size:9
Alignment explanation
Indices: 9762420--9762453 Score: 54
Period size: 8 Copynumber: 4.0 Consensus size: 9
9762410 ATTTATTTAA
9762420 TAAAAAAAG
1 TAAAAAAAG
9762429 T-AAAAAAG
1 TAAAAAAAG
9762437 TAAAAAAA-
1 TAAAAAAAG
9762445 TAAAAAAAG
1 TAAAAAAAG
9762454 GAAATTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (9 bp):
TAAAAAAAG
Found at i:9762442 original size:17 final size:16
Alignment explanation
Indices: 9762420--9762451 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
9762410 ATTTATTTAA
9762420 TAAAAAAAGTAAAAAAG
1 TAAAAAAA-TAAAAAAG
9762437 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
9762452 AGGAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
TAAAAAAATAAAAAAG
Found at i:9762723 original size:14 final size:14
Alignment explanation
Indices: 9762706--9762759 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
9762696 AATTTTTAAT
9762706 AAAAAATAAAATTA
1 AAAAAATAAAATTA
**
9762720 AAAAAACCAAATTA
1 AAAAAATAAAATTA
***
9762734 AAATGTTAAAATTAA
1 AAAAAATAAAATT-A
9762749 AAAAAATAAAA
1 AAAAAATAAAA
9762760 AATAAAAAAT
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
14 20 0.69
15 9 0.31
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (14 bp):
AAAAAATAAAATTA
Found at i:9762944 original size:12 final size:11
Alignment explanation
Indices: 9762925--9762981 Score: 78
Period size: 12 Copynumber: 4.9 Consensus size: 11
9762915 CACTTTCTCC
9762925 TTTTTTTTCTT
1 TTTTTTTTCTT
9762936 TTTTCTTTTCTT
1 TTTT-TTTTCTT
*
9762948 TTTCTTTTACTT
1 TTT-TTTTTCTT
9762960 TCTTTTTTTCTT
1 T-TTTTTTTCTT
9762972 TTTTTTTTCT
1 TTTTTTTTCT
9762982 CTTCCAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
11 13 0.32
12 25 0.61
13 3 0.07
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:9762949 original size:11 final size:11
Alignment explanation
Indices: 9762925--9762981 Score: 62
Period size: 11 Copynumber: 5.0 Consensus size: 11
9762915 CACTTTCTCC
9762925 TTTT-TTTTCTT
1 TTTTCTTTTC-T
9762936 TTTTCTTTTCT
1 TTTTCTTTTCT
9762947 TTTTCTTTTACT
1 TTTTCTTTT-CT
*
9762959 TTCTTTTTTTCT
1 TT-TTCTTTTCT
*
9762971 TTTTTTTTTCT
1 TTTTCTTTTCT
9762982 CTTCCAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
11 23 0.55
12 13 0.31
13 6 0.14
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:9763316 original size:22 final size:22
Alignment explanation
Indices: 9763276--9763333 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
9763266 AAAACACTAC
* *
9763276 ATTTATATATAATTATTATGTT
1 ATTTATATAAAATTATTATATT
9763298 ATTTATATTAAAATT-TTATATT
1 ATTTATA-TAAAATTATTATATT
*
9763320 -TTTAT-GAAAATTAT
1 ATTTATATAAAATTAT
9763334 ACTAAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.19
20 1 0.03
21 5 0.16
22 13 0.42
23 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (22 bp):
ATTTATATAAAATTATTATATT
Found at i:9763863 original size:12 final size:14
Alignment explanation
Indices: 9763843--9763884 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
9763833 ATATATTCTA
*
9763843 TTATTTATTTA-AT
1 TTATATATTTATAT
9763856 TT-TATATTTATAT
1 TTATATATTTATAT
9763869 TTATATATATTATAT
1 TTATATAT-TTATAT
9763884 T
1 T
