Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008252.1 Hibiscus syriacus cultivar Beakdansim tig00110904_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: 2928487
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 13
Found at i:1241 original size:52 final size:51
Alignment explanation
Indices: 1183--1282 Score: 116
Period size: 52 Copynumber: 1.9 Consensus size: 51
1173 GAAATAGAGA
*
1183 AAATTAA-ATAA-AA-TGAATAAAATAAAATAAAGACAAAGAAAAGAATAATAAT
1 AAATTAACATAACAAGTAAATAAAAT-AAA-AAAGA-AAA-AAAAGAATAATAAT
*
1235 AAATTAACGATAACAAGTAAATTAAATAAAAAAGAAAAAAAAGAATAA
1 AAATTAAC-ATAACAAGTAAATAAAATAAAAAAGAAAAAAAAGAATAA
1283 ATAAAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
52 17 0.40
53 3 0.07
54 9 0.21
55 5 0.12
56 8 0.19
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (51 bp):
AAATTAACATAACAAGTAAATAAAATAAAAAAGAAAAAAAAGAATAATAAT
Found at i:1291 original size:17 final size:16
Alignment explanation
Indices: 1269--1307 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
1259 AATAAAAAAG
1269 AAAAAAAAGA-ATAAA
1 AAAAAAAAGACATAAA
1284 TAAAAAAAAGACATAAA
1 -AAAAAAAAGACATAAA
1301 AAAAAAA
1 AAAAAAA
1308 GTCATAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.85, C:0.03, G:0.05, T:0.08
Consensus pattern (16 bp):
AAAAAAAAGACATAAA
Found at i:1313 original size:15 final size:15
Alignment explanation
Indices: 1269--1315 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1259 AATAAAAAAG
1269 AAAAAAAAGA-ATAAA
1 AAAAAAAAGACAT-AA
1284 TAAAAAAAAGACATAA
1 -AAAAAAAAGACATAA
*
1300 AAAAAAAAGTCATAA
1 AAAAAAAAGACATAA
1315 A
1 A
1316 GCAAATGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 15 0.52
16 12 0.41
17 2 0.07
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (15 bp):
AAAAAAAAGACATAA
Found at i:2324 original size:16 final size:17
Alignment explanation
Indices: 2286--2328 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
2276 AAAATAAAGA
*
2286 AAATAAAGACAACAATCG
1 AAATAAA-AAAACAATCG
2304 AAATAAAAAAACAAT-G
1 AAATAAAAAAACAATCG
2320 AAATAAAAA
1 AAATAAAAA
2329 CATGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.72, C:0.09, G:0.07, T:0.12
Consensus pattern (17 bp):
AAATAAAAAAACAATCG
Found at i:2610 original size:2 final size:2
Alignment explanation
Indices: 2603--2686 Score: 59
Period size: 2 Copynumber: 43.0 Consensus size: 2
2593 AAAATATTAA
* *
2603 AT AT AT AT AT AT AT AT ACT -T AT AT A- AG AT GAT A- AA AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT -AT AT AT AT AT AT
* * * * *
2644 AA AA AT AT AC AT AT AT AT AT AT AT AT AT AA AT A- AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2685 AT
1 AT
2687 TTAAATAAGT
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
1 4 0.06
2 59 0.89
3 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (2 bp):
AT
Found at i:2658 original size:45 final size:45
Alignment explanation
Indices: 2601--2691 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
2591 ATAAAATATT
* *
2601 AAATATATATATATATATACT-TATATAAGATGATA-AAATATATAA
1 AAATATACATATATATATA-TATATATAA-ATAATATAAATATATAA
*
2646 AAATATACATATATATATATATATATAAATAATATAAATATTTAA
1 AAATATACATATATATATATATATATAAATAATATAAATATATAA
2691 A
1 A
2692 TAAGTAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
44 6 0.15
45 35 0.85
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (45 bp):
AAATATACATATATATATATATATATAAATAATATAAATATATAA
Found at i:2691 original size:8 final size:8
Alignment explanation
Indices: 2594--2693 Score: 69
Period size: 8 Copynumber: 11.6 Consensus size: 8
2584 CGTATAAATA
2594 AAATAT-T
1 AAATATAT
2601 AAATATAT
1 AAATATAT
2609 ATATATATAT
1 A-A-ATATAT
**
2619 ACTTATAT
1 AAATATAT
2627 AAGATGATA-
1 AA-AT-ATAT
2636 AAATATAT
1 AAATATAT
*
2644 AAAAATAT
1 AAATATAT
2652 ACATATATAT
1 A-A-ATATAT
2662 ATATATATAT
1 A-A-ATATAT
2672 AAATAATAT
1 AAAT-ATAT
*
2681 AAATATTT
1 AAATATAT
2689 AAATA
1 AAATA
2694 AGTAAAAATA
Statistics
Matches: 76, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
7 9 0.12
8 28 0.37
9 14 0.18
10 25 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (8 bp):
AAATATAT
Found at i:2694 original size:17 final size:17
Alignment explanation
Indices: 2556--2694 Score: 71
Period size: 18 Copynumber: 8.4 Consensus size: 17
2546 AAAGAAAATC
2556 AAATAAT-TAAAATATAT
1 AAATAATAT-AAATATAT
* **
2573 AAAATAATAGACGTATA-
1 -AAATAATATAAATATAT
*
2590 AATAAAATATTAAATATAT
1 AA-ATAATA-TAAATATAT
* **
2609 ATATATATATACTTATAT
1 AAATA-ATATAAATATAT
*
2627 AAGATGATA-AAATATAT
1 AA-ATAATATAAATATAT
*
2644 AAA-AATATACATATAT
1 AAATAATATAAATATAT
2660 --AT-ATAT--ATATAT
1 AAATAATATAAATATAT
*
2672 AAATAATATAAATATTT
1 AAATAATATAAATATAT
2689 AAATAA
1 AAATAA
2695 GTAAAAATAA
Statistics
Matches: 90, Mismatches: 18, Indels: 27
0.67 0.13 0.20
Matches are distributed among these distances:
12 6 0.07
14 7 0.08
15 7 0.08
16 10 0.11
17 24 0.27
18 30 0.33
19 6 0.07
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATAATATAAATATAT
Found at i:8383 original size:75 final size:75
Alignment explanation
Indices: 8268--8452 Score: 293
Period size: 75 Copynumber: 2.5 Consensus size: 75
8258 TTTATTTAGT
* * *
8268 ATGGTATCGATACCCCCATATAGGGTACTGATACCCCTATGAACATTTTGGTT-TCGAGAAATAA
1 ATGGTACCGATACCCCC-TATAGGGTACCGATACCCCTATGAACATTTTGATTCT-GAGAAATAA
8332 CAGAATGCTCGG
64 CAGAATGCTCGG
8344 ATGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACATTTTGATTCTGAGAAATAACA
1 ATGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACATTTTGATTCTGAGAAATAACA
8409 GAATGCTCGG
66 GAATGCTCGG
*
8419 ATGGTACCGATACCCCCTAGTA-GGTATCGATACC
1 ATGGTACCGATACCCCCTA-TAGGGTACCGATACC
8453 ACCATGATAT
Statistics
Matches: 103, Mismatches: 4, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
75 84 0.82
76 19 0.18
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.26
Consensus pattern (75 bp):
ATGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACATTTTGATTCTGAGAAATAACA
GAATGCTCGG
Found at i:8449 original size:20 final size:23
Alignment explanation
Indices: 8419--8479 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 23
8409 GAATGCTCGG
*
8419 ATGGTACCGATACCCCCTA-G-T
1 ATGGTATCGATACCCCCTATGAT
*
8440 A-GGTATCGATACCACC-ATGAT
1 ATGGTATCGATACCCCCTATGAT
8461 ATGGTATCGATACCCCCTA
1 ATGGTATCGATACCCCCTA
8480 CTTAGGTACC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.42
21 3 0.09
22 14 0.42
23 1 0.03
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (23 bp):
ATGGTATCGATACCCCCTATGAT
Found at i:15077 original size:15 final size:16
Alignment explanation
Indices: 15053--15082 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15043 AAAAATAGTA
15053 AAACATAAAATAAAAT
1 AAACATAAAATAAAAT
15069 AAACA-AAAATAAAA
1 AAACATAAAATAAAA
15083 AATAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (16 bp):
AAACATAAAATAAAAT
Found at i:15077 original size:22 final size:22
Alignment explanation
Indices: 15052--15095 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
15042 AAAAAATAGT
*
15052 AAAACATAAAATAAAATAAACA
1 AAAACAAAAAATAAAATAAACA
*
15074 AAAATAAAAAATAAAATAAACA
1 AAAACAAAAAATAAAATAAACA
15096 TGCATTAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.14
Consensus pattern (22 bp):
AAAACAAAAAATAAAATAAACA
Found at i:17357 original size:8 final size:8
Alignment explanation
Indices: 17344--17368 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17334 ATGAAATTTC
17344 TTTCTCCT
1 TTTCTCCT
17352 TTTCTCCT
1 TTTCTCCT
17360 TTTCTCCT
1 TTTCTCCT
17368 T
1 T
17369 CACACTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTCTCCT
Found at i:19821 original size:17 final size:17
Alignment explanation
Indices: 19801--19839 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
19791 ATTAAAGAGT
* *
19801 TAGTTAGATTAACGAAC
1 TAGTTAAATGAACGAAC
*
19818 TAGTTAAATGAATGAAC
1 TAGTTAAATGAACGAAC
19835 TAGTT
1 TAGTT
19840 TAATTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (17 bp):
TAGTTAAATGAACGAAC
Found at i:19918 original size:17 final size:18
Alignment explanation
Indices: 19846--19942 Score: 67
Period size: 17 Copynumber: 5.6 Consensus size: 18
19836 AGTTTAATTA
* * *
19846 AAATGAACTAACTTTATT
1 AAATGAACTAAATTCACT
* *
19864 GAATGAACTAAGATGCA-T
1 AAATGAACTAA-ATTCACT
* **
19882 AAATGAAGTAGCTT-ACT
1 AAATGAACTAAATTCACT
19899 AAATGAACTAAATTCA-T
1 AAATGAACTAAATTCACT
* *
19916 AAATGAACT-ACTTCCCT
1 AAATGAACTAAATTCACT
19933 AAATGAACTA
1 AAATGAACTA
19943 GAAACTTAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
16 5 0.08
17 33 0.55
18 20 0.33
19 2 0.03
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.29
Consensus pattern (18 bp):
AAATGAACTAAATTCACT
Found at i:19922 original size:34 final size:35
Alignment explanation
Indices: 19846--19942 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 35
19836 AGTTTAATTA
* * *
19846 AAATGAACTAACTTTATTGAATGAACTAAGATGCAT
1 AAATGAACT-ACTTCACTAAATGAACTAAGATGCAT
* *
19882 AAATGAAGTAGCTT-ACTAAATGAACTAA-ATTCAT
