Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001584.1 Hibiscus syriacus cultivar Beakdansim tig00003160_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: 97532
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:422 original size:21 final size:21
Alignment explanation
Indices: 377--424 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
367 TGAGGGTTTT
* * **
377 ATGTAGTCCTCCGGGATAATT
1 ATGTGGTCCTCCGGGACAAAA
398 ATGTGGTCCTCCGGGACAAAA
1 ATGTGGTCCTCCGGGACAAAA
419 ATGTGG
1 ATGTGG
425 CACTTTGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (21 bp):
ATGTGGTCCTCCGGGACAAAA
Found at i:471 original size:23 final size:23
Alignment explanation
Indices: 419--471 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
409 CGGGACAAAA
*
419 ATGTGGCACTTTGGTGCAAACCT
1 ATGTGGTACTTTGGTGCAAACCT
442 ATGTGGTACTTTGGTGCAAACCT
1 ATGTGGTACTTTGGTGCAAACCT
465 ATGTGGT
1 ATGTGGT
472 CATTCGGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (23 bp):
ATGTGGTACTTTGGTGCAAACCT
Found at i:3178 original size:19 final size:22
Alignment explanation
Indices: 3154--3205 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 22
3144 ATGACAGATT
3154 GGTATCGGTACC-TTG-AG-GA
1 GGTATCGGTACCTTTGAAGAGA
*
3173 GGTATCGATACCTTTGAAGAGA
1 GGTATCGGTACCTTTGAAGAGA
*
3195 AGTATCGGTAC
1 GGTATCGGTAC
3206 TGGATGGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.41
20 3 0.11
21 2 0.07
22 11 0.41
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (22 bp):
GGTATCGGTACCTTTGAAGAGA
Found at i:10522 original size:108 final size:108
Alignment explanation
Indices: 10393--10609 Score: 251
Period size: 110 Copynumber: 2.0 Consensus size: 108
10383 ACTACAGGAG
**
10393 CTAAACAACAAATAATTCAAAATATATATAACATGCATAAAAG-TGGGTAAATTACAAAAACAA-
1 CTAAACAACAAATAAACCAAAA-ATATATAACATGCATAAAAGATGGGTAAATTACAAAAA-AAG
* ** *
10456 TCCATATAGGTGTTCATTTTGCAAAAACACGCAGAACTGAGGGGA
64 TCCATACAGGTGACCATTTTGCAAAAACACGCAGAACTAAGGGGA
* ** *
10501 CTAAACAA-AAATTAAACCAAAAATGTATAACATGCATATGAGATGGGTAAATTATAAAAAAATG
1 CTAAACAACAAA-TAAACCAAAAATATATAACATGCATAAAAGATGGGTAAATTACAAAAAAA--
* * *
10565 GTCCTTACATGTGACCATTTTGCAAAAACACGCATAACTAAGGGG
63 GTCCATACAGGTGACCATTTTGCAAAAACACGCAGAACTAAGGGG
10610 GACTTAACTG
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
107 22 0.24
108 32 0.35
110 37 0.41
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (108 bp):
CTAAACAACAAATAAACCAAAAATATATAACATGCATAAAAGATGGGTAAATTACAAAAAAAGTC
CATACAGGTGACCATTTTGCAAAAACACGCAGAACTAAGGGGA
Found at i:13468 original size:60 final size:61
Alignment explanation
Indices: 13355--13534 Score: 186
Period size: 60 Copynumber: 3.0 Consensus size: 61
13345 CATATGTCCC
* * * **
13355 AAAACTATAACCCTCATTTTATATTGGTCCTTAAACTTTTGAATATTCCAATTTCATCCC-T
1 AAAAC-ATGACCCTCATTATAAATTAATCCTTAAACTTTTGAATATTCCAATTTCATCCCAT
* ** * *
13416 AAACCATGATTCTCATTATAAATTAATCCTTAAACTTTTGAACATTCTAATTTCA-CCCAT
1 AAAACATGACCCTCATTATAAATTAATCCTTAAACTTTTGAATATTCCAATTTCATCCCAT
* * * **
13476 AAAATATGACCCTCATTGTAAATTGATCCCCAAACTTTT-AAGTATTCCAATTTCATCCC
1 AAAACATGACCCTCATTATAAATTAATCCTTAAACTTTTGAA-TATTCCAATTTCATCCC
13535 CAAATTCATC
Statistics
Matches: 96, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
59 5 0.05
60 84 0.88
61 7 0.07
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (61 bp):
AAAACATGACCCTCATTATAAATTAATCCTTAAACTTTTGAATATTCCAATTTCATCCCAT
Found at i:13814 original size:60 final size:60
Alignment explanation
Indices: 13655--13824 Score: 177
Period size: 60 Copynumber: 2.8 Consensus size: 60
13645 CATATAGCTT
* * * * * *
13655 GGGATGAAATTGGAATATTAAAAAAGTTTGGGGACCAATTTAGAATGAAGGTTATAGTTTG
1 GGGATGAAATTTGAATATT-AAAAAGTTTAGAGACTAATTTAGAATGAAGGTCATAGTTTA
* *
13716 GGGATGAAA-TTGAAATATTCAAAAGTTTA-AGGATTAATTTAGAATGATA-GTCATAGTTTA
1 GGGATGAAATTTG-AATATTAAAAAGTTTAGA-GACTAATTTAGAATGA-AGGTCATAGTTTA
* * *
13776 GTGATGAAATTTGAATATTTAAAAGTTTAGAGACTAATTTAAAAT-AAGG