9763885 AATAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 5 0.20
15 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATATATTTATAT
Found at i:9764787 original size:72 final size:71
Alignment explanation
Indices: 9764652--9764787 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 71
9764642 AACTAACAAC
*
9764652 GAAAGAATATTATTCTTTTACTTACTGATGAACATATTATACATAACAAAGGATTGAAAAAAAAG
1 GAAAGAATATTATTCTTTTACTTACTGATGAACATATTATACATAACAAAGGAATGAAAAAAAAG
9764717 TAATAA
66 TAATAA
* * * * * *
9764723 GAAAGAATTATTATAT-TTTTAGTTACTGATGAATATATTATACATTATAAAGTAATGAACAAAA
1 GAAAGAA-TATTAT-TCTTTTACTTACTGATGAACATATTATACATAACAAAGGAATGAAAAAAA
9764787 A
64 A
9764788 TTTAATAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
71 7 0.12
72 48 0.86
73 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.34
Consensus pattern (71 bp):
GAAAGAATATTATTCTTTTACTTACTGATGAACATATTATACATAACAAAGGAATGAAAAAAAAG
TAATAA
Found at i:9770347 original size:14 final size:14
Alignment explanation
Indices: 9770328--9770355 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9770318 TGAAATTTCG
9770328 TCTAAATTATTCCA
1 TCTAAATTATTCCA
9770342 TCTAAATTATTCCA
1 TCTAAATTATTCCA
9770356 CAATTTGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (14 bp):
TCTAAATTATTCCA
Found at i:9770736 original size:4 final size:4
Alignment explanation
Indices: 9770727--9770780 Score: 72
Period size: 4 Copynumber: 13.2 Consensus size: 4
9770717 AAAACTTTGA
* * *
9770727 AAAT AAAT AAACA AAAT AAAT AAAT ATAT AAAT GAAT AAAT AAAT AAAT
1 AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
9770776 AAAT A
1 AAAT A
9770781 CTAAAATAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
4 40 0.93
5 3 0.07
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:9770744 original size:13 final size:13
Alignment explanation
Indices: 9770726--9770750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9770716 AAAAACTTTG
9770726 AAAATAAATAAAC
1 AAAATAAATAAAC
9770739 AAAATAAATAAA
1 AAAATAAATAAA
9770751 TATATAAATG
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:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAAATAAAC
Found at i:9771226 original size:18 final size:18
Alignment explanation
Indices: 9771203--9771237 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9771193 CCATTCATTC
* *
9771203 TTTTTTTCAATTATCCAT
1 TTTTTTTAAAATATCCAT
9771221 TTTTTTTAAAATATCCA
1 TTTTTTTAAAATATCCA
9771238 GATACATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTTTAAAATATCCAT
Found at i:9771802 original size:89 final size:87
Alignment explanation
Indices: 9771647--9771899 Score: 278
Period size: 89 Copynumber: 2.9 Consensus size: 87
9771637 AAAATTTCTC
* * * *
9771647 TAAATAGAGGCTCAACAACTTTTGAAAAATAAACTAAGACTCTTATAAACAGAGGCTCAATGACT
1 TAAATAGAGGCTTAATAACTTTTGAAAAATAAA-TAAGGCTC-TCTAAACAGAGGCTCAATGACT
*
9771712 TTTGAAAATAAACTAGACCTCCTT
64 TTTGAAAATAAACTAAACCTCCTT
* * * ** * *
9771736 TAAATAGAGGGTTAATGACTTTTGAAAAATAAATTAGGGCTCATCTAAGTAGAAGCTCAATAAC-
1 TAAATAGAGGCTTAATAACTTTTGAAAAATAAA-TAAGGCTC-TCTAAACAGAGGCTCAATGACT
*
9771800 TTTGAAAAATAAA-TAAAGCTCCTT
64 TTTG-AAAATAAACTAAACCTCCTT
* * * *
9771824 TAAGTAGAGGCTTAATAAC-TTTGAAAAGTAAATAAGGCTTCTCTAAACAGAGGCTTAACGACTT
