Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002831.1 Hibiscus syriacus cultivar Beakdansim tig00005822_pilon, 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: 71668
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1541 original size:3 final size:3
Alignment explanation
Indices: 1533--1559 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1523 GGTCACTCCA
1533 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1560 TGGAGAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:2100 original size:33 final size:33
Alignment explanation
Indices: 2055--2124 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2045 CTTTACAAAC
* * *
2055 TCCCTAGTTTTTCTCGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
* **
2088 TCCCTAGCTTTTCACGGGATCAGTTAGAACCTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
2121 TCCC
1 TCCC
2125 CTTTACAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (33 bp):
TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
Found at i:3230 original size:17 final size:18
Alignment explanation
Indices: 3197--3230 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3187 TAGTGAACAG
*
3197 TAATGTCTACAGCATCAA
1 TAATGTCTACAGAATCAA
3215 TAATGT-TACAGAATCA
1 TAATGTCTACAGAATCA
3231 GCATACCAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (18 bp):
TAATGTCTACAGAATCAA
Found at i:8159 original size:20 final size:21
Alignment explanation
Indices: 8122--8160 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
8112 AATCAAAGAT
* *
8122 TTTAAGTTTGTTTTTAGTAAA
1 TTTAAGTTTGTATATAGTAAA
8143 TTTAAG-TTGTATATAGTA
1 TTTAAGTTTGTATATAGTA
8161 TTCCTAACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (21 bp):
TTTAAGTTTGTATATAGTAAA
Found at i:8687 original size:21 final size:20
Alignment explanation
Indices: 8641--8688 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
8631 TAATGTAAGT
* *
8641 GTATCGATACTGAGGGTTTG
1 GTATTGATACTGAGGGCTTG
*
8661 GAATTGATACTGAGGGGCTTG
1 GTATTGATACTGA-GGGCTTG
8682 GTATTGA
1 GTATTGA
8689 ACCTGGGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.23, C:0.08, G:0.35, T:0.33
Consensus pattern (20 bp):
GTATTGATACTGAGGGCTTG
Found at i:16539 original size:45 final size:45
Alignment explanation
Indices: 16488--16585 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
16478 TAGTTATTTA
** * * *
16488 TTAAAATAATTT-TAAATAAGGTTATTTATTTTAAAATAATTTATT
1 TTAAAATAATTTAT-AATAAAATAATTTACTTTAAAATAAATTATT
*
16533 TTAAAATAATTTATTATAAAATAATTTACTTTAAAATAAATTATT
1 TTAAAATAATTTATAATAAAATAATTTACTTTAAAATAAATTATT
*
16578 ATAAAATA
1 TTAAAATA
16586 TGGATTGATT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (45 bp):
TTAAAATAATTTATAATAAAATAATTTACTTTAAAATAAATTATT
Found at i:16622 original size:14 final size:15
Alignment explanation
Indices: 16511--16660 Score: 133
Period size: 15 Copynumber: 9.5 Consensus size: 15
16501 AAATAAGGTT
16511 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
16526 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
16541 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
16556 ATTTACTTTAAAATA
1 ATTTATTTTAAAATA
* *
16571 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
16590 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
16608 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
* * *
16622 ATTTATTAGTATGAATTG
1 ATTTATT--T-TAAAATA
16640 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
16654 ATTTATT
1 ATTTATT
16661 AGTATGGATT
Statistics
Matches: 112, Mismatches: 12, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
14 22 0.20
15 57 0.51
16 6 0.05
17 3 0.03
18 11 0.10
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.05
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:16645 original size:18 final size:18
Alignment explanation
Indices: 16622--16678 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
16612 ATTTTAAATA
16622 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
16640 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
16654 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
16672 ATTTATT
1 ATTTATT
16679 TTAAAATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:16647 original size:32 final size:32
Alignment explanation
Indices: 16608--16683 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
16598 TTTTAAAATA
16608 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
16640 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
16672 ATTTATTTTAAA
1 ATTTATTTTAAA
16684 ATATGGATTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:16700 original size:54 final size:54
Alignment explanation
Indices: 16631--17392 Score: 379
Period size: 54 Copynumber: 14.6 Consensus size: 54
16621 AATTTATTAG
*
16631 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
16685 TATGGATTGATTTA--TT--AT--TGTAGTT-GTGTGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
* * * * * * *
16732 TA---ATTTA-TTAGTATAGATTGATTTATTTTAAAATATGGGTTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTATTTTAAAA
** ** * ** * * * *
16786 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGAATTGATTTATTTTAAAA
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
16841 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
** ** * ** * ***
16895 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
* * * ***
16949 TATGGATTGATTTATTTT-AA-AA--TA-TAG-ATTGATTTA-TTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAA
*
16997 TATGGATTGATTT-GTTT---TAA---A--A-TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
17041 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* ** ** * ** * * *
17095 TATGAATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
*
17149 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
17203 TATGGATTGA-TTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTA-TTT---TAA---A--A
* * * **
17259 GTATGGATTGATTTATTTT-AA-AA--TA-TAG-ATTGATTTA-TTATTGTAGTTA
1 -TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAA
*
17308 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
17362 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
17393 TTGTAGTTGT
Statistics
Matches: 545, Mismatches: 92, Indels: 142
0.70 0.12 0.18
Matches are distributed among these distances:
43 3 0.01
44 25 0.05
45 12 0.02
46 2 0.00
47 26 0.05
48 69 0.13
49 12 0.02
50 13 0.02
51 8 0.01
52 14 0.03
53 44 0.08
54 245 0.45
55 23 0.04
56 6 0.01
57 13 0.02
58 14 0.03
59 7 0.01
60 7 0.01
61 2 0.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:16756 original size:32 final size:31
Alignment explanation
Indices: 16715--17201 Score: 179
Period size: 22 Copynumber: 17.5 Consensus size: 31
16705 TAGTTGTGTG
16715 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTAT
16746 AGATTGATTTATTTT-AA-AA--TA-T-G---
1 -GATTGATTTATTTTAAATAATTTATTAGTAT
*
16769 GGTTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTAT
16800 GGATTGATTTATTTT-AA-AA--TA-T-G-A-
1 -GATTGATTTATTTTAAATAATTTATTAGTAT
16824 -ATTGATTTATTTTAAA-A---TA-T-G---
1 GATTGATTTATTTTAAATAATTTATTAGTAT
16845 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTAT
16876 GGATTGATTTATTTT-AA-AA--TA-T-G---
1 -GATTGATTTATTTTAAATAATTTATTAGTAT
16899 GATTGATTTATTTTAAA--A--TA-T-G---
1 GATTGATTTATTTTAAATAATTTATTAGTAT
*
16921 GATTGATTTATTTTAAATAATTTATTTGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTAT
*
16952 GGATTGATTTATTTTAAAATATAGATTGATT--TAT
1 -GATTGATTTATTTT--AA-ATA-ATTTATTAGTAT
* * * * ** * *
16986 TATTGTAGTTGTATGGATTGATTTGTTT-TAAAATAT
1 GATTG-A-TT-TAT--TTTAAATAATTTAT-TAGTAT
17022 GGATTGATTTATTTT-AA-AA--TA-T-G---
1 -GATTGATTTATTTTAAATAATTTATTAGTAT
17045 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTAT
17076 GGATTGATTTATTTT-AA-AA--TA-T-G-A-
1 -GATTGATTTATTTTAAATAATTTATTAGTAT
17100 -ATTGATTTATTTTAAA-A---TA-T-G---
1 GATTGATTTATTTTAAATAATTTATTAGTAT
17121 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTAT
*
17152 GGATTGATTTATTTTAAATAATTTATTTGTAT
1 -GATTGATTTATTTTAAATAATTTATTAGTAT
17184 GGATTGATTTATTTTAAA
1 -GATTGATTTATTTTAAA
17202 ATATGGATTG
Statistics
Matches: 367, Mismatches: 19, Indels: 138
0.70 0.04 0.26
Matches are distributed among these distances:
22 129 0.35
23 14 0.04
24 5 0.01
25 2 0.01
26 14 0.04
27 9 0.02
28 14 0.04
30 8 0.02
31 9 0.02
32 119 0.32
33 5 0.01
34 11 0.03
35 8 0.02
36 14 0.04
37 4 0.01
38 2 0.01
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (31 bp):
GATTGATTTATTTTAAATAATTTATTAGTAT
Found at i:16774 original size:22 final size:22
Alignment explanation
Indices: 16747--17137 Score: 206
Period size: 22 Copynumber: 15.8 Consensus size: 22
16737 TATTAGTATA
16747 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
*
16769 GGTTGATTTATTTTAAATAATTTATTAG
1 GATTGATTTATTTT-AA-AA--TA-T-G
* * *
16797 TATGGATTGATTTATTTTAAAATATG
1 GATTGATTTA-TT---TTAAAATATG
*
16823 AATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
16845 GATTGATTTATTTTAAATAATTTATTAG
1 GATTGATTTATTTT-AA-AA--TA-T-G
* * *
16873 TATGGATTGATTTATTTTAAAATATG
1 GATTGATTTA-TT---TTAAAATATG
16899 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
16921 GATTGATTTATTTTAAATAATTTATTTG
1 GATTGATTTATTTT-AA-AA--TA--TG
* * * *
16949 TATGGATTGATTTATTTTAAAATATA
1 GATTGATTTA-TT---TTAAAATATG
***
16975 GATTGATTTATTATTGTAGTTGTATG
1 GATTGATTTA-T-TT-TA-AAATATG
*
17001 GATTGATTTGTTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
17023 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
17045 GATTGATTTATTTTAAATAATTTATTAG
1 GATTGATTTATTTT-AA-AA--TA-T-G
* * *
17073 TATGGATTGATTTATTTTAAAATATG
1 GATTGATTTA-TT---TTAAAATATG
*
17099 AATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
17121 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
17138 TAATTTATTA
Statistics
Matches: 288, Mismatches: 38, Indels: 86
0.70 0.09 0.21
Matches are distributed among these distances:
22 125 0.43
23 10 0.03
24 11 0.04
25 9 0.03
26 54 0.19
27 7 0.02
28 40 0.14
29 8 0.03
30 8 0.03
31 8 0.03
32 8 0.03
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATG
Found at i:16851 original size:76 final size:76
Alignment explanation
Indices: 16747--17382 Score: 716
Period size: 76 Copynumber: 8.2 Consensus size: 76
16737 TATTAGTATA
*
16747 GATTGATTTATTTTAAAATATGGGTTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
1 GATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
16812 TTTAAAATATG
66 TTTAAAATATG
*
16823 AATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
1 GATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
16888 TTTAAAATATG
66 TTTAAAATATG
*
16899 GATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTAT
1 GATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
*
16964 TTTAAAATATA
66 TTTAAAATATG
** * * * * * * *
16975 GATTGATTTATTATTGTAGT-TGTATGGATTGA-TTT--GT--TTTA-AAATATGGATTGATTTA
1 GATTGATTTATT-TTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA
17033 TTTTAAAATATG
65 TTTTAAAATATG
** ** * ** * * * *
17045 GATTGATTTATTTT-AAATAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGAATTGATT
1 GATTGATTTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATT
17107 TATTTTAAAATATG
63 TATTTTAAAATATG
*
17121 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGG
1 GATTGATTTA-TTT---TAA---A--A-TATGGATTGATTTATTTTAAATAATTTATTAGTATGG
17186 ATTGATTTATTTTAAAATATG
56 ATTGATTTATTTTAAAATATG
* ***
17207 GATTGATTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
1 GATTGA-T-TTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
*
17272 TATTTTAAAATATA
63 TATTTTAAAATATG
** *
17286 GATTGATTTATTATTGTAGTTATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
1 GATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
17351 TTATTTTAAAATATG
62 TTATTTTAAAATATG
17366 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
17383 TAATTTATTA
Statistics
Matches: 484, Mismatches: 48, Indels: 56
0.82 0.08 0.10
Matches are distributed among these distances:
68 2 0.00
69 2 0.00
70 41 0.08
71 5 0.01