1 GGGATGAAATTTGAATATTAAAAAGTTTAGAGACTAATTTAGAATGAAGG
13825 GTCCTACTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
58 1 0.01
59 2 0.02
60 68 0.75
61 20 0.22
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (60 bp):
GGGATGAAATTTGAATATTAAAAAGTTTAGAGACTAATTTAGAATGAAGGTCATAGTTTA
Found at i:14238 original size:75 final size:75
Alignment explanation
Indices: 14129--14275 Score: 276
Period size: 75 Copynumber: 2.0 Consensus size: 75
14119 TTTAGACACA
14129 TTCAGTCATTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATT
1 TTCAGTCATTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATT
14194 TTTTACCACG
66 TTTTACCACG
* *
14204 TTCAGTCGTTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCTTTTTCAATTAATT
1 TTCAGTCATTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATT
14269 TTTTACC
66 TTTTACC
14276 TCAACAGGCA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.54
Consensus pattern (75 bp):
TTCAGTCATTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATT
TTTTACCACG
Found at i:14294 original size:75 final size:75
Alignment explanation
Indices: 14135--14301 Score: 232
Period size: 75 Copynumber: 2.3 Consensus size: 75
14125 CACATTCAGT
*
14135 CATTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATTTTTTAC
1 CATTAATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATTTTTTAC
** *
14200 CACGTTCAGT
66 CACGAACAGG
* * *
14210 CGTTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCTTTTTCAATTAATTTTTTAC
1 CATTAATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATTTTTTAC
*
14275 CTC-AACAGG
66 CACGAACAGG
14284 CATCTAATTAT--ATATTAA
1 CAT-TAATTATCAATATTAA
14302 ATTGAATTAA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
73 7 0.08
74 5 0.06
75 71 0.86
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (75 bp):
CATTAATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATTTTTTAC
CACGAACAGG
Found at i:16831 original size:38 final size:37
Alignment explanation
Indices: 16715--16961 Score: 367
Period size: 37 Copynumber: 6.7 Consensus size: 37
16705 AAACAATCGT
*
16715 TTTTGAAAAATATATATAATATATAATTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
* *
16752 TTTTGAAAAATATATATAATATATAATTTTTAAATCA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
*
16789 TTTTGAAAAAT-TATATAATATATAGTTTTTAAAAACTT
1 TTTTGAAAAATATATATAATATATAGTTTTT-AAAAC-A
*
16827 TTTTGAAAACT-TATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
16863 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAA-ATATATATAATATATAGTTTTTAAAACA
*
16901 TTTT-AAAAATATATATATTATATAG-TTTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
*
16936 TTTTGAAATATATATATATATATATA
1 TTTTGAAAAATATATATA-ATATATA
16962 TTATAGTTTT
Statistics
Matches: 194, Mismatches: 10, Indels: 12
0.90 0.05 0.06
Matches are distributed among these distances:
35 14 0.07
36 55 0.28
37 67 0.35
38 58 0.30
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
Found at i:16993 original size:44 final size:40
Alignment explanation
Indices: 16715--16994 Score: 221
Period size: 38 Copynumber: 7.4 Consensus size: 40
16705 AAACAATCGT
* *
16715 TTTTGAAAAATATATATA-ATA-TATA-ATTTTTAAAACA
1 TTTTGAAACATATATATATATATTATATAGTTTTAAAACA
* * *
16752 TTTTGAAAAATATATATA-ATA-TATA-ATTTTTAAATCA
1 TTTTGAAACATATATATATATATTATATAGTTTTAAAACA
*
16789 TTTTGAAA-A-AT-TATATA-A-TATATAGTTTTTAAAAACTT
1 TTTTGAAACATATATATATATATTATATAG-TTTT-AAAAC-A
*
16827 TTTTGAAA-A-CT-TATATA-A-TATATAGTTTTTAAAACA
1 TTTTGAAACATATATATATATATTATATAG-TTTTAAAACA
16863 TTTTGAAA-ATATATATATA-A-TATATAGTTTTTAAAACA
1 TTTTGAAACATATATATATATATTATATAG-TTTTAAAACA
16901 TTTT--AA-A-A-ATATATATATTATATAGTTTTAAAACA
1 TTTTGAAACATATATATATATATTATATAGTTTTAAAACA
* **
16936 TTTTGAAATATATATATATATATATATTATAGTTTTAAAATGT
1 TTTTGAAACATATATATATATAT-TA-TATAGTTTTAAAA-CA
16979 TTTTGAAAACATATAT
1 TTTTG-AAACATATAT
16995 TCTATGGTTT
Statistics
Matches: 215, Mismatches: 10, Indels: 29