1 TAAATAGAGGCTTAATAACTTTTGAAAAATAAATAAGGC-TCTCTAAACAGAGGCTCAATGACTT
9771888 TTGAAAATAAAC
65 TTGAAAATAAAC
9771900 GAAGGCTCCT
Statistics
Matches: 134, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
86 28 0.21
87 18 0.13
88 29 0.22
89 59 0.44
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (87 bp):
TAAATAGAGGCTTAATAACTTTTGAAAAATAAATAAGGCTCTCTAAACAGAGGCTCAATGACTTT
TGAAAATAAACTAAACCTCCTT
Found at i:9771842 original size:43 final size:43
Alignment explanation
Indices: 9771644--9772033 Score: 266
Period size: 43 Copynumber: 8.9 Consensus size: 43
9771634 ATAAAAATTT
* *
9771644 CTCTAAATAGAGGCTCAACAACTTTTGAAAAATAAACT-AAGACTC
1 CTCTAAACAGAGGCTTAACAAC-TTTGAAAAATAAA-TAAAG-CTC
* * * ** * *
9771689 TTATAAACAGAGGCTCAATGACTTTTG-AAAATAAACTAGACCTC
1 CTCTAAACAGAGGCTTAACAAC-TTTGAAAAATAAA-TAAAGCTC
* * * ** **
9771733 CTTTAAATAGAGGGTTAATGACTTTTGAAAAATAAATTAGGGCTC
1 CTCTAAACAGAGGCTTAACAAC-TTTGAAAAATAAA-TAAAGCTC
* ** * * *
9771778 ATCTAAGTAGAAGCTCAATAACTTTGAAAAATAAATAAAGCTC
1 CTCTAAACAGAGGCTTAACAACTTTGAAAAATAAATAAAGCTC
* ** * * * *
9771821 CTTTAAGTAGAGGCTTAATAACTTTGAAAAGTAAATAAGGCTT
1 CTCTAAACAGAGGCTTAACAACTTTGAAAAATAAATAAAGCTC
* * *
9771864 CTCTAAACAGAGGCTTAACGACTTTTG-AAAATAAACGAAGGCTC
1 CTCTAAACAGAGGCTTAACAAC-TTTGAAAAATAAA-TAAAGCTC
* * * **
9771908 CTCTAAGCCGAGGCTCAACAACTTCAAAAAATAAATAAAGCTC
1 CTCTAAACAGAGGCTTAACAACTTTGAAAAATAAATAAAGCTC
* * * *
9771951 CTCTAAGCAAAGG-TTCAACAACTTTCAAAAATAAATAAAGCTT
1 CTCTAAACAGAGGCTT-AACAACTTTGAAAAATAAATAAAGCTC
* **
9771994 CTCTAAACAGAGGTTTAACAACTTCAAAAAATAAATAAAG
1 CTCTAAACAGAGGCTTAACAACTTTGAAAAATAAATAAAG
9772034 TTTAACAACT
Statistics
Matches: 281, Mismatches: 57, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.00
43 142 0.51
44 86 0.31
45 52 0.19
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.26
Consensus pattern (43 bp):
CTCTAAACAGAGGCTTAACAACTTTGAAAAATAAATAAAGCTC
Found at i:9771908 original size:87 final size:88
Alignment explanation
Indices: 9771651--9771956 Score: 264
Period size: 87 Copynumber: 3.5 Consensus size: 88
9771641 TTTCTCTAAA
* * *
9771651 TAGAGGCTCAACAACTTTTGAAAAATAAACTAAGACTCTTATAAACAGAGGCTCAATGACTTTTG
1 TAGAGGCTCAACAACTTTTGAAAAATAAACTAAGGCTCATCTAAACAGAGGCTCAATGACTTTTG
* * *
9771716 AAAATAAACTAGACCTCCTTTAAA
66 AAAATAAACAAG-GCTCCTTTAAG
* * ** * * ** * *
9771740 TAGAGGGTTAATGACTTTTGAAAAATAAATTAGGGCTCATCTAAGTAGAAGCTCAATAAC-TTTG
1 TAGAGGCTCAACAACTTTTGAAAAATAAACTAAGGCTCATCTAAACAGAGGCTCAATGACTTTTG
* *
9771804 AAAAATAAATAAAGCTCCTTTAAG
66 -AAAATAAACAAGGCTCCTTTAAG
* * * * *
9771828 TAGAGGCTTAATAAC-TTTGAAAAGTAAA-TAAGGCTTC-TCTAAACAGAGGCTTAACGACTTTT
1 TAGAGGCTCAACAACTTTTGAAAAATAAACTAAGGC-TCATCTAAACAGAGGCTCAATGACTTTT
*
9771890 GAAAATAAACGAAGGCTCCTCTAAG
65 GAAAATAAAC-AAGGCTCCTTTAAG
** ** * *
9771915 CCGAGGCTCAACAAC-TTCAAAAAATAAA-TAAAGCTCCTCTAA
1 TAGAGGCTCAACAACTTTTGAAAAATAAACTAAGGCTCATCTAA
9771957 GCAAAGGTTC
Statistics
Matches: 173, Mismatches: 39, Indels: 12
0.77 0.17 0.05
Matches are distributed among these distances:
86 30 0.17
87 61 0.35
88 26 0.15
89 56 0.32
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (88 bp):