1 AAATGAACTA-CTTCACTAAATGAACTAAGATGCAT
*
19916 AAATGAACTACTTCCCTAAATGAACTA
1 AAATGAACTACTTCACTAAATGAACTA
19943 GAAACTTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
33 3 0.06
34 26 0.49
35 13 0.25
36 11 0.21
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.29
Consensus pattern (35 bp):
AAATGAACTACTTCACTAAATGAACTAAGATGCAT
Found at i:24010 original size:30 final size:30
Alignment explanation
Indices: 23974--24034 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
23964 CGCCATCGAT
23974 CATTTTTGAATTAGGCGGATCAGACACCTA
1 CATTTTTGAATTAGGCGGATCAGACACCTA
* *
24004 CATTTTTTAATTAGGCGGATCGGACACCTA
1 CATTTTTGAATTAGGCGGATCAGACACCTA
24034 C
1 C
24035 TTACCAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (30 bp):
CATTTTTGAATTAGGCGGATCAGACACCTA
Found at i:25663 original size:18 final size:18
Alignment explanation
Indices: 25640--25683 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
25630 AAAACAGAAC
*
25640 AAAATAAATAAGTAAAT-A
1 AAAATAAATAA-AAAATAA
*
25658 AAAATACATAAAAAATAA
1 AAAATAAATAAAAAATAA
25676 AAAATAAA
1 AAAATAAA
25684 ACAAAGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (18 bp):
AAAATAAATAAAAAATAA
Found at i:25697 original size:29 final size:29
Alignment explanation
Indices: 25640--25697 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
25630 AAAACAGAAC
* *
25640 AAAATAAATAAGTAAATAAAAATACATAA
1 AAAATAAATAAATAAATAAAAATAAATAA
25669 AAAATAAA-AAATAAA-ACAAAGATAAATAA
1 AAAATAAATAAATAAATA-AAA-ATAAATAA
25698 TAACAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 1 0.04
28 9 0.36
29 15 0.60
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.17
Consensus pattern (29 bp):
AAAATAAATAAATAAATAAAAATAAATAA
Found at i:26920 original size:37 final size:38
Alignment explanation
Indices: 26860--26933 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 38
26850 TGTTCTTTTT
* *
26860 TGAGTGATGATTCAGTGAGTGATTGCTTTTTCTTATCTG
1 TGAGTGATGATTCAGT-AGTGATTCCGTTTTCTTATCTG
*
26899 TGAGTGATGATTCAGT-TTGATTCCGTTTTCTTATC
1 TGAGTGATGATTCAGTAGTGATTCCGTTTTCTTATC
26934 ATCACGATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 16 0.50
39 16 0.50
ACGTcount: A:0.18, C:0.12, G:0.23, T:0.47
Consensus pattern (38 bp):
TGAGTGATGATTCAGTAGTGATTCCGTTTTCTTATCTG
Found at i:28689 original size:117 final size:122
Alignment explanation
Indices: 28556--28774 Score: 308
Period size: 123 Copynumber: 1.8 Consensus size: 122
28546 AACAAAAATA
*
28556 ATTTACATATTTTTATTATTATGAATATC-TA-TGAAGAAT-TT-T-CACAA-TGTAA-ACATTT
1 ATTTACATATTTTTATTATTATGAATATCTTAGT-AA-AATGTTATGCAAAATTGTAATACATTT
28614 TTACATAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
64 TTACATAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
* * * * *
28673 ATTTACATCTTTTTATTATTATGAATATCTTAGTTAAATGTTGATGTAAAATTTTAATATATTTT
1 ATTTACATATTTTTATTATTATGAATATCTTAGTAAAATGTT-ATGCAAAATTGTAATACATTTT
28738 TACATAAATTATGTAAAATTTAATATTAATTAAAATA
65 TACATAAATTATGTAAAATTTAATATTAATTAAAATA
28775 AAAATAATAC
Statistics
Matches: 88, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
117 31 0.35
118 5 0.06
119 1 0.01
120 1 0.01
121 3 0.03
122 4 0.05
123 43 0.49
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (122 bp):
ATTTACATATTTTTATTATTATGAATATCTTAGTAAAATGTTATGCAAAATTGTAATACATTTTT
ACATAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
Found at i:32281 original size:4 final size:4
Alignment explanation
Indices: 32272--32301 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
32262 TCATATGATC
32272 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
32302 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:37381 original size:18 final size:17
Alignment explanation
Indices: 37360--37393 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
37350 CATTTATTTT
37360 TATCAAGTAATTTAATTA
1 TATCAA-TAATTTAATTA
*
37378 TATCAATTATTTAATT
1 TATCAATAATTTAATT
37394 TTAAATAGAA
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:0.06, G:0.03, T:0.50
Consensus pattern (17 bp):
TATCAATAATTTAATTA
Found at i:37441 original size:29 final size:30
Alignment explanation
Indices: 37383--37441 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
37373 AATTATATCA
* *
37383 ATTATTTAATTTTAAATAGAATACTAAATT
1 ATTATATAATTTTAAATAGAAAACTAAATT
*
37413 ATTATATAA-TTTAAAT-GTAAAACTTAATT
1 ATTATATAATTTTAAATAG-AAAACTAAATT
37442 TATTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 1 0.04
29 16 0.64
30 8 0.32
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (30 bp):
ATTATATAATTTTAAATAGAAAACTAAATT
Found at i:48211 original size:61 final size:61
Alignment explanation
Indices: 48139--48258 Score: 231
Period size: 61 Copynumber: 2.0 Consensus size: 61
48129 TTTACCATAT
*
48139 ATTAATAAAAAAATAGTGAATAAATACTTAATTTAAATCTATAATATATATATATATATAC
1 ATTAATAAAAAAATAGTGAATAAATACTTAACTTAAATCTATAATATATATATATATATAC
48200 ATTAATAAAAAAATAGTGAATAAATACTTAACTTAAATCTATAATATATATATATATAT
1 ATTAATAAAAAAATAGTGAATAAATACTTAACTTAAATCTATAATATATATATATATAT
48259 TAGCTTTAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (61 bp):
ATTAATAAAAAAATAGTGAATAAATACTTAACTTAAATCTATAATATATATATATATATAC
Found at i:48347 original size:33 final size:32
Alignment explanation
Indices: 48310--48438 Score: 97
Period size: 32 Copynumber: 4.0 Consensus size: 32
48300 TTTTATTAAA
*
48310 TTAATTTAAAAATATTTTATTTTAATTTTAATT
1 TTAATTTAAAAATA-TATATTTTAATTTTAATT
*
48343 TTAATTTAAAAATATATATTTT-ATTTTTATCT
1 TTAATTTAAAAATATATATTTTAATTTTAAT-T
* * * *
48375 ATACTTTTAAAA-ATATATTTT-ATTATT-GTT
1 TTAATTTAAAAATATATATTTTAATT-TTAATT
* * *
48405 TTAACTTTTTAAAGTATATATTTT-ATCTTAATT
1 TTAA--TTTAAAAATATATATTTTAATTTTAATT
48438 T
1 T
48439 ACTAAATATA
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
30 3 0.04
31 20 0.25
32 28 0.35
33 28 0.35
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (32 bp):
TTAATTTAAAAATATATATTTTAATTTTAATT
Found at i:48371 original size:32 final size:31
Alignment explanation
Indices: 48310--48430 Score: 109
Period size: 33 Copynumber: 3.8 Consensus size: 31
48300 TTTTATTAAA
* *
48310 TTAATTTAAAAATATTTTATTTTAATTTTAATT
1 TTAATTTAAAAATA-TATATTTT-ATTTTTATT
48343 TTAATTTAAAAATATATATTTTATTTTTATCT
1 TTAATTTAAAAATATATATTTTATTTTTAT-T
* * * * *
48375 ATACTTTTAAAA-ATATATTTTATTATTGTT
1 TTAATTTAAAAATATATATTTTATTTTTATT
* *
48405 TTAACTTTTTAAAGTATATATTTTAT
1 TTAA--TTTAAAAATATATATTTTAT
48431 CTTAATTTAC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
30 3 0.04
31 22 0.30
32 24 0.32
33 25 0.34
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (31 bp):
TTAATTTAAAAATATATATTTTATTTTTATT
Found at i:48500 original size:29 final size:29
Alignment explanation
Indices: 48458--48513 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
48448 ATTATAGGGT
* *
48458 AAAGTACATAAATGGTTCTTTGACTATCA
1 AAAGTACATAAATGGTCCTTCGACTATCA
48487 AAAGTTACA-AAATGGTCCTTCGACTAT
1 AAAG-TACATAAATGGTCCTTCGACTAT
48514 AGAATGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (29 bp):
AAAGTACATAAATGGTCCTTCGACTATCA
Found at i:49012 original size:20 final size:20
Alignment explanation
Indices: 48973--49023 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
48963 AACTTCAAAG
* *
48973 TATTTTAACA-TAAAATATA
1 TATTTTAAAATTAAAAAATA
48992 TATTTTAAAATTAAAAAATA
1 TATTTTAAAATTAAAAAATA
49012 T-TTTT-AAATTAA
1 TATTTTAAAATTAA
49024 GTTAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 7 0.24
19 13 0.45
20 9 0.31
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTTAAAATTAAAAAATA
Found at i:49014 original size:18 final size:20
Alignment explanation
Indices: 48973--49023 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
48963 AACTTCAAAG
*
48973 TATTTTAACA-TAAAATATA
1 TATTTTAAAATTAAAATATA
48992 TATTTTAAAATTAAAA-A-A
1 TATTTTAAAATTAAAATATA
*
49010 TATTTTTAAATTAA
1 TATTTTAAAATTAA
49024 GTTAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 14 0.48
19 10 0.34
20 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTTAAAATTAAAATATA
Found at i:54644 original size:19 final size:18
Alignment explanation
Indices: 54608--54647 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54598 AATGAAAACG
**
54608 TAATAAAAATATTTATTT
1 TAATAAAAATATAAATTT
54626 TAATAAAAATACTAAATTT
1 TAATAAAAATA-TAAATTT
54645 TAA
1 TAA
54648 AAACGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAAAAATATAAATTT
Found at i:56104 original size:18 final size:18
Alignment explanation
Indices: 56081--56120 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
56071 AATAAATTTC
56081 AAAATAAATACATTAT-AT
1 AAAATAAATA-ATTATCAT
56099 AAAATAAATAATTATCAT
1 AAAATAAATAATTATCAT
56117 AAAA
1 AAAA
56121 AATTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATAAATAATTATCAT
Found at i:57438 original size:20 final size:21
Alignment explanation
Indices: 57406--57445 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
57396 TGATTTTAAA
57406 AAAATTAAAAATTT-GATACT
1 AAAATTAAAAATTTAGATACT
57426 AAAA-TAAATAATTTAGATAC