72 6 0.01
73 1 0.00
74 1 0.00
75 3 0.01
76 210 0.43
77 12 0.02
78 4 0.01
79 64 0.13
80 72 0.15
81 1 0.00
84 6 0.01
85 10 0.02
86 37 0.08
87 4 0.01
88 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (76 bp):
GATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
TTTAAAATATG
Found at i:17193 original size:18 final size:18
Alignment explanation
Indices: 17140--17197 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
17130 ATTTTAAATA
*
17140 ATTTATTAGTATGGATTG
1 ATTTATTTGTATGGATTG
* *
17158 ATTTATTT-TA---AATA
1 ATTTATTTGTATGGATTG
17172 ATTTATTTGTATGGATTG
1 ATTTATTTGTATGGATTG
17190 ATTTATTT
1 ATTTATTT
17198 TAAAATATGG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 10 0.32
15 2 0.06
17 2 0.06
18 17 0.55
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
ATTTATTTGTATGGATTG
Found at i:17336 original size:80 final size:80
Alignment explanation
Indices: 17095--17377 Score: 435
Period size: 80 Copynumber: 3.5 Consensus size: 80
17085 TATTTTAAAA
*
17095 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGA
1 TATGAATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTTA-TATGGATTGA
*
17159 TTTATTTTAAATAATTTATTTG
59 TTTATTTTAAATAATTTATTAG
* *
17181 TATGGATTGATTTATTTTAAAATATGGATTGA-TTATTATTGTAGTTGTATGGATTGATTTATTT
1 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTATATGGATTGATTTATTT
17245 TAAATAATTTATTAG
66 TAAATAATTTATTAG
* *
17260 TATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTATATGGATTGATTTATTT
1 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTATATGGATTGATTTATTT
17325 TAAATAATTTATTAG
66 TAAATAATTTATTAG
17340 TATGAATTGATTTATTTTAAAATATGGATTGATTTATT
1 TATGAATTGATTTATTTTAAAATATGGATTGATTTATT
17378 TTAAATAATT
Statistics
Matches: 187, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
79 65 0.35
80 84 0.45
81 2 0.01
83 2 0.01
85 3 0.02
86 31 0.17
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTATATGGATTGATTTATTT
TAAATAATTTATTAG
Found at i:17365 original size:22 final size:22
Alignment explanation
Indices: 17340--17382 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
17330 AATTTATTAG
17340 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
17362 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
17383 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:17458 original size:31 final size:31
Alignment explanation
Indices: 17407--17465 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
17397 AGTTGTATGG
* * *
17407 ATTATTTAAATTTTAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
*
17438 ATTATTTAAATCTCATTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
17466 CTTTTAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:17506 original size:16 final size:16
Alignment explanation
Indices: 17485--17525 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
17475 TTAAAAAATC
17485 AGTTTATTTATATTTT
1 AGTTTATTTATATTTT
17501 AGTTTATTTATATTTT
1 AGTTTATTTATATTTT
*
17517 AGTTCATTT
1 AGTTTATTT
17526 TAGCAGTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (16 bp):
AGTTTATTTATATTTT
Found at i:19289 original size:15 final size:15
Alignment explanation
Indices: 19269--19299 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19259 CAGATTAATA
19269 TCTATTTTAGATAAC
1 TCTATTTTAGATAAC
19284 TCTATTTTAGATAAC
1 TCTATTTTAGATAAC
19299 T
1 T
19300 GTAAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.48
Consensus pattern (15 bp):
TCTATTTTAGATAAC
Found at i:20282 original size:41 final size:41
Alignment explanation
Indices: 20235--20337 Score: 115
Period size: 41 Copynumber: 2.5 Consensus size: 41
20225 ATTCGCGTTG
*
20235 CATTTCGCGTTGCGATAG-CTGAAAAT-TGCGTTGCGATTTTT
1 CATTTCGAGTTGCGATAGTCT-AAAATGT-CGTTGCGATTTTT
* *
20276 CATTTCGAGTTGCGATAGTCTACAATGTCGTTGCGATTTTC
1 CATTTCGAGTTGCGATAGTCTAAAATGTCGTTGCGATTTTT
*
20317 CAAATTC--GTTGCGATAGTCTA
1 C-ATTTCGAGTTGCGATAGTCTA
20338 CAGTTGTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 14 0.25
41 34 0.62
42 7 0.13
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (41 bp):
CATTTCGAGTTGCGATAGTCTAAAATGTCGTTGCGATTTTT
Found at i:20513 original size:5 final size:6
Alignment explanation
Indices: 20474--20510 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
20464 GACACGTATT
20474 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
20511 CGAGACGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.30, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:21055 original size:6 final size:6
Alignment explanation
Indices: 21019--21136 Score: 201
Period size: 6 Copynumber: 20.5 Consensus size: 6
21009 TCTCGTCTCG
21019 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
21062 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
21110 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
21137 AATACGTGTC
Statistics
Matches: 112, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 25 0.22
6 87 0.78
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:22570 original size:13 final size:13
Alignment explanation
Indices: 22552--22581 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22542 GCGATAAATG
22552 GTCAACGGGTCGC
1 GTCAACGGGTCGC
*
22565 GTCAACGGGTCGG
1 GTCAACGGGTCGC
22578 GTCA
1 GTCA
22582 GCCGGTTTAG
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:0.17, C:0.27, G:0.40, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGC
Found at i:23015 original size:22 final size:22
Alignment explanation
Indices: 22987--23061 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
22977 AATTTGGAAA
22987 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
23009 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
23031 ATCGCAACGATAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
23053 ATCGCAACG
1 ATCGCAACG
23062 CGAACTGGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:23700 original size:23 final size:23
Alignment explanation
Indices: 23670--23716 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