TAGAGGCTCAACAACTTTTGAAAAATAAACTAAGGCTCATCTAAACAGAGGCTCAATGACTTTTG
AAAATAAACAAGGCTCCTTTAAG
Found at i:9771925 original size:130 final size:130
Alignment explanation
Indices: 9771652--9772017 Score: 364
Period size: 130 Copynumber: 2.8 Consensus size: 130
9771642 TTCTCTAAAT
* * *
9771652 AGAGGCTCAACAACTTTTGAAAAATAAACT-AAGACT-CTTATAAACAGAGGCTCAATGACTTTT
1 AGAGGCTCAACAAC-TTTGAAAAATAAA-TAAAG-CTCCTT-TAAGCAGAGGCTTAATAAC-TTT
* * * * * * ** *
9771715 GAAAATAAACT-AGACCTCCTTTAAATAGAGGGTTAATGACTTTTGAAAAATAAATTAGGGCTCA
61 GAAAATAAA-TAAG-GCTTCTCTAAACAGAGGCTTAACGACTTTTGAAAAATAAACGAAGGCTCA
*
9771779 TCTAAGT
124 TCTAAGC
* * *
9771786 AGAAGCTCAATAACTTTGAAAAATAAATAAAGCTCCTTTAAGTAGAGGCTTAATAACTTTGAAAA
1 AGAGGCTCAACAACTTTGAAAAATAAATAAAGCTCCTTTAAGCAGAGGCTTAATAACTTTGAAAA
*
9771851 GTAAATAAGGCTTCTCTAAACAGAGGCTTAACGACTTTTG-AAAATAAACGAAGGCTCCTCTAAG
66 -TAAATAAGGCTTCTCTAAACAGAGGCTTAACGACTTTTGAAAAATAAACGAAGGCTCATCTAAG
9771915 C
130 C
* ** * * * *
9771916 CGAGGCTCAACAACTTCAAAAAATAAATAAAGCTCCTCTAAGCAAAGG-TTCAACAACTTTCAAA
1 AGAGGCTCAACAACTTTGAAAAATAAATAAAGCTCCTTTAAGCAGAGGCTT-AATAACTTT-GAA
* * *
9771980 AATAAATAAAGCTTCTCTAAACAGAGGTTTAACAACTT
64 AATAAATAAGGCTTCTCTAAACAGAGGCTTAACGACTT
9772018 CAAAAAATAA
Statistics
Matches: 196, Mismatches: 30, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
129 2 0.01
130 101 0.52
131 38 0.19
132 24 0.12
133 19 0.10
134 12 0.06
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.26
Consensus pattern (130 bp):
AGAGGCTCAACAACTTTGAAAAATAAATAAAGCTCCTTTAAGCAGAGGCTTAATAACTTTGAAAA
TAAATAAGGCTTCTCTAAACAGAGGCTTAACGACTTTTGAAAAATAAACGAAGGCTCATCTAAGC
Found at i:9772036 original size:27 final size:27
Alignment explanation
Indices: 9772006--9772062 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
9771996 CTAAACAGAG
9772006 GTTTAACAACTTCAAAAAATAAATAAA
1 GTTTAACAACTTCAAAAAATAAATAAA
9772033 GTTTAACAACTTCAAAAAATAAATAAA
1 GTTTAACAACTTCAAAAAATAAATAAA
9772060 GTT
1 GTT
9772063 CCTTTACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.28
Consensus pattern (27 bp):
GTTTAACAACTTCAAAAAATAAATAAA
Found at i:9772385 original size:33 final size:34
Alignment explanation
Indices: 9772339--9772410 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
9772329 TCCCTACTTC
* ** *
9772339 ATGCACTAGACATTC-TTAAATGCAATGTATGCT
1 ATGCACTAAACATTCAAAAAATGCAATGCATGCT
*
9772372 ATGCACTAAACATTCAAAAAATGTAATGCATGCT
1 ATGCACTAAACATTCAAAAAATGCAATGCATGCT
9772406 ATGCA
1 ATGCA
9772411 AATGTCATGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
33 14 0.42
34 19 0.58
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (34 bp):
ATGCACTAAACATTCAAAAAATGCAATGCATGCT
Found at i:9773594 original size:79 final size:78
Alignment explanation
Indices: 9773423--9773608 Score: 228
Period size: 78 Copynumber: 2.4 Consensus size: 78
9773413 ACTTGATCAC
* * * *
9773423 ATTTTCATCACTTGATTACAATTCACAAGCTTCACAACACTAGCAATTTAAGAAAAATTTTATTT
1 ATTTTCATCATTTGATCACAACTCACAAGCTTCACAACACTAGCAATTTAAGAAAAATTTTATCT
9773488 ACTAATTCACATT
66 ACTAATTCACATT
** * * * *
9773501 ATTTTTGTCATTTGATCACAACTCACAGGTTTCTCAACACTAGCAATTTCAGAACAAATTTTATC
1 ATTTTCATCATTTGATCACAACTCACAAGCTTCACAACACTAGCAATTTAAGAA-AAATTTTATC
* * **