1 AAAATTAAA-AATTTAGATAC
57446 CTAACACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
AAAATTAAAAATTTAGATACT
Found at i:58375 original size:2 final size:2
Alignment explanation
Indices: 58368--58406 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
58358 GTAGGTATTA
58368 AT AT AT AT AT AT AT AT AT AT A- 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
58407 GCAAAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58392 original size:21 final size:21
Alignment explanation
Indices: 58366--58406 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
58356 TTGTAGGTAT
58366 TAATATATATATATATATATA
1 TAATATATATATATATATATA
58387 TAATATATATATATATATAT
1 TAATATATATATATATATAT
58407 GCAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATATATATATATATATATA
Found at i:60263 original size:56 final size:53
Alignment explanation
Indices: 60181--60287 Score: 187
Period size: 56 Copynumber: 2.0 Consensus size: 53
60171 TTTTCGTTCG
60181 AGTCCTAAATTTATTTTACTTCGATATCGATCCCTATTTTACTTTCATTATCA
1 AGTCCTAAATTTATTTTACTTCGATATCGATCCCTATTTTACTTTCATTATCA
60234 AGTCCTAAATATTTATTTTTACTTCGATATCGATCCCTATTTTACTTTCATTAT
1 AGTCCT-AA-ATTTA-TTTTACTTCGATATCGATCCCTATTTTACTTTCATTAT
60288 TCAATTTAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
53 6 0.12
54 2 0.04
55 5 0.10
56 38 0.75
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.49
Consensus pattern (53 bp):
AGTCCTAAATTTATTTTACTTCGATATCGATCCCTATTTTACTTTCATTATCA
Found at i:61037 original size:17 final size:20
Alignment explanation
Indices: 61001--61044 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
60991 ATATGTATAG
61001 ATATATTTAAATTAACCAT-
1 ATATATTTAAATTAACCATA
*
61020 ATATATTTAAA-T-AGCATA
1 ATATATTTAAATTAACCATA
61038 ATATATT
1 ATATATT
61045 ATTTTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (20 bp):
ATATATTTAAATTAACCATA
Found at i:65618 original size:91 final size:91
Alignment explanation
Indices: 65463--65827 Score: 635
Period size: 91 Copynumber: 4.0 Consensus size: 91
65453 GCTCGTAAAA
* * *
65463 TGATAAGATTATATTCGAATCATATCATTTTAAAGATATTATGTAATCTCGATATCTTTTAAAAA
1 TGATAAGATTATATTTGAATCATATCATTTTAAAGATATAATGTAATCTCGATATCTTCTAAAAA
65528 TCGTCAAATATTATGGATGTCTTTTG
66 TCGTCAAATATTATGGATGTCTTTTG
*
65554 TGATAAGATTATATTTGAATCATATCATTTTAAAAATATAATGTAATCTCGATATCTTCTAAAAA
1 TGATAAGATTATATTTGAATCATATCATTTTAAAGATATAATGTAATCTCGATATCTTCTAAAAA
*
65619 TCATCAAATATTATGGATGTCTTTTG
66 TCGTCAAATATTATGGATGTCTTTTG
* *
65645 TGATAAGATTATATTTGAATCATATCATTTTAAAGATATAATATAATCTCGATATATTCTAAAAA
1 TGATAAGATTATATTTGAATCATATCATTTTAAAGATATAATGTAATCTCGATATCTTCTAAAAA
65710 TCGTCAAATATTATGGATGTCTTTTG
66 TCGTCAAATATTATGGATGTCTTTTG
* *
65736 TGATAAGATTATATTTAAATCATATCATTTTAAAGATATTATGTAATCTCGATATCTTCTAAAAA
1 TGATAAGATTATATTTGAATCATATCATTTTAAAGATATAATGTAATCTCGATATCTTCTAAAAA
65801 TCGTCAAATATTATGGATG--TTTTG
66 TCGTCAAATATTATGGATGTCTTTTG
65825 TGA
1 TGA
65828 CGTATTGTAG
Statistics
Matches: 261, Mismatches: 13, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
89 8 0.03
91 253 0.97
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.42
Consensus pattern (91 bp):
TGATAAGATTATATTTGAATCATATCATTTTAAAGATATAATGTAATCTCGATATCTTCTAAAAA
TCGTCAAATATTATGGATGTCTTTTG
Found at i:66626 original size:23 final size:24
Alignment explanation
Indices: 66600--66662 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
66590 GATGGATTTA
66600 ATCTTTGGTTTGTTTTGATTCAT-
1 ATCTTTGGTTTGTTTTGATTCATG
* **
66623 ATCTTTGCTGGGTTCTTGATTCATG
1 ATCTTTGGTTTGTT-TTGATTCATG
* *
66648 ATTTTTTGTTTGTTT
1 ATCTTTGGTTTGTTT
66663 GTTTGTATTT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
23 11 0.37
24 10 0.33
25 9 0.30
ACGTcount: A:0.11, C:0.10, G:0.19, T:0.60
Consensus pattern (24 bp):
ATCTTTGGTTTGTTTTGATTCATG
Found at i:69261 original size:4 final size:4
Alignment explanation
Indices: 69247--69281 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
69237 AATCATGCAA
69247 TTCT ATTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
69282 AATTGACATC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:77436 original size:12 final size:13
Alignment explanation
Indices: 77419--77457 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
77409 ATGTAGGAGT
*
77419 TTTTTCTT-TTTC
1 TTTTTCTTCTTTA
77431 TTTTTCTTCTTTA
1 TTTTTCTTCTTTA
77444 TTTTT-TTCTTTA
1 TTTTTCTTCTTTA
77456 TT
1 TT
77458 GCAACACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTCTTCTTTA
Found at i:88103 original size:50 final size:51
Alignment explanation
Indices: 88008--88109 Score: 118
Period size: 50 Copynumber: 2.0 Consensus size: 51
87998 AATGTTCAAG
* * * * *
88008 AAACTCGTTACGTTGAGGTGACGAGTTTCAATAAAACAT-TTTTTTTATTA
1 AAACTCGTCACGTCGAGGTGACAAGTTTCAATAAAACATAATTTTTAATTA
* *
88058 AAACTCGTCACGTCGAGGTTACAAG-TTCTAATAAAATATAATTTTTAATTA
1 AAACTCGTCACGTCGAGGTGACAAGTTTC-AATAAAACATAATTTTTAATTA
88109 A
1 A
88110 TTTTTATCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
49 3 0.07
50 30 0.70
51 10 0.23
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (51 bp):
AAACTCGTCACGTCGAGGTGACAAGTTTCAATAAAACATAATTTTTAATTA
Found at i:88349 original size:32 final size:33
Alignment explanation
Indices: 88313--88384 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 33
88303 AAACACATAT
88313 CGTAATTCATTTTGTTGTAAAAAATGAC-TTAA
1 CGTAATTCATTTTGTTGTAAAAAATGACTTTAA
88345 CGTAATTCATTTTGTTGTAAAAAATGACTTTTAA
1 CGTAATTCATTTTGTTGTAAAAAATGAC-TTTAA
88379 CGTAAT
1 CGTAAT
88385 CTGGTTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 28 0.74
34 10 0.26
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (33 bp):
CGTAATTCATTTTGTTGTAAAAAATGACTTTAA
Found at i:96068 original size:54 final size:54
Alignment explanation
Indices: 96052--96502 Score: 762
Period size: 54 Copynumber: 8.4 Consensus size: 54
96042 TAAATTCTGC
* * * *
96052 GAAATGCACACTTAGTGCCGAAACAGTTATTCATTCATATAGGATGAATTCTGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* ** *
96106 GAAATACACACTTAGTGCCGAAACAATTATTCATCTACATAGGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
*
96160 GAAATACACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* * *
96214 GAAATGAACACTTAGTGCCGAAACGGTTATTCATCCACCTAGGAT-AATTCAGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
96267 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
*
96321 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACCTAGGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
*
96375 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCTGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
96429 GAAATGCACACTTAGTGCC-AAACGGTTATTCATCCACATAGGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
96482 GAAATGCACACTTAGTGCCGA
1 GAAATGCACACTTAGTGCCGA
96503 TTTGGAAATC
Statistics
Matches: 375, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
53 102 0.27
54 273 0.73
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (54 bp):
GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
Found at i:96309 original size:161 final size:162
Alignment explanation
Indices: 96052--96502 Score: 780
Period size: 161 Copynumber: 2.8 Consensus size: 162
96042 TAAATTCTGC
* * * *
96052 GAAATGCACACTTAGTGCCGAAACAGTTATTCATTCATATAGGATGAATTCTGTGAAATACACAC
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACAC
** * *
96117 TTAGTGCCGAAACAATTATTCATCTACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAA
66 TTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
96182 ACGGTTATTCATCCACATAGGATGAATTCCGT
131 ACGGTTATTCATCCACATAGGATGAATTCCGT
* * *
96214 GAAATGAACACTTAGTGCCGAAACGGTTATTCATCCACCTAGGAT-AATTCAGTGAAATGCACAC
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACAC
96278 TTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
66 TTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
*
96343 ACGGTTATTCATCCACCTAGGATGAATTCCGT
131 ACGGTTATTCATCCACATAGGATGAATTCCGT
96375 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACAC
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACAC
96440 TTAGTGCC-AAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGA
66 TTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGA
96503 TTTGGAAATC
Statistics
Matches: 273, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
161 207 0.76
162 66 0.24
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (162 bp):
GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACAC
TTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
ACGGTTATTCATCCACATAGGATGAATTCCGT
Found at i:96423 original size:215 final size:215
Alignment explanation
Indices: 96052--96502 Score: 760
Period size: 215 Copynumber: 2.1 Consensus size: 215
96042 TAAATTCTGC
* * *
96052 GAAATGCACACTTAGTGCCGAAACAGTTATTCATTCATATAGGATGAATTCTGTGAAATACACAC
1 GAAATGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAATACACAC
*
96117 TTAGTGCCGAAACAATTATTCATCTACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAA
66 TTAGTGCCGAAACAATTATTCATCCACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAA
96182 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGAACACTTAGTGCCGAAACGGTTATTCA
131 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGAACACTTAGTGCC-AAACGGTTATTCA
*
96247 TCCACCTAGGAT-AATTCAGT
195 TCCACATAGGATGAATTCAGT
* *
96267 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC
1 GAAATGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAATACACAC
** * *
96332 TTAGTGCCGAAACGGTTATTCATCCACCTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
66 TTAGTGCCGAAACAATTATTCATCCACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAA
* *
96397 ACGGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGCCAAACGGTTATTCAT
131 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGAACACTTAGTGCCAAACGGTTATTCAT
*
96462 CCACATAGGATGAATTCCGT
196 CCACATAGGATGAATTCAGT
96482 GAAATGCACACTTAGTGCCGA
1 GAAATGCACACTTAGTGCCGA
96503 TTTGGAAATC
Statistics
Matches: 221, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
214 24 0.11
215 197 0.89
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (215 bp):
GAAATGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAATACACAC
TTAGTGCCGAAACAATTATTCATCCACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAA
ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGAACACTTAGTGCCAAACGGTTATTCAT
CCACATAGGATGAATTCAGT
Found at i:96908 original size:20 final size:20
Alignment explanation
Indices: 96883--96953 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
96873 TACTATGCTA
96883 TGGTATCGATACCTTCCCTT
1 TGGTATCGATACCTTCCCTT
*
96903 TGGTATCGATACCTTCCCAT
1 TGGTATCGATACCTTCCCTT
*
96923 TGGTATCGATA-CTCCCCTT
1 TGGTATCGATACCTTCCCTT
*
96942 TCGATATCGATA
1 T-GGTATCGATA
96954 TCGATTAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.15
20 39 0.85
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (20 bp):
TGGTATCGATACCTTCCCTT
Found at i:97825 original size:27 final size:26
Alignment explanation
Indices: 97794--97881 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 26
97784 TACATATATA
97794 GTTTATATAAATTATATATCAACTATT
1 GTTTATATAAATTATATAT-AACTATT
97821 GTTTATAGACTATACATTATATAT-A-TA--
1 GTTTAT--A-TA-A-ATTATATATAACTATT
97848 GTTTATATAAATTATATATAAACTATT
1 GTTTATATAAATTATATAT-AACTATT
*
97875 CTTTATA
1 GTTTATA
97882 AACTATAGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 20
0.70 0.01 0.28
Matches are distributed among these distances:
22 9 0.18
23 1 0.02
24 3 0.06
25 3 0.06
27 18 0.36
29 3 0.06
30 3 0.06
31 1 0.02
32 9 0.18
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (26 bp):
GTTTATATAAATTATATATAACTATT
Found at i:97851 original size:54 final size:55
Alignment explanation
Indices: 97787--97921 Score: 200
Period size: 54 Copynumber: 2.5 Consensus size: 55
97777 GTGTTTATAC
* * *
97787 ATATATAGTTTATATAAATTATATATCAACTATTGTTTATAGACTATACATT-AT
1 ATATATAGTTTATATAAATTATATATAAACTATTCTTTATAAACTATACATTAAT
**
97841 ATATATAGTTTATATAAATTATATATAAACTATTCTTTATAAACTATAGGTTACAT
1 ATATATAGTTTATATAAATTATATATAAACTATTCTTTATAAACTATACATTA-AT
*
97897 ATATATAGTTTATATAAACTATATA
1 ATATATAGTTTATATAAATTATATA
97922 GATTACATAT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
54 47 0.64
56 26 0.36
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (55 bp):
ATATATAGTTTATATAAATTATATATAAACTATTCTTTATAAACTATACATTAAT
Found at i:97853 original size:13 final size:13
Alignment explanation
Indices: 97837--98036 Score: 73
Period size: 13 Copynumber: 14.3 Consensus size: 13
97827 AGACTATACA
97837 TTATATATATAGT
1 TTATATATATAGT
*
97850 TTATATAAATTA-T
1 TTATATATA-TAGT
* * **
97863 ATATAAACTATTCT
1 TTATATA-TATAGT
*
97877 TTATAAACTATAGGT
1 TTATATA-TATA-GT
*
97892 TACATATATATAGT
1 T-TATATATATAGT
*
97906 TTATATAAACTATATAGA
1 TTATAT--A---TATAGT
* *
97924 TTACATATATAAT
1 TTATATATATAGT
* *
97937 TTATACATATGTAGC
1 TTAT--ATATATAGT
*
97952 TTATATATATAGA
1 TTATATATATAGT
97965 TTATATATATAGT
1 TTATATATATAGT
97978 TTATACATATATAGT
1 TTAT--ATATATAGT
*
97993 TTATA-ATA-ACT
1 TTATATATATAGT
* * *
98004 ATATAATTTATATT
1 TTAT-ATATATAGT
98018 ATATATATATATAGT
1 -T-TATATATATAGT
98033 TTAT
1 TTAT
98037 GCATAGTGTT
Statistics
Matches: 139, Mismatches: 29, Indels: 38
0.67 0.14 0.18
Matches are distributed among these distances:
11 5 0.04
12 4 0.03
13 55 0.40
14 20 0.14
15 37 0.27
16 8 0.06
18 10 0.07
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (13 bp):
TTATATATATAGT
Found at i:97943 original size:15 final size:15
Alignment explanation
Indices: 97925--97997 Score: 82
Period size: 15 Copynumber: 5.1 Consensus size: 15
97915 CTATATAGAT
*
97925 TACATATATAATTTA
1 TACATATATAGTTTA
* *
97940 TACATATGTAGCTTA
1 TACATATATAGTTTA
*
97955 T--ATATATAGATTA
1 TACATATATAGTTTA
97968 T--ATATATAGTTTA
1 TACATATATAGTTTA
97981 TACATATATAGTTTA
1 TACATATATAGTTTA
97996 TA
1 TA
97998 ATAACTATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
13 23 0.46
15 27 0.54
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (15 bp):
TACATATATAGTTTA
Found at i:97973 original size:41 final size:41
Alignment explanation
Indices: 97916--97997 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
97906 TTATATAAAC
*
97916 TATATAGATTACATATATAATTTATACATATGTAGCTTATA
1 TATATAGATTACATATATAATTTATACATATATAGCTTATA
* * *
97957 TATATAGATTATATATATAGTTTATACATATATAGTTTATA
1 TATATAGATTACATATATAATTTATACATATATAGCTTATA
97998 ATAACTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (41 bp):
TATATAGATTACATATATAATTTATACATATATAGCTTATA
Found at i:98024 original size:18 final size:18
Alignment explanation
Indices: 97964--98026 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 18
97954 ATATATATAG
*
97964 ATTATATATAT-AGTT-T
1 ATTATATATATAATTTAT
* *
97980 A-TACATATATAGTTTAT
1 ATTATATATATAATTTAT
*
97997 AATA-ACTATATAATTTAT
1 ATTATA-TATATAATTTAT
98015 ATTATATATATA
1 ATTATATATATA
98027 TATAGTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
15 8 0.22
16 3 0.08
17 3 0.08
18 22 0.59
19 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTATATATATAATTTAT
Found at i:98058 original size:53 final size:57
Alignment explanation
Indices: 97966--98108 Score: 147
Period size: 55 Copynumber: 2.6 Consensus size: 57
97956 ATATATAGAT
97966 TATATATATAGTTTATACATATATAGTTTATAATAACTATATAATTTA-TA-TTATA
1 TATATATATAGTTTATACATATATAGTTTATAATAACTATATAATTTATTACTTATA
* * * * *
98021 TATATATATAGTTTATGCATA-GT-GTTTCT-ATAAACTATGTACTTTATTACTTTATA
1 TATATATATAGTTTATACATATATAGTTTATAAT-AACTATATAATTTATTAC-TTATA
* * *
98077 TATATATATA-TATATATATATATA-TATATAAT
1 TATATATATAGTTTATACATATATAGTTTATAAT
98109 CTATAGATTA
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
52 2 0.03
53 17 0.24
54 3 0.04
55 27 0.39
56 19 0.27
57 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (57 bp):
TATATATATAGTTTATACATATATAGTTTATAATAACTATATAATTTATTACTTATA
Found at i:98080 original size:2 final size:2
Alignment explanation
Indices: 98073--98155 Score: 93
Period size: 2 Copynumber: 43.0 Consensus size: 2
98063 TTTATTACTT
*
98073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
98114 GA T- TA CA TA TA T- TA GT- TA TA CA 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
98154 TA
1 TA
98156 CTAAATTAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
1 4 0.06
2 63 0.93
3 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:98253 original size:18 final size:18
Alignment explanation
Indices: 98242--98277 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
98232 TATAATAATT
98242 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
98260 ATATAGTTTATATATATA
1 ATATAGTTTATA-ATATA
98278 GTTTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
ATATAGTTTATAATATAA
Found at i:98276 original size:13 final size:13
Alignment explanation
Indices: 98255--98288 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
98245 TAGTTTATAA
*
98255 TATAAATATAGTT
1 TATATATATAGTT
98268 TATATATATAGTT
1 TATATATATAGTT
98281 TATATATA
1 TATATATA
98289 AACTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
TATATATATAGTT
Found at i:98452 original size:2 final size:2
Alignment explanation
Indices: 98441--98500 Score: 52
Period size: 2 Copynumber: 30.0 Consensus size: 2
98431 TATGTACTTA
* * *
98441 AT AT ACT AT AT AT AT ACT AT AT AC AT AA AT CT -T AT AT AT -T AT
1 AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
98483 AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
98501 TACATAGTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
1 2 0.04
2 41 0.87
3 4 0.09
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:98573 original size:2 final size:2
Alignment explanation
Indices: 98568--98628 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
98558 TTTCTCTCTT
98568 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
98610 TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA
98629 AGTGTTTTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:102113 original size:32 final size:32