23660 AGATTAATAA
23670 TTTTTCTACTAAAATTAAAACAT
1 TTTTTCTACTAAAATTAAAACAT
23693 TTTTTCTACTAAAATTAAAACAT
1 TTTTTCTACTAAAATTAAAACAT
23716 T
1 T
23717 AAACTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTTTCTACTAAAATTAAAACAT
Found at i:26511 original size:30 final size:30
Alignment explanation
Indices: 26477--26533 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
26467 CACTATTGTA
*
26477 CTTCTTTTTTATTTATTTCTCAAGTGTGTT
1 CTTCTATTTTATTTATTTCTCAAGTGTGTT
26507 CTTCTATTTTATTTATTTCTCAAGTGT
1 CTTCTATTTTATTTATTTCTCAAGTGT
26534 TTTTATTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (30 bp):
CTTCTATTTTATTTATTTCTCAAGTGTGTT
Found at i:26540 original size:26 final size:29
Alignment explanation
Indices: 26477--26541 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
26467 CACTATTGTA
*
26477 CTTCTTTTTTATTTATTTCTCAAGTGTGTT
1 CTTCTATTTTATTTATTTCTCAAG-GTGTT
26507 CTTCTATTTTATTTATTTCTCAA-GTGTT
1 CTTCTATTTTATTTATTTCTCAAGGTGTT
26535 -TT-TATTT
1 CTTCTATTT
26542 GCTCTAGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.15
27 2 0.06
28 5 0.15
30 22 0.65
ACGTcount: A:0.15, C:0.12, G:0.08, T:0.65
Consensus pattern (29 bp):
CTTCTATTTTATTTATTTCTCAAGGTGTT
Found at i:30900 original size:23 final size:23
Alignment explanation
Indices: 30870--30950 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
30860 ATTATGCCCA
*
30870 TGTTGCACGTTTATCTCTG-CTT
1 TGTTGCACGTTTATCTATGCCTT
* *
30892 GTGTTGCACGTTTATATATGTCTT
1 -TGTTGCACGTTTATCTATGCCTT
*
30916 TG-TGACACGTTTATCTTTGCCTT
1 TGTTG-CACGTTTATCTATGCCTT
*
30939 TGTGGCACGTTT
1 TGTTGCACGTTT
30951 TTCAATTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
22 2 0.04
23 43 0.88
24 4 0.08
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (23 bp):
TGTTGCACGTTTATCTATGCCTT
Found at i:31790 original size:35 final size:35
Alignment explanation
Indices: 31744--31867 Score: 185
Period size: 35 Copynumber: 3.5 Consensus size: 35
31734 TCTGTCATCG
31744 AGAATCGAAAGTGTTATGCCTCTTTTCGTTCTACT
1 AGAATCGAAAGTGTTATGCCTCTTTTCGTTCTACT
*
31779 AGAATCGAAAGTGATATGCCTCTTTTCGTTCTACT
1 AGAATCGAAAGTGTTATGCCTCTTTTCGTTCTACT
* *
31814 AGAATCGAAAGTGCTATACCTCTTTTCGTTCTACT
1 AGAATCGAAAGTGTTATGCCTCTTTTCGTTCTACT
** * *
31849 CTAATCAAAAGTGTGATGC
1 AGAATCGAAAGTGTTATGC
31868 TTTCTTCTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 80 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (35 bp):
AGAATCGAAAGTGTTATGCCTCTTTTCGTTCTACT
Found at i:31930 original size:42 final size:42
Alignment explanation
Indices: 31851--31945 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
31841 GTTCTACTCT
* * * *
31851 AATCAAAAGTGTGATGCTTTCTTCTGTTATACATTAGACGAG
1 AATCGAAAGTGTGATCCTTCCTTCCGTTATACATTAGACGAG
* * *
31893 AATCGAAAGTGTGATCCTTCCTTCCGTTCTACTTTAGATGAG
1 AATCGAAAGTGTGATCCTTCCTTCCGTTATACATTAGACGAG
*
31935 AATTGAAAGTG
1 AATCGAAAGTG
31946 CTATGCCTCC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (42 bp):
AATCGAAAGTGTGATCCTTCCTTCCGTTATACATTAGACGAG
Found at i:31957 original size:42 final size:42
Alignment explanation
Indices: 31851--31968 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
31841 GTTCTACTCT
* * * * *
31851 AATCAAAAGTGTGATGCTTTCTTCTGTT-ATACATTAGACGAG
1 AATCGAAAGTGTGATCCTTCCTTCCGTTCA-ACTTTAGACGAG
* *
31893 AATCGAAAGTGTGATCCTTCCTTCCGTTCTACTTTAGATGAG
1 AATCGAAAGTGTGATCCTTCCTTCCGTTCAACTTTAGACGAG
* *
31935 AATTGAAAGTGCT-ATGCC-TCCTTTCGTTCAACTT
1 AATCGAAAGTG-TGAT-CCTTCCTTCCGTTCAACTT
31969 GAATCGAAAG
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
42 60 0.95
43 3 0.05
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (42 bp):
AATCGAAAGTGTGATCCTTCCTTCCGTTCAACTTTAGACGAG
Found at i:35555 original size:35 final size:35
Alignment explanation
Indices: 35507--35621 Score: 140
Period size: 35 Copynumber: 3.3 Consensus size: 35
35497 CAAAACAGTC
* *
35507 TTCAATTTCATTCTAAACCCCAAATTATAAAGTAA
1 TTCAATTTAATTCTAAACCCCAAATTATAAAATAA
* * **
35542 TTCAATTTTATTCTAAACCCTAAATTCCAAAATAA
1 TTCAATTTAATTCTAAACCCCAAATTATAAAATAA
* * * *
35577 TTCAATTAAATTCTAAATCCCAAATTTTAAAATAC
1 TTCAATTTAATTCTAAACCCCAAATTATAAAATAA
35612 TTCAATTTAA
1 TTCAATTTAA
35622 GGTTTAGAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.43, C:0.18, G:0.01, T:0.37
Consensus pattern (35 bp):
TTCAATTTAATTCTAAACCCCAAATTATAAAATAA
Found at i:35661 original size:35 final size:35
Alignment explanation
Indices: 35615--35689 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
35605 AAAATACTTC
* * *
35615 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
*
35650 AATTTAGGGTTTAAAATGAAATTGAATTACTTTGG
1 AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
35685 AATTT
1 AATTT
35690 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
Found at i:35693 original size:24 final size:24
Alignment explanation
Indices: 35666--35737 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
35656 GGGTTTAAAA
35666 TGAAATTGAATTACTTTGGAATTT
1 TGAAATTGAATTACTTTGGAATTT
*
35690 TGAACA-TGAATTTACTATTTAGAA---
1 TGAA-ATTGAA-TTAC--TTTGGAATTT
*
35714 TAAAATTGAATTACTTTGGAATTT
1 TGAAATTGAATTACTTTGGAATTT
35738 GGGGTTTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 16
0.66 0.05 0.29
Matches are distributed among these distances:
21 6 0.16
23 5 0.14
24 15 0.41
25 5 0.14
27 6 0.16
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.43
Consensus pattern (24 bp):
TGAAATTGAATTACTTTGGAATTT
Found at i:35940 original size:29 final size:29
Alignment explanation
Indices: 35888--35947 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
35878 GCAAACGGAA
* * *
35888 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAAAGTTGGGGGACTGTAATGCAAGCTT
35917 TAAAAGTTGGGGGACT-TAAATGCAAGCTT
1 TAAAAGTTGGGGGACTGT-AATGCAAGCTT
35946 TA
1 TA
35948 GAAATGTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.33
Consensus pattern (29 bp):
TAAAAGTTGGGGGACTGTAATGCAAGCTT
Found at i:38542 original size:2 final size:2
Alignment explanation