9773566 TATTGATTTGCATT
65 TACTAATTCACATT
*
9773580 ATTTCCATCATTTGATCACAACTCACAAG
1 ATTTTCATCATTTGATCACAACTCACAAG
9773609 TTATGTTGAT
Statistics
Matches: 89, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
78 45 0.51
79 44 0.49
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (78 bp):
ATTTTCATCATTTGATCACAACTCACAAGCTTCACAACACTAGCAATTTAAGAAAAATTTTATCT
ACTAATTCACATT
Found at i:9774226 original size:8 final size:8
Alignment explanation
Indices: 9774215--9774307 Score: 68
Period size: 8 Copynumber: 11.8 Consensus size: 8
9774205 ATTTTACATT
9774215 TTTTTTTA
1 TTTTTTTA
9774223 -TTTTTTA
1 TTTTTTTA
9774230 TTTTTTTCA
1 TTTTTTT-A
*
9774239 -TTCTTTA
1 TTTTTTTA
*
9774246 TTCTTTTA
1 TTTTTTTA
* *
9774254 TTCTTTCA
1 TTTTTTTA
9774262 TTTTTTT-
1 TTTTTTTA
9774269 TCTTTTTTCA
1 T-TTTTTT-A
* * *
9774279 -TATCTCA
1 TTTTTTTA
9774286 TTTTTTTA
1 TTTTTTTA
9774294 TTTTTTTA
1 TTTTTTTA
9774302 TTTTTT
1 TTTTTT
9774308 CCTTCATTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
7 10 0.15
8 55 0.83
9 1 0.02
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTTA
Found at i:9774260 original size:23 final size:23
Alignment explanation
Indices: 9774217--9774274 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
9774207 TTTACATTTT
*
9774217 TTTTTATT-TTTTATTTTTTTCA
1 TTTTTATTCTTTTATTTCTTTCA
9774239 TTCTTTATTCTTTTA-TTCTTTCA
1 TT-TTTATTCTTTTATTTCTTTCA
*
9774262 TTTTTTTTCTTTT
1 TTTTTATTCTTTT
9774275 TTCATATCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 12 0.38
23 15 0.47
24 5 0.16
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTATTCTTTTATTTCTTTCA
Found at i:9774276 original size:40 final size:39
Alignment explanation
Indices: 9774222--9774307 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 39
9774212 ATTTTTTTTT
*
9774222 ATTTTTTATTTTTTTCAT-TCTTTATTCTTTTATTCTTTC
1 ATTTTTTATTTTTTTCATATC-TCATTCTTTTATTCTTTC
* * * *
9774261 ATTTTTTTTCTTTTTTCATATCTCATTTTTTTATTTTTTT
1 ATTTTTTAT-TTTTTTCATATCTCATTCTTTTATTCTTTC
9774301 ATTTTTT
1 ATTTTTT
9774308 CCTTCATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 8 0.20
40 30 0.75
41 2 0.05
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (39 bp):
ATTTTTTATTTTTTTCATATCTCATTCTTTTATTCTTTC
Found at i:9774329 original size:31 final size:32
Alignment explanation
Indices: 9774257--9774330 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
9774247 TCTTTTATTC
*
9774257 TTTCATTTTTTTTCTTTTTTCATATCTCATTTT
1 TTTCATTTTTTTTATTTTTTCA-ATCTCATTTT
*
9774290 TTT-A-TTTTTTTATTTTTTC-CT-TCATTTT
1 TTTCATTTTTTTTATTTTTTCAATCTCATTTT
*
9774318 TTTCAATTTTTTT
1 TTTCATTTTTTTT
9774331 CTTTAATCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 10 0.27
29 2 0.05
30 7 0.19
31 14 0.38
32 1 0.03
33 3 0.08
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTCATTTTTTTTATTTTTTCAATCTCATTTT
Found at i:9779797 original size:5 final size:5
Alignment explanation
Indices: 9779778--9779847 Score: 54
Period size: 5 Copynumber: 13.2 Consensus size: 5
9779768 AATAAGCAAG
9779778 ATAAA ATAAGTA ATAAA ATAAA ATAAA ATAAAA ATGATAA ATAAA A-AAA
1 ATAAA ATAA--A ATAAA ATAAA ATAAA AT-AAA AT-A-AA ATAAA ATAAA
* *
9779827 ATATAG AT-AA ATAAA GTAAA A