Alignment explanation
Indices: 102071--102215 Score: 170
Period size: 32 Copynumber: 4.5 Consensus size: 32
102061 ATCGGATCGG
*
102071 TCGGATGATTTTGGGTTCGGATTAATATCGAA
1 TCGGTTGATTTTGGGTTCGGATTAATATCGAA
102103 TCGGTTGATTTTGGGTTCGGATTAATATCGAA
1 TCGGTTGATTTTGGGTTCGGATTAATATCGAA
* * *
102135 TCGGTTGATTTTTGGG-TCGGGTTAATAACGGA
1 TCGGTTGA-TTTTGGGTTCGGATTAATATCGAA
* * *
102167 TCGGTTAGA-TTTCGATTCGGGTTAATATC-ATA
1 TCGGTT-GATTTTGGGTTCGGATTAATATCGA-A
*
102199 TCGGTTGATTTTCGGTT
1 TCGGTTGATTTTGGGTT
102216 TACGTCAACC
Statistics
Matches: 99, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.06
32 84 0.85
33 9 0.09
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41
Consensus pattern (32 bp):
TCGGTTGATTTTGGGTTCGGATTAATATCGAA
Found at i:106046 original size:14 final size:14
Alignment explanation
Indices: 106027--106056 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
106017 TTGATCTTTT
106027 AAGTTTTATTAAGA
1 AAGTTTTATTAAGA
*
106041 AAGTTTTATTGAGA
1 AAGTTTTATTAAGA
106055 AA
1 AA
106057 CTCAATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (14 bp):
AAGTTTTATTAAGA
Found at i:107197 original size:46 final size:46
Alignment explanation
Indices: 107130--107222 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
107120 CCGCTATGTG
* * *
107130 TTTTCATTTGTGGCATCCTTTCATGTCAATTATGCACTGTTATTCA
1 TTTTCATTTATAGCATCCTTTCATGCCAATTATGCACTGTTATTCA
* *
107176 TTTTCATTTATAGCATCCTTTCATGCCAATTATGCATTGTTCTTCA
1 TTTTCATTTATAGCATCCTTTCATGCCAATTATGCACTGTTATTCA
107222 T
1 T
107223 CTAACTTGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.48
Consensus pattern (46 bp):
TTTTCATTTATAGCATCCTTTCATGCCAATTATGCACTGTTATTCA
Found at i:107627 original size:55 final size:55
Alignment explanation
Indices: 107506--107771 Score: 442
Period size: 55 Copynumber: 4.8 Consensus size: 55
107496 CCCACTATCA
* * **
107506 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCAT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCC
*
107562 ATACGGAAATTCATAAACTTATTATGAATTTCTTACTTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
*
107617 ATATGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* *
107672 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTCACACACAATGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
*
107727 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACA
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACA
107772 TATATAGTGC
Statistics
Matches: 198, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
55 164 0.83
56 34 0.17
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (55 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
Found at i:108224 original size:20 final size:20
Alignment explanation
Indices: 108199--108248 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
108189 GTTATCAATG
108199 GTATCGATATCTTCCTCATA
1 GTATCGATATCTTCCTCATA
* ** *
108219 GTATCGATACCTTCCTTTTG
1 GTATCGATATCTTCCTCATA
108239 GTATCGATAT
1 GTATCGATAT
108249 TGCTTAGCTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (20 bp):
GTATCGATATCTTCCTCATA
Found at i:113448 original size:55 final size:54
Alignment explanation
Indices: 113327--113591 Score: 406
Period size: 55 Copynumber: 4.8 Consensus size: 54
113317 CCCACAATCA
* *
113327 ATACGGAAATTCATAAACTTATTATGAATTTTTTAGTTTTTGCACACAAAGTGCCC
1 ATAC-GAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCC
* *
113383 ATACGAAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACACAGTGTCC
1 ATACG-AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
*
113438 ATACTGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTCACACACAGTGCCC
1 ATAC-GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* *
113493 ATACGAAAATTCATAAACTTATTATAAATTTCTTAGTTTTGCACACACAGTGCTC
1 ATACG-AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
113548 ATACAGAAATTCATAAACTTATTAT-AATTTCTTAGTTTTGCACA
1 ATAC-GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACA
113592 TATATAGTGT
Statistics
Matches: 196, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
54 20 0.10
55 141 0.72
56 35 0.18
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (54 bp):
ATACGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
Found at i:114957 original size:2 final size:2
Alignment explanation
Indices: 114950--114976 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
114940 CACATTATTA
114950 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
114977 ATAACTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:115151 original size:32 final size:32
Alignment explanation
Indices: 115084--115192 Score: 110
Period size: 32 Copynumber: 3.4 Consensus size: 32
115074 CTTTCGGATT
* * * * * *
115084 GGTTTCTTTCGGTTCGGATTAATTTTTGTTTA
1 GGTTGCTTTCGGATCGGGTTAAATTTGGTTCA
*
115116 GGTTGCTTTCGGGTCGGGTTAAATTTGGTTCA
1 GGTTGCTTTCGGATCGGGTTAAATTTGGTTCA
* * *
115148 GGTTGATTTCGGATCGGGTTAAAATTCGGTTCG
1 GGTTGCTTTCGGATCGGGTT-AAATTTGGTTCA
*
115181 GGTTTCTTTCGG
1 GGTTGCTTTCGG
115193 CTCAGGTTGC
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
32 44 0.69
33 20 0.31
ACGTcount: A:0.13, C:0.12, G:0.30, T:0.45
Consensus pattern (32 bp):
GGTTGCTTTCGGATCGGGTTAAATTTGGTTCA
Found at i:115191 original size:33 final size:32
Alignment explanation
Indices: 115115--115192 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 32
115105 ATTTTTGTTT
* *
115115 AGGTTGCTTTCGGGTCGGGTTAAATTTGGTTC
1 AGGTTGCTTTCGGATCGGGTTAAATTCGGTTC
*
115147 AGGTTGATTTCGGATCGGGTTAAAATTCGGTTC
1 AGGTTGCTTTCGGATCGGGTT-AAATTCGGTTC
* *
115180 GGGTTTCTTTCGG
1 AGGTTGCTTTCGG
115193 CTCAGGTTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 19 0.49
33 20 0.51
ACGTcount: A:0.14, C:0.13, G:0.33, T:0.40
Consensus pattern (32 bp):
AGGTTGCTTTCGGATCGGGTTAAATTCGGTTC
Found at i:115229 original size:16 final size:16
Alignment explanation
Indices: 115208--115245 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
115198 GTTGCTTTCA
*
115208 GTTCGGGCTAGTTTTG
1 GTTCGGGCTAATTTTG
*
115224 GTTCGGGTTAATTTTG
1 GTTCGGGCTAATTTTG
115240 GTTCGG
1 GTTCGG
115246 ATTAATTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.11, G:0.37, T:0.45
Consensus pattern (16 bp):
GTTCGGGCTAATTTTG
Found at i:115250 original size:16 final size:16
Alignment explanation
Indices: 115219--115258 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
115209 TTCGGGCTAG
*
115219 TTTTGGTTCGGGTTAA
1 TTTTGGTTCGGATTAA
115235 TTTTGGTTCGGATTAA
1 TTTTGGTTCGGATTAA
*
115251 TTTCGGTT
1 TTTTGGTT
115259 TCGCTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.07, G:0.28, T:0.53
Consensus pattern (16 bp):
TTTTGGTTCGGATTAA
Found at i:116094 original size:3 final size:3
Alignment explanation
Indices: 116081--116127 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
116071 AAATAATTTA
116081 AAT AA- 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 AAT AAT
116128 TTAAAGTTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:116957 original size:25 final size:25
Alignment explanation
Indices: 116923--116974 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
116913 TATAAAGAGA
*
116923 ATGACATCAAATTTTAATTGACAGT
1 ATGACATCAAACTTTAATTGACAGT
116948 ATGACATCAAACTTTAATTGACAGT
1 ATGACATCAAACTTTAATTGACAGT
116973 AT
1 AT
116975 TAATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (25 bp):
ATGACATCAAACTTTAATTGACAGT
Found at i:119358 original size:3 final size:3
Alignment explanation
Indices: 119350--119435 Score: 147
Period size: 3 Copynumber: 29.0 Consensus size: 3
119340 TCCGGAGACC
119350 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
119398 ATT ATT A-T ATT ACT ATT ATT ATT ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
119436 TATATTTATA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:123116 original size:31 final size:31
Alignment explanation
Indices: 123081--123164 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
123071 TTAAGTATTA
* *
123081 TTGAGCTCGACTCTACTTGAAAA-TATTAAAG
1 TTGAGCTAGACTCAACTTGAAAAGT-TTAAAG
* ** *
123112 TTGAGCTAAACTCGGCTCGAAAAGTTTAAAG
1 TTGAGCTAGACTCAACTTGAAAAGTTTAAAG
123143 TTGAGCTAGACTCAACTTGAAA
1 TTGAGCTAGACTCAACTTGAAA
123165 GATCGCAAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (31 bp):
TTGAGCTAGACTCAACTTGAAAAGTTTAAAG
Found at i:123243 original size:67 final size:67
Alignment explanation
Indices: 123155--123280 Score: 162
Period size: 67 Copynumber: 1.9 Consensus size: 67
123145 GAGCTAGACT
* * ** * *
123155 CAACTTGAAAGATCGCAAGCTTAAATTTATTACGCTCGACTCAAACTCGAAATAAAAAATTGAAG
1 CAACTCGAAAGATCACAAGCTTAAAACTATCAAGCTCGACTCAAACTCGAAATAAAAAATTGAAG
123220 TC
66 TC
* * * *
123222 CAACTCGAAAGTTCACAAGCTTAAAACTGTCAAGCTTGACTCGAACTCGAAATAAAAAA
1 CAACTCGAAAGATCACAAGCTTAAAACTATCAAGCTCGACTCAAACTCGAAATAAAAAA
123281 ATTAAAGCTT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
67 49 1.00
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (67 bp):