Indices: 38535--38583 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
38525 CTACAGGGAT
38535 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38577 TA TA TA T
1 TA TA TA T
38584 TGAAAATTGA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39529 original size:35 final size:35
Alignment explanation
Indices: 39472--39666 Score: 219
Period size: 35 Copynumber: 5.5 Consensus size: 35
39462 TAGTAAACCA
* * * * *
39472 TCCGTTCTAGTTGAATCAAAAGTGCGGTGCCTCCT
1 TCCGTTCGACTTGAATCGAAAGTGCGATGCTTCCT
** * *
39507 TTTGTTCGACTTGAATCGAAAGTGCGGTGTTTCCT
1 TCCGTTCGACTTGAATCGAAAGTGCGATGCTTCCT
*
39542 TCCGTTCGACTTGAATCGAAAGTGTGATGCTTCCT
1 TCCGTTCGACTTGAATCGAAAGTGCGATGCTTCCT
* * *
39577 TCCGTTTGACTTGAATCAAAAGTGCCAATGCTTCCT
1 TCCGTTCGACTTGAATCGAAAGTG-CGATGCTTCCT
* * *
39613 TCCGTTCAACTTGAATCGAAAGTGCGATTCCTCCT
1 TCCGTTCGACTTGAATCGAAAGTGCGATGCTTCCT
* *
39648 TCCGTTTGACTTAAATCGA
1 TCCGTTCGACTTGAATCGA
39667 TGAAAACTTT
Statistics
Matches: 134, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
35 104 0.78
36 30 0.22
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.34
Consensus pattern (35 bp):
TCCGTTCGACTTGAATCGAAAGTGCGATGCTTCCT
Found at i:39635 original size:71 final size:70
Alignment explanation
Indices: 39472--39664 Score: 233
Period size: 71 Copynumber: 2.7 Consensus size: 70
39462 TAGTAAACCA
* * * * ** * * ** *
39472 TCCGTTCTAGTTGAATCAAAAGTGCGGTGCCTCCTTTTGTTCGACTTGAATCGAAAGTGCGGTGT
1 TCCGTTCAACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTTGACTTGAATCAAAAGTGCAATGC
39537 TTCCT
66 TTCCT
* * *
39542 TCCGTTCGACTTGAATCGAAAGTGTGATGCTTCCTTCCGTTTGACTTGAATCAAAAGTGCCAATG
1 TCCGTTCAACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTTGACTTGAATCAAAAGTG-CAATG
39607 CTTCCT
65 CTTCCT
* *
39613 TCCGTTCAACTTGAATCGAAAGTGCGATTCCTCCTTCCGTTTGACTTAAATC
1 TCCGTTCAACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTTGACTTGAATC
39665 GATGAAAACT
Statistics
Matches: 104, Mismatches: 18, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
70 49 0.47
71 55 0.53
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (70 bp):
TCCGTTCAACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTTGACTTGAATCAAAAGTGCAATGC
TTCCT
Found at i:41246 original size:26 final size:25
Alignment explanation
Indices: 41216--41271 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
41206 TTATCATTTT
* * *
41216 AATTATTATTATTTTATTATTAATA
1 AATTAGTATTATATTATCATTAATA
41241 ATATTAGTATTATATTATCATTAATA
1 A-ATTAGTATTATATTATCATTAATA
41267 AATTA
1 AATTA
41272 CAAATACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
AATTAGTATTATATTATCATTAATA
Found at i:41265 original size:23 final size:23
Alignment explanation
Indices: 41205--41266 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
41195 GATCCATTTC
* *
41205 ATTATCATTTTAATTATTATTATTTT
1 ATTATCA--TTAA-TATTAGTATTAT
* *
41231 ATTATTAATAATATTAGTATTAT
1 ATTATCATTAATATTAGTATTAT
41254 ATTATCATTAATA
1 ATTATCATTAATA
41267 AATTACAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 21 0.70
24 3 0.10
26 6 0.20
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTATCATTAATATTAGTATTAT
Found at i:42608 original size:15 final size:17
Alignment explanation
Indices: 42588--42620 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42578 TAAAATACTA
42588 TATTT-AATT-TATTTT
1 TATTTAAATTATATTTT
42603 TATTTAAATTATATTTT
1 TATTTAAATTATATTTT
42620 T
1 T
42621 TAAGAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 4 0.25
17 7 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTAAATTATATTTT
Found at i:42778 original size:148 final size:147
Alignment explanation
Indices: 42500--42771 Score: 377
Period size: 148 Copynumber: 1.8 Consensus size: 147
42490 TAAATAATAG
* *
42500 TATTTATTTATTTTTTAATATTAAAGAAATGAACTATCTTAAAGTAATTAGATGTCCTTTTCTAA
1 TATTTATTTATTTTTTAATATTAAAGAAATGAACTATCTTAAAGTAACTAGATGTCATTTTCTAA
* * *** * *
42565 TTTTTTAAATAAATAAAATACTATATTTAATTTATTTTTATTTAAATTATATTTTTTAAGAAAAA
66 TTTTTTAAAT-AATAAAATACTATATTTAATATATTTTTACTTAAATTATACGATTGAACAAAAA
42630 TTATCATATTCTTATTAA
130 TTATCATATTCTTATTAA
* *
42648 TATTTATTTATTTTTTAATATTAAAGAAATGAGCTTTCTTAAAGTAACTAGATGTCATTTTCTAA
1 TATTTATTTATTTTTTAATATTAAAGAAATGAACTATCTTAAAGTAACTAGATGTCATTTTCTAA
* * *
42713 TATTTTTAAAT-ATAAAA-ATTATTTTTAATATATTTTTCCTTAGAATTATACGATTGAAC
66 T-TTTTTAAATAATAAAATACTATATTTAATATATTTTTACTTA-AATTATACGATTGAAC
42772 CTAAAATAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
146 20 0.19
147 17 0.16
148 62 0.57
149 9 0.08
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (147 bp):
TATTTATTTATTTTTTAATATTAAAGAAATGAACTATCTTAAAGTAACTAGATGTCATTTTCTAA
TTTTTTAAATAATAAAATACTATATTTAATATATTTTTACTTAAATTATACGATTGAACAAAAAT
TATCATATTCTTATTAA
Found at i:44930 original size:6 final size:6
Alignment explanation
Indices: 44919--45001 Score: 53
Period size: 6 Copynumber: 13.0 Consensus size: 6
44909 TCCTTCGTTG
*
44919 CATTTT CATTTT CATTTT GCATTCTT -ACTTTT -ATGTTT GCATTTG CATTTTT
1 CATTTT CATTTT CATTTT -CATT-TT CA-TTTT CAT-TTT -CATTTT CA-TTTT
* * *
44971 ATATTTT CATTTT CATTTG CATTTT TATTTT
1 -CATTTT CATTTT CATTTT CATTTT CATTTT
45002 ATATTTTGCT
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
5 1 0.02
6 41 0.66
7 15 0.24
8 5 0.08
ACGTcount: A:0.17, C:0.13, G:0.06, T:0.64
Consensus pattern (6 bp):
CATTTT
Found at i:44963 original size:26 final size:23
Alignment explanation
Indices: 44920--45003 Score: 87
Period size: 26 Copynumber: 3.3 Consensus size: 23
44910 CCTTCGTTGC
*
44920 ATTTTCATTTTCATTTTGCATTCTT
1 ATTTT-ATTTTCA-TTTGCATTTTT
44945 ACTTTTATGTTTGCATTTGCATTTTTAT
1 A-TTTTAT-TTT-CATTTGCA-TTTT-T
44973 ATTTTCATTTTCATTTGCATTTTT
1 ATTTT-ATTTTCATTTGCATTTTT
44997 ATTTTAT
1 ATTTTAT
45004 ATTTTGCTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
23 2 0.04
24 6 0.12
25 7 0.13
26 21 0.40
27 12 0.23
28 4 0.08
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (23 bp):
ATTTTATTTTCATTTGCATTTTT
Found at i:44970 original size:20 final size:19
Alignment explanation