0.85 0.04 0.11
Matches are distributed among these distances:
34 16 0.07
35 20 0.09
36 24 0.11
37 56 0.26
38 59 0.27
39 1 0.00
40 10 0.05
41 2 0.01
42 13 0.06
43 5 0.02
44 9 0.04
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (40 bp):
TTTTGAAACATATATATATATATTATATAGTTTTAAAACA
Found at i:17082 original size:4 final size:4
Alignment explanation
Indices: 17060--17127 Score: 58
Period size: 4 Copynumber: 17.8 Consensus size: 4
17050 AAAATGTTTT
17060 TTTA TTATA TTTA --TA TTTA TTTA TTTA -TTA TTTA TTTTA TTT- TATTA
1 TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA T-TTA
*
17107 TTTA -TTA CTTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT
17128 TTATTTTTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
2 2 0.04
3 10 0.18
4 34 0.62
5 9 0.16
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:17131 original size:24 final size:25
Alignment explanation
Indices: 17061--17133 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 25
17051 AAATGTTTTT
*
17061 TTATTATATTTATATTTATTTATTTA
1 TTATT-TATTTATTTTTATTTATTTA
17087 TTATTTATTT-TATTTTA-TTATTTA
1 TTATTTATTTAT-TTTTATTTATTTA
17111 TTACTTATTATTTATTTTTATTT
1 TTA--T-TTATTTATTTTTATTT
17134 TTCAGGTCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
24 11 0.28
25 9 0.22
26 6 0.15
27 11 0.28
28 3 0.08
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (25 bp):
TTATTTATTTATTTTTATTTATTTA
Found at i:18154 original size:23 final size:23
Alignment explanation
Indices: 18128--18174 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
18118 TTTATGCATG
18128 TTTTAATTTAGCCATTATTATTT
1 TTTTAATTTAGCCATTATTATTT
* *
18151 TTTTGATTTAGCCATTGTTATTT
1 TTTTAATTTAGCCATTATTATTT
18174 T
1 T
18175 AATTTTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (23 bp):
TTTTAATTTAGCCATTATTATTT
Found at i:19469 original size:15 final size:15
Alignment explanation
Indices: 19451--19480 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19441 TAATTTAATC
19451 AAAAATTAAAATGTT
1 AAAAATTAAAATGTT
*
19466 AAAAGTTAAAATGTT
1 AAAAATTAAAATGTT
19481 CTAAAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (15 bp):
AAAAATTAAAATGTT
Found at i:20527 original size:3 final size:3
Alignment explanation
Indices: 20519--20573 Score: 101
Period size: 3 Copynumber: 18.0 Consensus size: 3
20509 TTGACGTTAC
20519 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
20567 GAGA GAA
1 GA-A GAA
20574 ATGAGACACC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:23435 original size:37 final size:37
Alignment explanation
Indices: 23380--23452 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
23370 GGGGTAAGTA
*
23380 TCTCGTTGTTATTACTCTTAAACTAGCTTCGAGTGTC
1 TCTCCTTGTTATTACTCTTAAACTAGCTTCGAGTGTC
* *
23417 TCTCCTTGTTATTACTCTTAAATTAGCTTTGAGTGT
1 TCTCCTTGTTATTACTCTTAAACTAGCTTCGAGTGT
23453 ATTTCTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (37 bp):
TCTCCTTGTTATTACTCTTAAACTAGCTTCGAGTGTC
Found at i:26006 original size:3 final size:3
Alignment explanation
Indices: 25998--26072 Score: 114
Period size: 3 Copynumber: 25.0 Consensus size: 3
25988 ATTGATTTAT
* * *
25998 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
26046 ATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
26073 AATATATTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:26080 original size:12 final size:14
Alignment explanation
Indices: 26005--26081 Score: 81
Period size: 15 Copynumber: 5.6 Consensus size: 14
25995 TATTTATTAT
26005 TATTATTATTATAA
1 TATTATTATTATAA
26019 TTATTATTATTAT--
1 -TATTATTATTATAA
*
26032 TATAATTATTATAAA
1 TATTATTATTAT-AA
*
26047 TATTATTATTATTAT
1 TATTATTATTA-TAA
26062 TATTATTATTA-AA
1 TATTATTATTATAA
26075 TA-TATTA
1 TATTATTA
26082 AATATATATA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
12 16 0.30
13 3 0.06
15 34 0.63
16 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTATTATTATAA
Found at i:28700 original size:9 final size:9
Alignment explanation
Indices: 28686--28710 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28676 TTACATGTAA
28686 ATTTAAATT
1 ATTTAAATT
28695 ATTTAAATT
1 ATTTAAATT
28704 ATTTAAA
1 ATTTAAA
28711 AGCATGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTTAAATT
Found at i:31487 original size:15 final size:15
Alignment explanation
Indices: 31467--31498 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31457 ATCAATACCT
31467 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
31482 TTTTGCATACATTCA
1 TTTTGCATACATGCA
31497 TT
1 TT
31499 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:39184 original size:16 final size:16
Alignment explanation
Indices: 39158--39202 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
39148 TTTGAAAACA
*
39158 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
39175 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
39190 ATTCAATTTATTT
1 ATTCAATTTATTT
39203 TCGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:40131 original size:83 final size:83
Alignment explanation
Indices: 39987--40461 Score: 815
Period size: 83 Copynumber: 5.7 Consensus size: 83
39977 ATTAGCTGGA
* * * *
39987 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
*
40052 ACTAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
40070 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
40135 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
** * *
40153 AAGAATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
*
40218 ACTAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
40236 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
40301 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
** * *
40319 AAGAATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
40384 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
*
40402 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTTG
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
40462 ATATGAAACC
Statistics
Matches: 368, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 368 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (83 bp):
AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
ACCAATCATTGAATTTGG
Found at i:40267 original size:166 final size:166
Alignment explanation
Indices: 39993--40461 Score: 911
Period size: 166 Copynumber: 2.8 Consensus size: 166
39983 TGGAAAGATG
*
39993 AATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAAT
40058 CATTGAATTTGGAAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
66 CATTGAATTTGGAAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
40123 TGGTTTGGTAAAACCAATCATTGAATTTGGAAGAAT
131 TGGTTTGGTAAAACCAATCATTGAATTTGGAAGAAT
40159 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAAT
40224 CATTGAATTTGGAAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
66 CATTGAATTTGGAAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
40289 TGGTTTGGTAAAACCAATCATTGAATTTGGAAGAAT
131 TGGTTTGGTAAAACCAATCATTGAATTTGGAAGAAT
*
40325 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAAT
*
40390 CATTGAATTTGGAAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATC
66 CATTGAATTTGGAAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
40455 TGGTTTG
131 TGGTTTG
40462 ATATGAAACC
Statistics
Matches: 300, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 300 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (166 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAAT
CATTGAATTTGGAAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTAAAACCAATCATTGAATTTGGAAGAAT
Found at i:41493 original size:23 final size:23
Alignment explanation
Indices: 41463--41506 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
41453 AGTTCATAAT
*
41463 GAGAAGAACTCATCTGAAGAAGG
1 GAGAAGAACTCATCTAAAGAAGG
41486 GAGAAGAACTCATCTAAAGAA
1 GAGAAGAACTCATCTAAAGAA