1 ATA-AA ATAAA ATAAA ATAAA A
9779848 ACACAATTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
4 7 0.13
5 27 0.51
6 10 0.19
7 9 0.17
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:9779804 original size:22 final size:22
Alignment explanation
Indices: 9779778--9779847 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 22
9779768 AATAAGCAAG
9779778 ATAAAATAAGTAATAAAATAAA
1 ATAAAATAAGTAATAAAATAAA
*
9779800 ATAAAATAA-AAATGATAAATAAA
1 ATAAAATAAGTAAT-A-AAATAAA
*
9779823 A-AAAATATAGATAAATAAAGTAAA
1 ATAAAATA-AG-T-AATAAAATAAA
9779847 A
1 A
9779848 ACACAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
21 3 0.08
22 16 0.41
23 9 0.23
24 7 0.18
25 1 0.03
26 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (22 bp):
ATAAAATAAGTAATAAAATAAA
Found at i:9779824 original size:19 final size:19
Alignment explanation
Indices: 9779798--9779841 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
9779788 TAATAAAATA
*
9779798 AAATAAAATAAAAAT-GAT
1 AAATAAAAAAAAAATAGAT
*
9779816 AAATAAAAAAAATATAGAT
1 AAATAAAAAAAAAATAGAT
9779835 AAATAAA
1 AAATAAA
9779842 GTAAAAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
AAATAAAAAAAAAATAGAT
Found at i:9780404 original size:12 final size:12
Alignment explanation
Indices: 9780379--9780456 Score: 54
Period size: 12 Copynumber: 6.4 Consensus size: 12
9780369 TATATACAAA
9780379 AATTATTT-TTT
1 AATTATTTATTT
9780390 AATTATTTATTT
1 AATTATTTATTT
9780402 AATT-TTATATTT
1 AATTATT-TATTT
* *
9780414 ATTTATATATTTT
1 AATTATTTA-TTT
** *
9780427 TTTTATATATTT
1 AATTATTTATTT
9780439 AATT-TTATATTT
1 AATTATT-TATTT
9780451 ATATTA
1 A-ATTA
9780457 AAAAATAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
11 11 0.20
12 28 0.52
13 15 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
AATTATTTATTT
Found at i:9780419 original size:24 final size:23
Alignment explanation
Indices: 9780387--9780452 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
9780377 AAAATTATTT
*
9780387 TTTAATTATTTATTTAATTTTATA
1 TTTAATTATATATTT-ATTTTATA
* *
9780411 TTTATTTATATATTTTTTTTATATA
1 TTTAATTATATA-TTTATTT-TATA
*
9780436 TTTAATTTTATATTTAT
1 TTTAATTATATATTTAT
9780453 ATTAAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 17 0.50
25 17 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTAATTATATATTTATTTTATA
Found at i:9780433 original size:13 final size:14
Alignment explanation
Indices: 9780392--9780448 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 14
9780382 TATTTTTTAA
*
9780392 TTATTTATTTAA-T
1 TTATATATTTAATT
9780405 TT-TATATTT-A-T
1 TTATATATTTAATT
*
9780416 TTATATATTT-TTT
1 TTATATATTTAATT
9780429 TTATATATTTAATT
1 TTATATATTTAATT
9780443 TTATAT
1 TTATAT
9780449 TTATATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
11 4 0.11
12 13 0.34
13 13 0.34
14 8 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:9780453 original size:20 final size:20
Alignment explanation
Indices: 9780392--9780454 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
9780382 TATTTTTTAA
*
9780392 TTATTTATTTAATTTTATAT
1 TTATATATTTAATTTTATAT
* *
9780412 TTATTTATAT-ATTTT-T-T
1 TTATATATTTAATTTTATAT
9780429 TTATATATTTAATTTTATAT