Indices: 44916--44988 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
44906 AACTCCTTCG
*
44916 TTGCATTTTCATTTTCATT
1 TTGCATTTTCATTTTTATT
*
44935 TTGCATTCTT-ACTTTTATGT
1 TTGCATT-TTCATTTTTAT-T
*
44955 TTGCATTTGCATTTTTATAT
1 TTGCATTTTCATTTTTAT-T
*
44975 TTTCATTTTCATTT
1 TTGCATTTTCATTT
44989 GCATTTTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 14 0.32
20 30 0.68
ACGTcount: A:0.16, C:0.14, G:0.07, T:0.63
Consensus pattern (19 bp):
TTGCATTTTCATTTTTATT
Found at i:47045 original size:3 final size:3
Alignment explanation
Indices: 47032--47089 Score: 98
Period size: 3 Copynumber: 19.0 Consensus size: 3
47022 GGGCATGCTC
47032 GAA GTAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
47078 AAA GAA GAA GAA
1 GAA GAA GAA GAA
47090 AAAAGAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:47090 original size:12 final size:12
Alignment explanation
Indices: 47032--47106 Score: 89
Period size: 12 Copynumber: 6.2 Consensus size: 12
47022 GGGCATGCTC
*
47032 GAAGTAAGAAGAA
1 GAAG-AAGAAAAA
*
47045 GAAGAAGAAGAA
1 GAAGAAGAAAAA
*
47057 GAAGAAGAAGAA
1 GAAGAAGAAAAA
47069 GAAGAAGAAAAA
1 GAAGAAGAAAAA
47081 GAAGAAGAAAAAA
1 GAAGAAG-AAAAA
*
47094 GAA-AAAAAAAA
1 GAAGAAGAAAAA
47105 GA
1 GA
47107 GGGATTGATT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
11 7 0.12
12 40 0.68
13 12 0.20
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:47803 original size:26 final size:27
Alignment explanation
Indices: 47774--47824 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
47764 TCATTTTAAT
* *
47774 TATTATTATTTTATTATTAA-AAATAA
1 TATTATTATATTATCATTAATAAATAA
47800 TATTATTATATTATCATTAATAAAT
1 TATTATTATATTATCATTAATAAAT
47825 TACAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
TATTATTATATTATCATTAATAAATAA
Found at i:48647 original size:30 final size:28
Alignment explanation
Indices: 48594--48658 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
48584 ATGAGGGAGT
* *
48594 TTAGAGATAAGTGAGAGCTTCTCTCTCC
1 TTAGAGAGAAGTAAGAGCTTCTCTCTCC
48622 TTAGAGAGAAGTAAGAGCTTCTCTCTCC
1 TTAGAGAGAAGTAAGAGCTTCTCTCTCC
*
48650 ATAGAGAGA
1 TTAGAGAGA
48659 GAAGCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (28 bp):
TTAGAGAGAAGTAAGAGCTTCTCTCTCC
Found at i:50810 original size:10 final size:11
Alignment explanation
Indices: 50795--50834 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
50785 AAGAAAGAAA
*
50795 GAAAAAAAAAG
1 GAAAATAAAAG
50806 G-AAA-AAAAG
1 GAAAATAAAAG
50815 GAAAATAAAA-
1 GAAAATAAAAG
50825 GAAAATAAAA
1 GAAAATAAAA
50835 CAGGTTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 6 0.22
10 16 0.59
11 5 0.19
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (11 bp):
GAAAATAAAAG
Found at i:50828 original size:19 final size:18
Alignment explanation
Indices: 50778--50829 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
50768 TCTTGGGACA
* *
50778 AAAATTAAAGAAAGAAAG
1 AAAATAAAAGAAAAAAAG
*
50796 AAAAAAAAAGGAAAAAAAGG
1 AAAATAAAA-GAAAAAAA-G
50816 AAAATAAAAGAAAA
1 AAAATAAAAGAAAA
50830 TAAAACAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 7 0.25
19 12 0.43
20 9 0.32
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (18 bp):
AAAATAAAAGAAAAAAAG
Found at i:51984 original size:38 final size:36
Alignment explanation
Indices: 51942--52166 Score: 206
Period size: 38 Copynumber: 6.0 Consensus size: 36
51932 AAAAAACCAT
51942 TTTTAAAAATATTTTTTAAAAACTATATAATATATATA
1 TTTTAAAAA-A-TTTTTAAAAACTATATAATATATATA
*
51980 TTTTAAAAACA--TTTAAAAACTATATATTATATATAA
1 TTTTAAAAA-ATTTTTAAAAACTATATAATATATAT-A
* *
52016 GTTTTCAAAAA-TTTCAAAAACTATATAATATATATA
1 -TTTTAAAAAATTTTTAAAAACTATATAATATATATA
* *
52052 TTTT-CAAAATGTTTTAAAAACTATATAATATATAAA
1 TTTTAAAAAAT-TTTTAAAAACTATATAATATATATA
* * *
52088 TATTTCAAAAATGTTTTAAAAACTATATAATTTATAAATG
1 T-TTTAAAAAAT-TTTTAAAAACTATATAA--TATATATA
* ** *
52128 TTTTCAAAAATGTTTTTCAAACCATATATATATATATA
1 TTTTAAAAAAT-TTTTAAAAACTATATA-ATATATATA
52166 T
1 T
52167 ATATATATAT
Statistics
Matches: 160, Mismatches: 17, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
34 4 0.03
35 26 0.16
36 27 0.17
37 32 0.20
38 40 0.25
39 24 0.15
40 7 0.04
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.43
Consensus pattern (36 bp):
TTTTAAAAAATTTTTAAAAACTATATAATATATATA
Found at i:52035 original size:37 final size:36
Alignment explanation
Indices: 51955--52165 Score: 216
Period size: 37 Copynumber: 5.7 Consensus size: 36
51945 TAAAAATATT
51955 TTTTAAAAACTATATAATATATAT-ATTTT-AAAAA
1 TTTTAAAAACTATATAATATATATAATTTTCAAAAA
* *
51989 CATTTAAAAACTATATATTATATATAAGTTTTCAAAAA
1 -TTTTAAAAACTATATAATATATATAA-TTTTCAAAAA
* *
52027 TTTCAAAAACTATATAATATATAT-ATTTTCAAAATG
1 TTTTAAAAACTATATAATATATATAATTTTCAAAA-A
52063 TTTTAAAAACTATATAATATATA-AATATTTCAAAAA
1 TTTTAAAAACTATATAATATATATAAT-TTTCAAAAA
*
52099 TGTTTTAAAAACTATATAATTTATA-AATGTTTTCAAAAA
1 --TTTTAAAAACTATATAATATATATAA--TTTTCAAAAA
** *
52138 TGTTTTTCAAACCATATATATATATATA
1 --TTTTAAAAACTATATA-ATATATATA
52166 TATATATATA
Statistics
Matches: 151, Mismatches: 13, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
35 31 0.21
36 26 0.17
37 33 0.22
38 29 0.19
39 24 0.16
40 7 0.05
41 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (36 bp):
TTTTAAAAACTATATAATATATATAATTTTCAAAAA
Found at i:52040 original size:72 final size:73
Alignment explanation
Indices: 51959--52137 Score: 229
Period size: 72 Copynumber: 2.4 Consensus size: 73
51949 AATATTTTTT
*
51959 AAAAACTATATAATATATATATTTT-AAAAACATTTAAAAACTATATATTATATATAAGT-TTTC
1 AAAAACTATATAATATATATATTTTCAAAAACATTTAAAAACTATATA--ATATATAAATATTTC
52022 AAAAA-TTTC
64 AAAAAGTTTC
***
52031 AAAAACTATATAATATATATATTTTCAAAATGTTTTAAAAACTATATAATATATAAATATTTCAA
1 AAAAACTATATAATATATATATTTTCAAAAACATTTAAAAACTATATAATATATAAATATTTCAA
*
52096 AAATGTTTT
66 AAA-GTTTC
* *
52105 AAAAACTATATAATTTATAAATGTTTTCAAAAA
1 AAAAACTATATAA--TATATATATTTTCAAAAA
52138 TGTTTTTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
71 9 0.10
72 34 0.37
73 19 0.20
74 16 0.17