41507 CTTGTTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.14, G:0.25, T:0.14
Consensus pattern (23 bp):
GAGAAGAACTCATCTAAAGAAGG
Found at i:41678 original size:113 final size:113
Alignment explanation
Indices: 41304--41970 Score: 847
Period size: 113 Copynumber: 6.0 Consensus size: 113
41294 GCAAAGATTT
* * **** *
41304 AAATCCATCA-TTCAATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATTTGAA
1 AAATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
41368 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
41417 AAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * * * *
41482 AAGGGAGAAG-AACTCAT-CT-A-AAGAACTTGTTTAACCCTTTTGTTC
66 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-CCTTTTGCTC
41527 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
41592 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGCTC
66 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
41640 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * *
41705 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGTTT
66 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * * * * *
41753 AAATTCATCATTTGATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCAT-C
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATC-TGA
*
41816 TG-AAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
64 AGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
41865 AAATCCATCACTTGATGGAGCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCT----
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * ** *
41925 AAAGAAGAAGAAGTTCATAATAAGAAGAGCTTGTTCAACTTTTTGC
66 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
41971 ATAATTCTAT
Statistics
Matches: 484, Mismatches: 60, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
108 40 0.08
109 12 0.02
110 82 0.17
111 30 0.06
112 75 0.15
113 230 0.48
114 15 0.03
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:41692 original size:223 final size:224
Alignment explanation
Indices: 41304--41969 Score: 931
Period size: 223 Copynumber: 3.0 Consensus size: 224
41294 GCAAAGATTT
* ** *
41304 AAATCCATCATTCAATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATTTGAAG
1 AAATCCATCATT-GATGGATCAACTTTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
41369 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
64 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
* * *
41434 GATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGGAGAAGAA-CTCA
129 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGCTCA
* *
41498 T-CT-A-AAGAACTTGTTTAACCCTTTTGTTC
194 TAATAAGAAGAACTTGTTCAA-CCTTTTGTTC
* *
41527 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCA-TTGATGGATCAACTTTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
41592 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGCTCAAATCCATCATTTGATG
64 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
*
41657 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
129 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGCTCA
* *
41722 TAATAAGAAGAATTTGTTCAACCTTTTGTTT
194 TAATAAGAAGAACTTGTTCAACCTTTTGTTC
* * * * * **
41753 AAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCAT-CT
1 AAATCCATCA-TTGATGGATCAACTTTTCCAGG-AGAGTTCATAATGAGAAGAACTCATC-TGAA
41817 G-AAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGAT
63 GAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGAT
* *
41881 GGAGCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCT--A-AA-GAAGAAGAAGTTC
128 GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGCTC
* *
41941 ATAATAAGAAGAGCTTGTTCAACTTTTTG
193 ATAATAAGAAGAACTTGTTCAACCTTTTG
41970 CATAATTCTA
Statistics
Matches: 402, Mismatches: 34, Indels: 17
0.89 0.08 0.04
Matches are distributed among these distances:
220 39 0.10
221 2 0.00
222 1 0.00
223 174 0.43
224 32 0.08
225 80 0.20
226 61 0.15
227 13 0.03
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (224 bp):