CAACTCGAAAGATCACAAGCTTAAAACTATCAAGCTCGACTCAAACTCGAAATAAAAAATTGAAG
TC
Found at i:125207 original size:20 final size:20
Alignment explanation
Indices: 125182--125220 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
125172 CTACCTCCAA
125182 CAATTTCCACAATAATCATT
1 CAATTTCCACAATAATCATT
125202 CAATTTCCACAATAATCAT
1 CAATTTCCACAATAATCAT
125221 CTTTTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.33
Consensus pattern (20 bp):
CAATTTCCACAATAATCATT
Found at i:126032 original size:16 final size:16
Alignment explanation
Indices: 126007--126037 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
125997 TAAAGCTCGT
*
126007 ATTGATCTTGAAAAAA
1 ATTGAACTTGAAAAAA
126023 ATTGAACTTGAAAAA
1 ATTGAACTTGAAAAA
126038 TTCTCAGACT
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:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (16 bp):
ATTGAACTTGAAAAAA
Found at i:127374 original size:52 final size:52
Alignment explanation
Indices: 127268--127381 Score: 126
Period size: 52 Copynumber: 2.2 Consensus size: 52
127258 TGTTAAGCTC
* * * *
127268 GACTCGAACTCGAAATAAAAAAATTGAAGTTCGACTTGAAAGCTCACAAACTT
1 GACTCGAACTCGAAATAAAAAAATTAAAGCTCGACTCG-AAGCTCAAAAACTT
127321 GACTCGAACTCGAAAT-AAAAAATTAAAGCTCGTA-TCG-AGCTCGAAAAAACTT
1 GACTCGAACTCGAAATAAAAAAATTAAAGCTCG-ACTCGAAGCTC--AAAAACTT
127373 GAACTCGAA
1 G-ACTCGAA
127382 ACATTCTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
50 5 0.09
52 24 0.45
53 24 0.45
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (52 bp):
GACTCGAACTCGAAATAAAAAAATTAAAGCTCGACTCGAAGCTCAAAAACTT
Found at i:127934 original size:18 final size:18
Alignment explanation
Indices: 127911--127950 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
127901 ATGTCGGGTT
127911 CGGTCTTGGGTTGTTGGC
1 CGGTCTTGGGTTGTTGGC
127929 CGGTCTTGGGTTGTTGGC
1 CGGTCTTGGGTTGTTGGC
127947 CGGT
1 CGGT
127951 TACACTTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.17, G:0.45, T:0.38
Consensus pattern (18 bp):
CGGTCTTGGGTTGTTGGC
Found at i:128652 original size:31 final size:31
Alignment explanation
Indices: 128589--128654 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
128579 AACTTGATTT
**
128589 GAAAAGTTTAAAGTTGAGCTAAACTCGGCTC
1 GAAAAGTTTAAAGTTGAGCTAAACTCAACTC
**
128620 GAAAAGTTTAAAGTTGAGCTCGACTCAACTC
1 GAAAAGTTTAAAGTTGAGCTAAACTCAACTC
128651 GAAA
1 GAAA
128655 TCTCGCAAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (31 bp):
GAAAAGTTTAAAGTTGAGCTAAACTCAACTC
Found at i:132865 original size:21 final size:21
Alignment explanation
Indices: 132797--132875 Score: 54
Period size: 21 Copynumber: 3.6 Consensus size: 21
132787 GTGTAGAATT
132797 GGAGAAGAAGAAGGCGCAGGCTG
1 GGAGAAGAAGAAGGCGCAGG--G
*** **
132820 GAGAGAAGAAG-AGAGTAAAACG
1 G-GAGAAGAAGAAG-GCGCAGGG
132842 GGAGAAGAAGAAGGCGCAGGG
1 GGAGAAGAAGAAGGCGCAGGG
132863 GGAGGAAG-AGAAG
1 GGA-GAAGAAGAAG
132876 AAGAGAGTAG
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
21 20 0.48
22 8 0.19
23 3 0.07
24 11 0.26
ACGTcount: A:0.43, C:0.08, G:0.47, T:0.03
Consensus pattern (21 bp):
GGAGAAGAAGAAGGCGCAGGG
Found at i:132873 original size:48 final size:46
Alignment explanation
Indices: 132769--132884 Score: 137
Period size: 45 Copynumber: 2.5 Consensus size: 46
132759 CAGACAGCGG
* * * **
132769 AGGCA-GAAGAGAAGAGGAGTGTAGAATTGGAGAAGAAGAAGGCGC
1 AGGCAGGAAGAGAAGAAGAGAGTAAAACGGGAGAAGAAGAAGGCGC
*
132814 AGGCTGG-AGAGAAGAAGAGAGTAAAACGGGAGAAGAAGAAGGCGC
1 AGGCAGGAAGAGAAGAAGAGAGTAAAACGGGAGAAGAAGAAGGCGC
*
132859 AGGGGGAGGAAGAGAAGAAGAGAGTA
1 A--GGCAGGAAGAGAAGAAGAGAGTA
132885 GCATATCTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
45 38 0.64
46 1 0.02
47 4 0.07
48 16 0.27
ACGTcount: A:0.44, C:0.06, G:0.44, T:0.06
Consensus pattern (46 bp):
AGGCAGGAAGAGAAGAAGAGAGTAAAACGGGAGAAGAAGAAGGCGC
Found at i:133614 original size:30 final size:32
Alignment explanation
Indices: 133552--133620 Score: 88
Period size: 36 Copynumber: 2.1 Consensus size: 32
133542 TGGGGAGCAT
133552 GTGCAATCAAATATACCAAGAAGCAGAAGCAGGCAA
1 GTGCAATCAAATATACC-A-AAGC--AAGCAGGCAA
133588 GTGCAATCAAATATACC-AAGC-AGCAGGCAA
1 GTGCAATCAAATATACCAAAGCAAGCAGGCAA
133618 GTG
1 GTG
133621 ACGCACCGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 12 0.36
33 4 0.12
36 17 0.52
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (32 bp):
GTGCAATCAAATATACCAAAGCAAGCAGGCAA
Found at i:139934 original size:23 final size:23
Alignment explanation
Indices: 139908--139955 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
139898 CTCATAATTG
*
139908 AAAGAACACCAAAAGAAAAACTT
1 AAAGAAAACCAAAAGAAAAACTT
** *
139931 AAAGAAAACTTAATGAAAAACTT
1 AAAGAAAACCAAAAGAAAAACTT
139954 AA
1 AA
139956 TGTCAAACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.65, C:0.12, G:0.08, T:0.15
Consensus pattern (23 bp):
AAAGAAAACCAAAAGAAAAACTT
Found at i:139938 original size:11 final size:12
Alignment explanation
Indices: 139919--139955 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
139909 AAGAACACCA
139919 AAAGAAAAACTT
1 AAAGAAAAACTT
139931 AAAG-AAAACTT
1 AAAGAAAAACTT
*
139942 AATGAAAAACTT
1 AAAGAAAAACTT
139954 AA
1 AA
139956 TGTCAAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (12 bp):
AAAGAAAAACTT
Found at i:141994 original size:6 final size:6
Alignment explanation
Indices: 141983--142011 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
141973 AAATCAAGGA
141983 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
142012 GAATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:145706 original size:23 final size:23
Alignment explanation
Indices: 145680--145727 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
145670 CTCATAATTG
*
145680 AAAGAACACCAAAAGAAAAACTT
1 AAAGAAAACCAAAAGAAAAACTT
** *
145703 AAAGAAAACTTAATGAAAAACTT
1 AAAGAAAACCAAAAGAAAAACTT
145726 AA
1 AA
145728 TGTCAAACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.65, C:0.12, G:0.08, T:0.15
Consensus pattern (23 bp):
AAAGAAAACCAAAAGAAAAACTT
Found at i:145728 original size:12 final size:12
Alignment explanation
Indices: 145694--145750 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
145684 AACACCAAAA
*
145694 GAAAAACTTAAA
1 GAAAAACTTAAT
145706 G-AAAACTTAAT
1 GAAAAACTTAAT
145717 GAAAAACTTAAT
1 GAAAAACTTAAT
** *
145729 GTCAAACTTGAT
1 GAAAAACTTAAT
*
145741 GTAAAACTTA
1 GAAAAACTTA
145751 TGCCCTAGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 10 0.26
12 28 0.74
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (12 bp):
GAAAAACTTAAT
Found at i:145735 original size:24 final size:23
Alignment explanation
Indices: 145694--145750 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
145684 AACACCAAAA
145694 GAAAAACTTAAAGAAAACTTAAT
1 GAAAAACTTAAAGAAAACTTAAT
* * *
145717 GAAAAACTTAATGTCAAACTTGAT
1 GAAAAACTTAAAG-AAAACTTAAT
*
145741 GTAAAACTTA
1 GAAAAACTTA
145751 TGCCCTAGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (23 bp):
GAAAAACTTAAAGAAAACTTAAT
Found at i:149237 original size:26 final size:26
Alignment explanation
Indices: 149201--149256 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
149191 AAACATTTCT
*
149201 AAAATATATATAATAAATATTTTTGA
1 AAAATATATATAATAAATAGTTTTGA
*
149227 AAAATATATATAATATATAGTTTTGA
1 AAAATATATATAATAAATAGTTTTGA
149253 AAAA
1 AAAA
149257 CATTTTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (26 bp):
AAAATATATATAATAAATAGTTTTGA
Found at i:149269 original size:37 final size:37
Alignment explanation
Indices: 149219--149350 Score: 207
Period size: 37 Copynumber: 3.6 Consensus size: 37
149209 TATAATAAAT
149219 ATTTTTGAAAAATATATATAATATATAGTTTTGAAAAAC
1 ATTTTTG-AAAATATATATAATATATAGTTTTG-AAAAC
149258 ATTTTTG-AAATATATATAATATATAGTTTTGAAAAC
1 ATTTTTGAAAATATATATAATATATAGTTTTGAAAAC
*
149294 ATTTCTG-AAATATATATAATATATAGTTTTTGAAAAC
1 ATTTTTGAAAATATATATAATATATAG-TTTTGAAAAC
149331 A-TTTTGAAAATATATATAAT
1 ATTTTTGAAAATATATATAAT
149351 TTTTGAAAAC
Statistics
Matches: 89, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
36 34 0.38
37 48 0.54
39 7 0.08
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (37 bp):
ATTTTTGAAAATATATATAATATATAGTTTTGAAAAC
Found at i:149356 original size:19 final size:19
Alignment explanation
Indices: 149332--149401 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
149322 TTTGAAAACA
149332 TTTTGAAAATATATATAAT
1 TTTTGAAAATATATATAAT
* *
149351 TTTTGAAAACATATATAGT
1 TTTTGAAAATATATATAAT
* *
149370 TTTTTAAAA-A-A-ATGAT
1 TTTTGAAAATATATATAAT
149386 TTTTGAAAATATATAT
1 TTTTGAAAATATATAT
149402 GATATAGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 11 0.26
17 2 0.05
18 2 0.05
19 27 0.64
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (19 bp):
TTTTGAAAATATATATAAT
Found at i:149423 original size:35 final size:34
Alignment explanation
Indices: 149384--149512 Score: 120
Period size: 35 Copynumber: 3.7 Consensus size: 34
149374 TAAAAAAATG
*
149384 ATTTTTGAAAATATATATGATATAGTTTTTAAAA
1 ATTTTTGAAAACATATATGATATAGTTTTTAAAA