76 15 0.16
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (73 bp):
AAAAACTATATAATATATATATTTTCAAAAACATTTAAAAACTATATAATATATAAATATTTCAA
AAAGTTTC
Found at i:52158 original size:2 final size:2
Alignment explanation
Indices: 52151--52252 Score: 72
Period size: 2 Copynumber: 52.5 Consensus size: 2
52141 TTTTCAAACC
* * * *
52151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA AA AT GT -T TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
52191 CAA AA ACT AT AT -T ACT AT AT AT AT AT AT AT A- AT A- AA AT A-
1 -AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
52230 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
52253 AACAAAATAA
Statistics
Matches: 84, Mismatches: 7, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
1 6 0.07
2 75 0.89
3 3 0.04
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (2 bp):
AT
Found at i:52210 original size:46 final size:47
Alignment explanation
Indices: 52133--52221 Score: 130
Period size: 46 Copynumber: 1.9 Consensus size: 47
52123 AAATGTTTTC
*
52133 AAAAATGTTTTTCAAACCATATATATATATATATATATATATATATT
1 AAAAATGTTTTTCAAAACATATATATATATATATATATATATATATT
52180 AAAAATG-TTTTCAAAA-ACTATAT-TACTATATATATATATATA
1 AAAAATGTTTTTCAAAACA-TATATATA-TATATATATATATATA
52222 ATAAAATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
45 3 0.08
46 29 0.74
47 7 0.18
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (47 bp):
AAAAATGTTTTTCAAAACATATATATATATATATATATATATATATT
Found at i:53005 original size:36 final size:36
Alignment explanation
Indices: 52918--53365 Score: 339
Period size: 36 Copynumber: 12.8 Consensus size: 36
52908 TTGTTTTGTG
* * *
52918 TGTTTTAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAATT
* * *
52955 TATTTCAAGGGAAACTGTCTTAAGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
*
52991 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAATT
* * * * *
53028 AGTTCCAAAAGAAACTGTCTCAAGGGAGAATAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
* *
53064 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGAAAAAATT
* * * *
53093 TCTTTCAAGGGAAACTTTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
*
53129 TGTTTCTAG-GTAAACTGTCTCAAGAGAG--AAAATT
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGAAAAAATT
*
53163 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAATT
* * * * **
53200 AG-TTCTAAAAGAAATTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGAAAAAATT
* *
53236 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGAAAAAATT
* * *
53265 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
* *
53301 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
*
53337 TGTTTAAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA
53366 TAACTTTGTT
Statistics
Matches: 329, Mismatches: 50, Indels: 65
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.01
29 31 0.09
30 5 0.02
31 2 0.01
32 4 0.01
33 4 0.01
34 31 0.09
35 7 0.02
36 153 0.47
37 88 0.27
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
Found at i:53190 original size:17 final size:17
Alignment explanation
Indices: 53140--53191 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
53130 GTTTCTAGGT
53140 AAACTGTCTCAAGAGAG
1 AAACTGTCTCAAGAGAG
* *
53157 AAAATTTGTTTC-A-AGAG
1 -AAA-CTGTCTCAAGAGAG
53174 AAACTGTCTCAAGAGAG
1 AAACTGTCTCAAGAGAG
53191 A
1 A
53192 CAAAACTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
15 5 0.19
16 4 0.15
17 9 0.33
18 4 0.15
19 5 0.19
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.23
Consensus pattern (17 bp):
AAACTGTCTCAAGAGAG
Found at i:53224 original size:172 final size:173
Alignment explanation
Indices: 52928--53365 Score: 709
Period size: 172 Copynumber: 2.5 Consensus size: 173
52918 TGTTTTAAGA
* * *
52928 GAAATTGTCTCAAGAGAGACAAAACTTTATTTCAAGGGAAACTGTCTTAAGAGAGAAAAAATTTG
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAG-AAAAATTTG
52993 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGAA
64 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGAA
* *
53058 TAAATTTGTTTCAA-GGAAAACATATTCAAAGATTTTCTTTCAAGG
129 GAAATTTGTTT-AATGGAAAACATATTCAAAGATTTTATTTCAAGG
* * *
53103 GAAACTTTCTCAAGAGAGACAAAATTTGTTTCTAGGTAAACTGTCTCAAGAGAG-AAAATTTGTT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAATTTGTT
* * *
53167 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAATTGTCTCAAGGGAGACGA
66 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGAAGA
*
53232 AATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAAGG
131 AATTTGTTTAATGGAAAACATATTCAAAGATTTTATTTCAAGG
53275 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA-AAAATTTGT
*
53340 TTAAAGAGAAACTGTCTCAAGAGAGA
65 TTCAAGAGAAACTGTCTCAAGAGAGA
53366 TAACTTTGTT
Statistics
Matches: 244, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
171 2 0.01
172 160 0.66
174 60 0.25
175 22 0.09
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (173 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAATTTGTT
TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGAAGA
AATTTGTTTAATGGAAAACATATTCAAAGATTTTATTTCAAGG
Found at i:54867 original size:88 final size:88
Alignment explanation
Indices: 54718--54897 Score: 279
Period size: 88 Copynumber: 2.0 Consensus size: 88
54708 ATTGTATAGA
* * * *
54718 TATTATAACCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTT
1 TATTATAACCACCTTTATCAGGCTAACTGAATATTATCCATAAAGCCAGAGCGTTTAACCAATTG
54783 CTCTAGAGGGACAACTCAAGCTT
66 CTCTAGAGGGACAACTCAAGCTT
* * * *
54806 TATTATAATCACCTTTATCAGGCTAACTGAATCTTATCCATAAAGTCAGAGTGTTTAACCAATTG
1 TATTATAACCACCTTTATCAGGCTAACTGAATATTATCCATAAAGCCAGAGCGTTTAACCAATTG
*
54871 CTTTAGAGGGACAACTCAAGCTT
66 CTCTAGAGGGACAACTCAAGCTT
54894 TATT
1 TATT
54898 GTATATATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 83 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (88 bp):
TATTATAACCACCTTTATCAGGCTAACTGAATATTATCCATAAAGCCAGAGCGTTTAACCAATTG
CTCTAGAGGGACAACTCAAGCTT
Found at i:57766 original size:20 final size:20