1 TTATATATTTAATTTTATAT
9780449 TTATAT
1 TTATAT
9780455 TAAAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 9 0.24
18 6 0.16
19 6 0.16
20 16 0.43
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATATATTTAATTTTATAT
Found at i:9780501 original size:21 final size:20
Alignment explanation
Indices: 9780448--9780513 Score: 114
Period size: 20 Copynumber: 3.2 Consensus size: 20
9780438 TAATTTTATA
9780448 TTTATATTAAAAAATAATAT
1 TTTATATTAAAAAATAATAT
9780468 TTTATATTAAAAAATAATAT
1 TTTATATTAAAAAATAATAT
*
9780488 TTTATATTTTAAAAATAATAT
1 TTTATA-TTAAAAAATAATAT
9780509 TTTAT
1 TTTAT
9780514 TAATTTTGGG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 26 0.59
21 18 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTATATTAAAAAATAATAT
Found at i:9783584 original size:2 final size:2
Alignment explanation
Indices: 9783538--9783567 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9783528 ACCTCCCCCA
9783538 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9783568 ATCATAGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9784103 original size:3 final size:3
Alignment explanation
Indices: 9784095--9784136 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
9784085 GATGAACTTC
9784095 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9784137 TATTATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9784709 original size:52 final size:54
Alignment explanation
Indices: 9784648--9784752 Score: 133
Period size: 52 Copynumber: 2.0 Consensus size: 54
9784638 ATGAAACTTT
* * * * *
9784648 AATAATAATAAAATATATCTTAGAAAAAATTTA-TAAGAAAA-AAACAAATTGC
1 AATAATAATAAAATATACCTTAAAAAAAAGTTACTAAAAAAATAAAAAAATTGC
* *
9784700 AATAGTAATAGAATATACCTTAAAAAAAAGTTACTAAAAAAATAAAAAAATTG
1 AATAATAATAAAATATACCTTAAAAAAAAGTTACTAAAAAAATAAAAAAATTG
9784753 ATGTATAACA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 28 0.64
53 7 0.16
54 9 0.20
ACGTcount: A:0.62, C:0.06, G:0.07, T:0.26
Consensus pattern (54 bp):
AATAATAATAAAATATACCTTAAAAAAAAGTTACTAAAAAAATAAAAAAATTGC
Found at i:9785425 original size:2 final size:2
Alignment explanation
Indices: 9785420--9785468 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
9785410 ATATAATATA
9785420 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
9785462 TG TG TG T
1 TG TG TG T
9785469 ATATATATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:9788408 original size:13 final size:13
Alignment explanation
Indices: 9788390--9788419 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
9788380 CATTTGTCTC
9788390 TTTTTTCTTTATT
1 TTTTTTCTTTATT
9788403 TTTTTTCTTTATT
1 TTTTTTCTTTATT
9788416 TTTT
1 TTTT
9788420 GCTTTTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTCTTTATT
Found at i:9788424 original size:12 final size:12
Alignment explanation
Indices: 9788390--9788424 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
9788380 CATTTGTCTC
9788390 TTTTTTCTTTATT
1 TTTTTTCTTTA-T
9788403 TTTTTTCTTTAT
1 TTTTTTCTTTAT
*
9788415 TTTTTGCTTT
1 TTTTTTCTTT
9788425 TTGCTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTTTCTTTAT
Found at i:9788432 original size:21 final size:19
Alignment explanation
Indices: 9788382--9788467 Score: 66