* *
149418 TATTTTTTAAAACGTATAAT-ATATAGTTTTTAAAGA
1 -ATTTTTGAAAACATAT-ATGATATAGTTTTTAAA-A
* * *
149454 AGGTTTTTAAAAACATATA-GCATGTAGTTTTTTAAA
1 A--TTTTTGAAAACATATATG-ATATAGTTTTTAAAA
*
149490 A-TTTTGAAAACGTATATGATATA
1 ATTTTTGAAAACATATATGATATA
149513 TATATTTTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
33 17 0.22
34 1 0.01
35 28 0.36
36 6 0.08
37 25 0.32
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (34 bp):
ATTTTTGAAAACATATATGATATAGTTTTTAAAA
Found at i:149482 original size:72 final size:74
Alignment explanation
Indices: 149361--149514 Score: 174
Period size: 72 Copynumber: 2.1 Consensus size: 74
149351 TTTTGAAAAC
* * *
149361 ATATATAGTTTTTTAAAAAAATGATTTTTGAAAATATATATGATATAGTTTTTAAAATATTTTTT
1 ATATATAGTTTTTTAAAAAAATGATTTTTAAAAACATATATGATATAGTTTTTAAAA-A-TTTTG
149426 AAAACGTATA-
64 AAAACGTATAG
* * * *
149436 ATATATAG-TTTTT-AAAGAA-GGTTTTTAAAAACATATA-GCATGTAGTTTTTTAAAATTTTGA
1 ATATATAGTTTTTTAAAAAAATGATTTTTAAAAACATATATG-ATATAGTTTTTAAAAATTTTGA
149497 AAACGTATATG
65 AAACGTATA-G
149508 ATATATA
1 ATATATA
149515 TATTTTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
70 14 0.20
71 2 0.03
72 35 0.51
73 5 0.07
74 5 0.07
75 8 0.12
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (74 bp):
ATATATAGTTTTTTAAAAAAATGATTTTTAAAAACATATATGATATAGTTTTTAAAAATTTTGAA
AACGTATAG
Found at i:150886 original size:9 final size:9
Alignment explanation
Indices: 150821--150883 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 9
150811 GATTTGAATG
150821 TTATTTTAT
1 TTATTTTAT
*
150830 TTATTTTTT
1 TTATTTTAT
150839 TGTATTTTA-
1 T-TATTTTAT
*
150848 TTAATTT-T
1 TTATTTTAT
*
150856 TTATTTAAT
1 TTATTTTAT
* *
150865 TTACTTTAA
1 TTATTTTAT
150874 TT-TTTTAT
1 TTATTTTAT
150882 TT
1 TT
150884 TTTCTATACT
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
8 16 0.39
9 19 0.46
10 6 0.15
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (9 bp):
TTATTTTAT
Found at i:151451 original size:16 final size:17
Alignment explanation
Indices: 151421--151452 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
151411 TGAATTTTAA
151421 ACTAAATATAATTGATC
1 ACTAAATATAATTGATC
151438 ACTAAATA-AATTGAT
1 ACTAAATATAATTGAT
151453 GGCATTTATT
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:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (17 bp):
ACTAAATATAATTGATC
Found at i:152534 original size:185 final size:183
Alignment explanation
Indices: 152222--152590 Score: 720
Period size: 185 Copynumber: 2.0 Consensus size: 183
152212 GAATGTCGAT
152222 GAGTTCTACTTTGACCTTTGCTGGTCCATTGAAAGGGCAAAACACCCATACAGCTATGTCGGTAT
1 GAGTTCTACTTTGACCTTTGCTGGTCCATTGAAAGGGCAAAACACCCATACAGCTATGTCGGTAT
152287 ACGTGGCGCCAAACATGGGTTTTACATGCAAATAAACTTGGGAGTTTTGCAAATCTCCTTTCTTT
66 ACGTGGCGCCAAACATGGGTTTTACATGCAAATAAACTTGGGAGTTTTGCAAATCTCCTTTCTTT
152352 ACTCTTTTCCCTTGTTTGCTTCGTCCACTGGAAGATCCAGCCAGTAATTGCCGTC
131 ACTCTTTT--CTTGTTTGCTTCGTCCACTGGAAGATCCAGCCAGTAATTGCCGTC
152407 GAGTTCTACTTTGACCTTTGCTGGTCCATTGAAAGGGCAAAACACCCATACAGCTATGTCGGTAT
1 GAGTTCTACTTTGACCTTTGCTGGTCCATTGAAAGGGCAAAACACCCATACAGCTATGTCGGTAT
152472 ACGTGGCGCCAAACATGGGTTTTACATGCAAATAAACTTGGGAGTTTTGCAAATCTCCTTTCTTT
66 ACGTGGCGCCAAACATGGGTTTTACATGCAAATAAACTTGGGAGTTTTGCAAATCTCCTTTCTTT
152537 ACTCTTTTCTTGTTTGCTTCGTCCACTGGAAGATCCAGCCAGTAATTGCCGTC
131 ACTCTTTTCTTGTTTGCTTCGTCCACTGGAAGATCCAGCCAGTAATTGCCGTC
152590 G
1 G
152591 TTCGAACCGC
Statistics
Matches: 184, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
183 46 0.25
185 138 0.75
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (183 bp):
GAGTTCTACTTTGACCTTTGCTGGTCCATTGAAAGGGCAAAACACCCATACAGCTATGTCGGTAT
ACGTGGCGCCAAACATGGGTTTTACATGCAAATAAACTTGGGAGTTTTGCAAATCTCCTTTCTTT
ACTCTTTTCTTGTTTGCTTCGTCCACTGGAAGATCCAGCCAGTAATTGCCGTC
Found at i:155085 original size:22 final size:22
Alignment explanation
Indices: 155057--155119 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
155047 TGTCCTGCGC
155057 CTTGCTCCCCGTTGCATGCTCG
1 CTTGCTCCCCGTTGCATGCTCG
155079 CTTGCTCCCCGTTGCATGCTCG
1 CTTGCTCCCCGTTGCATGCTCG
**
155101 CTTGCTCCCCACTGCATGC
1 CTTGCTCCCCGTTGCATGC
155120 AAGCGACCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.06, C:0.43, G:0.21, T:0.30
Consensus pattern (22 bp):
CTTGCTCCCCGTTGCATGCTCG
Found at i:166111 original size:28 final size:28
Alignment explanation
Indices: 166077--166163 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
166067 AAAATTTACT
166077 TGGAAATTAAGTTTTTTTTCTTGAATCA
1 TGGAAATTAAGTTTTTTTTCTTGAATCA
* * * * *
166105 TGGAAATTAAGTAATATTTTCATG-TTACT
1 TGGAAATTAAGT-TTTTTTTCTTGAAT-CA
*
166134 TGGAAATTAAGGTTTTTTTCTTGAATCA
1 TGGAAATTAAGTTTTTTTTCTTGAATCA
166162 TG
1 TG
166164 AAGAGGGAGG
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
28 24 0.53
29 21 0.47
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (28 bp):
TGGAAATTAAGTTTTTTTTCTTGAATCA
Found at i:167324 original size:14 final size:14
Alignment explanation
Indices: 167305--167336 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
167295 TATTAGTGAA
167305 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
167319 CGTTCGGTTTTGTT
1 CGTTCGGTTATGTT
167333 CGTT
1 CGTT
167337 TATGTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.28, T:0.53
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:168458 original size:16 final size:16
Alignment explanation
Indices: 168439--168481 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
168429 TTTATGTTTG
168439 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
* *
168455 TTTATGTTCTTGTTCG
1 TTTATGTTCGTGTTCA
168471 TTTATGTTCGT
1 TTTATGTTCGT
168482 TAATTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.09, C:0.12, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:171012 original size:14 final size:14
Alignment explanation
Indices: 170993--171020 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
170983 CGTAAGGATA
170993 TATGTATAAATGAT
1 TATGTATAAATGAT
171007 TATGTATAAATGAT
1 TATGTATAAATGAT
171021 GATATGAAAG
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:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
TATGTATAAATGAT
Found at i:173371 original size:20 final size:20
Alignment explanation
Indices: 173346--173466 Score: 91
Period size: 20 Copynumber: 5.8 Consensus size: 20
173336 AACCCGACGG
*
173346 GTGTATCGGTACACTGCAGA
1 GTGTATCGATACACTGCAGA
*
173366 GTGTATCGATACATTGCAGA
1 GTGTATCGATACACTGCAGA
*
173386 GTGTATCGATACACATTCAAGGA
1 GTGTATCGATACAC-TGC-A-GA
* * * * *
173409 ATGCATCGGTACACTATCATA
1 GTGTATCGATACACT-GCAGA
* *
173430 GTGTATCGATACA-TAGTGAGG
1 GTGTATCGATACACT-G-CAGA
173451 GTGTATCGATACACTG
1 GTGTATCGATACACTG
173467 TGCACAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
20 33 0.41
21 28 0.35
22 4 0.05
23 15 0.19
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (20 bp):
GTGTATCGATACACTGCAGA
Found at i:175475 original size:59 final size:59
Alignment explanation
Indices: 175383--175505 Score: 237
Period size: 59 Copynumber: 2.1 Consensus size: 59
175373 AAGGGATTTC
*
175383 CCTTTCTTCAATGGTTAAATTCTCAAGAACATCGTGAGTTTCTTCATCTTTCATTTCTT
1 CCTTTCTTCAATGGTTAAATTCTAAAGAACATCGTGAGTTTCTTCATCTTTCATTTCTT
175442 CCTTTCTTCAATGGTTAAATTCTAAAGAACATCGTGAGTTTCTTCATCTTTCATTTCTT
1 CCTTTCTTCAATGGTTAAATTCTAAAGAACATCGTGAGTTTCTTCATCTTTCATTTCTT
175501 CCTTT
1 CCTTT
175506 GATGATGGTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (59 bp):
CCTTTCTTCAATGGTTAAATTCTAAAGAACATCGTGAGTTTCTTCATCTTTCATTTCTT
Found at i:176569 original size:31 final size:31
Alignment explanation
Indices: 176545--176686 Score: 248
Period size: 31 Copynumber: 4.6 Consensus size: 31
176535 CCATAGATTT
*
176545 CGAAGAACCTAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
*
176576 CGAAGAACATAGGTAAACAATCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
* *
176607 CGAAGAATATAGGTAAACGGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
176638 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
176669 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
176687 CCTCGACCCT
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:180222 original size:19 final size:21
Alignment explanation
Indices: 180198--180245 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
180188 ATATACGTTT
*
180198 TATGAATAGT-AA-AATATGG
1 TATGAACAGTGAACAATATGG
*
180217 TATGAACAGTGAACAATATTG
1 TATGAACAGTGAACAATATGG
180238 TATGAACA
1 TATGAACA
180246 ATACCATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 2 0.08
21 14 0.56
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (21 bp):
TATGAACAGTGAACAATATGG
Found at i:181021 original size:31 final size:31
Alignment explanation
Indices: 180998--181138 Score: 246
Period size: 31 Copynumber: 4.5 Consensus size: 31
180988 CATAGATTCT
* *
180998 GAAGAACCTAGGTAAACAGTCCATATGTCTC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
181029 GAAGAATATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