Alignment explanation
Indices: 57725--57766 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
57715 ACAAACAAAC
* *
57725 AATAAATAAGCAAATAAGTA
1 AATAAATAAGCAAAAAAATA
57745 AATAAATAAG-AATAAAAATA
1 AATAAATAAGCAA-AAAAATA
57765 AA
1 AA
57767 ACAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (20 bp):
AATAAATAAGCAAAAAAATA
Found at i:59081 original size:12 final size:12
Alignment explanation
Indices: 59038--59080 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
59028 TATATAATAT
59038 ATATTTTAAAAA
1 ATATTTTAAAAA
59050 ATA-TTTAAAAA
1 ATATTTTAAAAA
* *
59061 ACCATTTTTAAAA
1 A-TATTTTAAAAA
59074 ATATTTT
1 ATATTTT
59081 TTAAAAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 9 0.35
12 9 0.35
13 8 0.31
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATTTTAAAAA
Found at i:59200 original size:41 final size:39
Alignment explanation
Indices: 59134--59253 Score: 117
Period size: 39 Copynumber: 3.2 Consensus size: 39
59124 TATATATAAG
* **
59134 TTTTC-AAAA-ATTTCAAAAACTATA---TATATATCTA
1 TTTTCAAAAATATTTTAAAAACTATAGAATATATAAATA
* *
59168 TTTTC-AAAATGTTTTTAAAAACTATAGAATATATAAATG
1 TTTTCAAAAAT-ATTTTAAAAACTATAGAATATATAAATA
* * *
59207 TTTTCAAAAATATTTTAAAAACTATATAATAAATAAATG
1 TTTTCAAAAATATTTTAAAAACTATAGAATATATAAATA
59246 TTTTCAAA
1 TTTTCAAA
59254 CCATATATTA
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
34 9 0.12
36 13 0.18
39 45 0.62
40 5 0.07
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (39 bp):
TTTTCAAAAATATTTTAAAAACTATAGAATATATAAATA
Found at i:59272 original size:39 final size:38
Alignment explanation
Indices: 59190--59307 Score: 114
Period size: 39 Copynumber: 3.1 Consensus size: 38
59180 TTTTAAAAAC
* * * * *
59190 TATAGAATATATAAATGTTTTCAAAAATATTTTAAAAA
1 TATATAATAAATAAATGTTTTCAAAAATATATTATATA
*
59228 CTATATAATAAATAAATGTTTTCAAACCATATATTATATA
1 -TATATAATAAATAAATGTTTTCAAA-AATATATTATATA
* *
59268 TATAT-TTTAA-AAATGTTTTCAAAAACTATATTACTATA
1 TATATAATAAATAAATGTTTTCAAAAA-TATATTA-TATA
59306 TA
1 TA
59308 CATGCATACA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
36 1 0.01
37 20 0.30
38 9 0.13
39 28 0.42
40 9 0.13
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (38 bp):
TATATAATAAATAAATGTTTTCAAAAATATATTATATA
Found at i:59329 original size:4 final size:4
Alignment explanation
Indices: 59305--59348 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
59295 ATATTACTAT
* *
59305 ATAC ATGC ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
59349 CCCCCACCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:59375 original size:2 final size:2
Alignment explanation
Indices: 59368--59770 Score: 783
Period size: 2 Copynumber: 202.5 Consensus size: 2
59358 ACCCACCACC
59368 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
59410 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C- CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
59451 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
59493 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
*
59535 C- CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA AA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
59576 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
59618 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
59660 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
59702 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
59744 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
59771 CTACACCTAC
Statistics
Matches: 397, Mismatches: 2, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
1 2 0.01
2 395 0.99
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:59801 original size:4 final size:4
Alignment explanation
Indices: 59782--60143 Score: 625
Period size: 4 Copynumber: 90.5 Consensus size: 4
59772 TACACCTACC
*
59782 TACA TACA TACC TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
59830 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
59878 TACA TACA TACA TACA TACA TACA TACA TACA TACC TACC TACA TACC
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * * *
59926 TACC TACC TACA TACC TACC TACA TACC TACC TACA TACA TACC TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
59974 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
60022 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
60070 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
60118 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
60144 TATAAATAAC
Statistics
Matches: 346, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 346 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:63013 original size:18 final size:18
Alignment explanation
Indices: 62986--63024 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
62976 TATATCATGA
*
62986 AAATTAGCGGTGTTTTTT
1 AAATTAGCGGTGTTTGTT
*
63004 AAATTCGCGGTGTTTGTT
1 AAATTAGCGGTGTTTGTT
63022 AAA
1 AAA
63025 AAAAACCGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.44
Consensus pattern (18 bp):
AAATTAGCGGTGTTTGTT
Found at i:63912 original size:2 final size:2
Alignment explanation
Indices: 63905--63944 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
63895 GTATTTTTAA
63905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63945 TTTATGCAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64390 original size:13 final size:13
Alignment explanation
Indices: 64360--64384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64350 TCTATGACAC
64360 GCATTTATGACGT
1 GCATTTATGACGT
64373 GCATTTATGACG
1 GCATTTATGACG
64385 CTCATTGTGC
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:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (13 bp):
GCATTTATGACGT
Found at i:64555 original size:2 final size:2
Alignment explanation
Indices: 64548--64574 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64538 TTTCGTCAAT
64548 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
64575 TGTAGATTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.