Period size: 22 Copynumber: 4.2 Consensus size: 19
9788372 TTTTTCCTCA
*
9788382 TTTGTCTCTTTTTTCTTTATT
1 TTTG-CTCTTTTTT-TTTCTT
**
9788403 TTTTTTCTTTATTTTTTGCTT
1 TTTGCTCTTT-TTTTTT-CTT
9788424 TTTGCTCTTTTTTTTTTTACTT
1 TTTGCTC--TTTTTTTTT-CTT
9788446 TTTGCT-TTTTTTTCTTCTT
1 TTTGCTCTTTTTTT-TTCTT
9788465 TTT
1 TTT
9788468 TTTTGTACAC
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
19 13 0.24
20 10 0.19
21 13 0.24
22 15 0.28
23 3 0.06
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (19 bp):
TTTGCTCTTTTTTTTTCTT
Found at i:9788439 original size:22 final size:21
Alignment explanation
Indices: 9788390--9788458 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
9788380 CATTTGTCTC
*
9788390 TTTTTTCTTTA-TTTTT--TT
1 TTTTTTTTTTACTTTTTGCTT
*
9788408 TCTTTATTTTTTGCTTTTTGCTCT
1 T-TTT-TTTTTTACTTTTTGCT-T
9788432 TTTTTTTTTTACTTTTTGCTT
1 TTTTTTTTTTACTTTTTGCTT
9788453 TTTTTT
1 TTTTTT
9788459 CTTCTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 5 0.12
21 12 0.29
22 15 0.36
23 4 0.10
24 2 0.05
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.81
Consensus pattern (21 bp):
TTTTTTTTTTACTTTTTGCTT
Found at i:9788447 original size:29 final size:29
Alignment explanation
Indices: 9788401--9788471 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
9788391 TTTTTCTTTA
*
9788401 TTTTTTTTCTTTATTTTTTGCTTTTTGCTC
1 TTTTTTTT-TTTACTTTTTGCTTTTTGCTC
**
9788431 TTTTTTTTTTTACTTTTTGCTTTTTTTTC
1 TTTTTTTTTTTACTTTTTGCTTTTTGCTC
9788460 TTCTTTTTTTTT
1 TT-TTTTTTTTT
9788472 GTACACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.03, C:0.11, G:0.04, T:0.82
Consensus pattern (29 bp):
TTTTTTTTTTTACTTTTTGCTTTTTGCTC
Found at i:9788448 original size:41 final size:42
Alignment explanation
Indices: 9788382--9788467 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 42
9788372 TTTTTCCTCA
*
9788382 TTTGTCTCTTTTTTCTTTATTTTTTTTCTTTATTTTT-TGCTT
1 TTTGTCTCTTTTTTCTTTATTTTTTTGCTTT-TTTTTCTGCTT
*
9788424 TTTG-CTCTTTTTT-TTT-TTACTTTTTGCTTTTTTTTCTTCTT
1 TTTGTCTCTTTTTTCTTTATT--TTTTTGCTTTTTTTTCTGCTT
9788465 TTT
1 TTT
9788468 TTTTGTACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.05
40 8 0.21
41 25 0.64
42 4 0.10
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (42 bp):
TTTGTCTCTTTTTTCTTTATTTTTTTGCTTTTTTTTCTGCTT
Found at i:9788788 original size:66 final size:64
Alignment explanation
Indices: 9788707--9788859 Score: 175
Period size: 66 Copynumber: 2.3 Consensus size: 64
9788697 ATTTTGACAT
9788707 TTTTGCCCCATCAATTTTTTTCTTTTTATTTT-TGT-TTGTTTTTTGTTTAGGTAAAGCACATTG
1 TTTTGCCCCATCAATTTTTTTCTTTTTATTTTCT-TCTT-TTTTTT-TTT-GGTAAAGCACATTG
9788770 GCA
62 GCA
* * * * ** *
9788773 TTTTGCCCCACCAATTTCCTTTCCTTTTTCTTTTCTTCTTTTTTTTTTTTGTGGAGTACATTGGC
1 TTTTGCCCCATCAATTT--TTTTCTTTTTATTTTCTTCTTTTTTTTTTTGGTAAAGCACATTGGC
9788838 A
64 A
9788839 TTTTGCCCCATCAATTTTTTT
1 TTTTGCCCCATCAATTTTTTT
9788860 TTTCTTTTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
64 3 0.04
66 45 0.61
67 3 0.04
68 20 0.27
69 3 0.04
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.56
Consensus pattern (64 bp):
TTTTGCCCCATCAATTTTTTTCTTTTTATTTTCTTCTTTTTTTTTTTGGTAAAGCACATTGGCA
Done.