181060 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
181091 GAAAAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
181122 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
181139 CCTCGACCCT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:186499 original size:17 final size:16
Alignment explanation
Indices: 186471--186510 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
186461 TTTAATTTTT
*
186471 AAATAAAATTATTTAA
1 AAATAAAATTATTCAA
*
186487 AATATAAAGTTATTCAA
1 AA-ATAAAATTATTCAA
186504 AAATAAA
1 AAATAAA
186511 TAAATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
AAATAAAATTATTCAA
Found at i:186766 original size:28 final size:29
Alignment explanation
Indices: 186697--186768 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 29
186687 ATAAAAAATT
*
186697 AAAAATATATTTAAA-ATACAAAGTTATTA
1 AAAAATA-ATTTAAATATACAAAGTTACTA
*
186726 AAAAATAA-ATAAATATTA-AAA-TTACTA
1 AAAAATAATTTAAATA-TACAAAGTTACTA
186753 AAAAATAATTTAAATA
1 AAAAATAATTTAAATA
186769 AAACTTGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 17 0.46
28 11 0.30
29 9 0.24
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAAATAATTTAAATATACAAAGTTACTA
Found at i:187761 original size:25 final size:25
Alignment explanation
Indices: 187728--187776 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
187718 AATTATACAC
187728 CTAAACCCTAAATCCCCAAATTATA
1 CTAAACCCTAAATCCCCAAATTATA
187753 CTAAACCCTAAATCCCCAAATTAT
1 CTAAACCCTAAATCCCCAAATTAT
187777 CTCTCACCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (25 bp):
CTAAACCCTAAATCCCCAAATTATA
Found at i:189029 original size:150 final size:153
Alignment explanation
Indices: 188736--189034 Score: 577
Period size: 150 Copynumber: 2.0 Consensus size: 153
188726 ACAATGCTAA
188736 CGTTTTTATTTTACAATAATTATATTTTCTAACAATTTAGAAGTAATTTCATTTGAATTGATATA
1 CGTTTTTATTTTACAATAATTATATTTTCTAACAATTTAGAAGTAATTTCATTTGAATTGATATA
188801 ATATTGAAAATAGACGTTCGTCCCTAAGATTAACACAATTTTTTATACTTCGTTCATTCAAAGTG
66 ATATTGAAAATAGACGTTCGTCCCTAAGATTAACACAATTTTTTATACTTCGTTCATTCAAAGTG
188866 AGGAAGTGAAATTCACTTGGTTT
131 AGGAAGTGAAATTCACTTGGTTT
188889 CGTTTTTA-TTTACAATAA-T-TATTTTCTAACAATTTAGAAGTAATTTCATTTGAATTGATATA
1 CGTTTTTATTTTACAATAATTATATTTTCTAACAATTTAGAAGTAATTTCATTTGAATTGATATA
188951 ATATTGAAAATAGACGTTCGTCCCTAAGATTAACACAATTTTTTATACTTCGTTCATTCAAAGTG
66 ATATTGAAAATAGACGTTCGTCCCTAAGATTAACACAATTTTTTATACTTCGTTCATTCAAAGTG
189016 AGGAAGTGAAATTCACTTG
131 AGGAAGTGAAATTCACTTG
189035 TGTTGTTCTC
Statistics
Matches: 146, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
150 127 0.87
151 1 0.01
152 10 0.07
153 8 0.05
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (153 bp):
CGTTTTTATTTTACAATAATTATATTTTCTAACAATTTAGAAGTAATTTCATTTGAATTGATATA
ATATTGAAAATAGACGTTCGTCCCTAAGATTAACACAATTTTTTATACTTCGTTCATTCAAAGTG
AGGAAGTGAAATTCACTTGGTTT
Found at i:197681 original size:42 final size:42
Alignment explanation
Indices: 197613--197693 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
197603 ATAATGAGTT
*
197613 TGATCTTTTGCGGCATTTGTAGGAAAAACGCCGCTATAGGAA
1 TGATCTTTTGCGGCATTTGTAAGAAAAACGCCGCTATAGGAA
* * *
197655 TGATCTTTTGCGTCGTTTTTAAGAAAAACGCCGCTATAG
1 TGATCTTTTGCGGCATTTGTAAGAAAAACGCCGCTATAG
197694 AGCTTGACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (42 bp):
TGATCTTTTGCGGCATTTGTAAGAAAAACGCCGCTATAGGAA
Found at i:198437 original size:18 final size:19
Alignment explanation
Indices: 198399--198440 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
198389 TTTTCAATAC
*
198399 AAAATATATAATATTTTTT
1 AAAATATATAATATATTTT
*
198418 AAAATATATGATA-ATTTT
1 AAAATATATAATATATTTT
198436 AAAAT
1 AAAAT
198441 TTTAGAAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AAAATATATAATATATTTT
Found at i:199321 original size:44 final size:43
Alignment explanation
Indices: 199256--199562 Score: 180
Period size: 44 Copynumber: 7.1 Consensus size: 43
199246 TATAAATTTT
* * *
199256 AAAAAATTAAGAACTTCAATTATAAAGGTAAAAAGTGAGATTG
1 AAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAGATTG
* * ** *
199299 AAGGAACTTAGGAGCCTCAATTATAAATATAAAAAGTGAGATTT
1 AA-AAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAGATTG
* * *
199343 AAAAAATTAACGA-CCTCAATTATAAAGGTAGAAAGTGAAATTG
1 AAAAAATT-AGGAGCCTCAATTATAAAGGTAAAAAGTGAGATTG
* * ** *
199386 AAAAAACTCAAGG-GCCTTAATTATAAATTTAAAAAGT-ATG-TTT
1 AAAAAA-T-TAGGAGCCTCAATTATAAAGGTAAAAAGTGA-GATTG
* * * *
199429 AAAAAAATAGGAGCCTCAATTATAACGGTAAAAAAAATGAAATTG
1 AAAAAATTAGGAGCCTCAATTATAAAGGT--AAAAAGTGAGATTG
* * * * * * *
199474 GAAAAATCA-GAGACTTAAATTGTAAAGATAAAAACTGAGATT-
1 AAAAAATTAGGAG-CCTCAATTATAAAGGTAAAAAGTGAGATTG
* * * * * *
199516 AAAAAAATA-GAACCACAATTATAAATGTGAAAAA-TAAGATTT
1 AAAAAATTAGGAGCCTCAATTATAAAGGT-AAAAAGTGAGATTG
199558 AAAAA
1 AAAAA
199563 TAAGGGACTC
Statistics
Matches: 196, Mismatches: 54, Indels: 29
0.70 0.19 0.10
Matches are distributed among these distances:
41 19 0.10
42 31 0.16
43 57 0.29
44 69 0.35
45 20 0.10
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.25
Consensus pattern (43 bp):
AAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAGATTG
Found at i:199408 original size:87 final size:85
Alignment explanation
Indices: 199253--199590 Score: 271
Period size: 87 Copynumber: 3.9 Consensus size: 85
199243 TTTTATAAAT
* * ** * *
199253 TTTAAAAAATTAAGAACTTCAATTATAAAGGTAAAAAGTGAGATTGAAGGAACTTAGGAGCCTCA
1 TTTAAAAAATTAAG-ACCTCAATTATAAAGGTAAAAAGTGAAATTGAAAAAACTCAGG-GCCTTA
199318 ATTATAAATATAAAAAGTGAGA
64 ATTATAAATATAAAAAGTGAGA
*
199340 TTTAAAAAATTAACGACCTCAATTATAAAGGTAGAAAGTGAAATTGAAAAAACTCAAGGGCCTTA
1 TTTAAAAAATTAA-GACCTCAATTATAAAGGTAAAAAGTGAAATTGAAAAAACTC-AGGGCCTTA
*
199405 ATTATAAATTTAAAAAGT-ATG-
64 ATTATAAATATAAAAAGTGA-GA
* * * * * * *
199426 TTTAAAAAAATAGGAGCCTCAATTATAACGGTAAAAAAAATGAAATTGGAAAAA-TCAGAGACTT
1 TTTAAAAAATTAAGA-CCTCAATTATAAAGGT--AAAAAGTGAAATTGAAAAAACTCAGGGCCTT
* * *
199490 AAATTGTAAAGATAAAAACTGAGA
63 -AATTATAAATATAAAAAGTGAGA
* * * * * *
199514 -TTAAAAAAAT-AGAACCACAATTATAAATGTGAAAAA-T-AAGATT-TAAAAA-TAAGGGACTC
1 TTTAAAAAATTAAG-ACCTCAATTATAAAGGT-AAAAAGTGAA-ATTGAAAAAACTCAGGGCCT-
*
199573 TAATTACAAATATAAAAA
62 TAATTATAAATATAAAAA
199591 AATAAAGACC
Statistics
Matches: 208, Mismatches: 31, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
83 28 0.13
84 5 0.02
85 7 0.03
86 47 0.23
87 99 0.48
88 22 0.11
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25
Consensus pattern (85 bp):
TTTAAAAAATTAAGACCTCAATTATAAAGGTAAAAAGTGAAATTGAAAAAACTCAGGGCCTTAAT
TATAAATATAAAAAGTGAGA
Found at i:199604 original size:29 final size:30
Alignment explanation
Indices: 199558--199619 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
199548 AATAAGATTT
* * *
199558 AAAAATAAGGGACTCTAATTACAAATATAA
1 AAAAATAAGAGACCCTAATTACAAAGATAA
*
199588 AAAAATAA-AGACCCTAATTGCAAAGATAA
1 AAAAATAAGAGACCCTAATTACAAAGATAA
199617 AAA
1 AAA
199620 GTAGGGACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.60, C:0.11, G:0.10, T:0.19
Consensus pattern (30 bp):
AAAAATAAGAGACCCTAATTACAAAGATAA
Found at i:199628 original size:28 final size:27
Alignment explanation
Indices: 199557--199628 Score: 63
Period size: 29 Copynumber: 2.5 Consensus size: 27
199547 AAATAAGATT
* *
199557 TAAAAATAAGGGACTCTAATTACAAATA
1 TAAAAAT-AGGGACCCTAATTACAAAGA
** *
199585 TAAAAAAATAAAGACCCTAATTGCAAAGA
1 T--AAAAATAGGGACCCTAATTACAAAGA
199614 TAAAAAGTAGGGACC
1 TAAAAA-TAGGGACC
199629 ACGAGGAGTC
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
27 5 0.15
28 7 0.21
29 16 0.47
30 6 0.18
ACGTcount: A:0.54, C:0.12, G:0.14, T:0.19
Consensus pattern (27 bp):
TAAAAATAGGGACCCTAATTACAAAGA
Found at i:200113 original size:20 final size:20
Alignment explanation
Indices: 200088--200128 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
200078 TTTGAACCAT
200088 GCTAATTCCCGTTAAAAACC
1 GCTAATTCCCGTTAAAAACC
200108 GCTAATTCCCGTTAAAAACC
1 GCTAATTCCCGTTAAAAACC
200128 G
1 G
200129 GCTTGTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (20 bp):
GCTAATTCCCGTTAAAAACC
Found at i:214261 original size:19 final size:19
Alignment explanation
Indices: 214239--214278 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
214229 GCCCAACAAC
* *
214239 CCCAAATAAATCCAATAGT
1 CCCAAATAAACCCAACAGT
214258 CCCAAATAAACCCAACAGT
1 CCCAAATAAACCCAACAGT
214277 CC
1 CC
214279 AACCCGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.45, C:0.35, G:0.05, T:0.15
Consensus pattern (19 bp):
CCCAAATAAACCCAACAGT
Found at i:215278 original size:21 final size:20
Alignment explanation
Indices: 215245--215305 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 20
215235 ATTTAATCTA
*
215245 ATATATTTATATATTTATTTT
1 ATATTTTTATATA-TTATTTT
*
215266 ATATTTTTTTATA-TATTTT
1 ATATTTTTATATATTATTTT
215285 ATATTTTTATATATGTATTTT
1 ATATTTTTATATAT-TATTTT
215306 TTTATTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.51
21 17 0.49
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
ATATTTTTATATATTATTTT
Done.