AAATCCATCATTGATGGATCAACTTTTCCAGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
AGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGA
TCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGCTCATA
ATAAGAAGAACTTGTTCAACCTTTTGTTC
Found at i:41935 original size:336 final size:332
Alignment explanation
Indices: 41304--41967 Score: 928
Period size: 336 Copynumber: 2.0 Consensus size: 332
41294 GCAAAGATTT
**** *
41304 AAATCCATCATTCAATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATTTGAAG
1 AAATCCATCATTCAATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
41369 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
66 AAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
* * *
41434 GATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGGAGAAGAACTCAT
131 GATTAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAACTCAT
* * * *
41499 CTAAAGAACTTGTTTAACCCTTTTGTTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAA
196 ATAAAGAACTTGTTCAACCCTTTTGCTCAAATCCATCACTTGATGGAGCAGCTTTTCCAGAGAAA
* * *
41564 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
261 GTTCATAATGAGAAGAACTCATCTAAAGAAAGAAGAAG---TTCATAATAAGAAGAACTTGTTCA
41629 ATCTTTTGCTC
323 A-CTTTTGCTC
** *
41640 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCAATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * *
41705 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATG
66 AAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
* *
41770 GATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AAT
131 GATTAACATTGCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAC
*
41831 TCATAATGAGAAGAATTTGTTCAA-CCTTTTGCTCAAATCCATCACTTGATGGAGCAGCTTTTCC
192 TCAT-AT-A-AAGAACTTGTTCAACCCTTTTGCTCAAATCCATCACTTGATGGAGCAGCTTTTCC
*
41895 AGAG-AAGTTCATAATGAGAAGAACTCATCTAAAG-AAGAAGAAGTTCATAATAAGAAGAGCTTG
254 AGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAAGAAGAAGTTCATAATAAGAAGAACTTG
41958 TTCAACTTTT
319 TTCAACTTTT
41968 TGCATAATTC
Statistics
Matches: 293, Mismatches: 28, Indels: 18
0.86 0.08 0.05
Matches are distributed among these distances:
332 5 0.02
333 22 0.08
335 1 0.00
336 163 0.56
337 31 0.11
338 47 0.16
339 24 0.08
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (332 bp):
AAATCCATCATTCAATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
GATTAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAACTCAT
ATAAAGAACTTGTTCAACCCTTTTGCTCAAATCCATCACTTGATGGAGCAGCTTTTCCAGAGAAA
GTTCATAATGAGAAGAACTCATCTAAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACT
TTTGCTC
Found at i:41951 original size:17 final size:17
Alignment explanation
Indices: 41897--41952 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
41887 GCTTTTCCAG
*
41897 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATAAGA
* *
41914 AGAA-CTCATCTAAAGAAGA
1 AGAAGTTCA--T-AATAAGA
41933 AGAAGTTCATAATAAGA
1 AGAAGTTCATAATAAGA
41950 AGA
1 AGA
41953 GCTTGTTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 3 0.10
17 13 0.43
18 2 0.07
19 9 0.30
20 3 0.10
ACGTcount: A:0.52, C:0.09, G:0.20, T:0.20
Consensus pattern (17 bp):
AGAAGTTCATAATAAGA
Found at i:42089 original size:84 final size:82
Alignment explanation
Indices: 41935--42118 Score: 208
Period size: 84 Copynumber: 2.2 Consensus size: 82
41925 AAAGAAGAAG
* * * * * * *
41935 AAGTTCATAATAAGAAGAGCTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTA
1 AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAAAAGATCA
*
42000 GCATCAGCCTTTCCAG-AGA
66 ACATCAGCC---CCAGTAGA
* * * *
42019 AAGTTCATAATGAGAAGAGCTTATTTAACCTTTTGAATGACTCTATCACAGAAGGAAAAAGGTCA
1 AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAAAAGATCA
* *
42084 ACATCATCCCCAGTGGA
66 ACATCAGCCCCAGTAGA
42101 AAGTTCATAATAAGAAGA
1 AAGTTCATAATAAGAAGA
42119 ACTCATCTGA
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
81 4 0.05
82 19 0.23
84 61 0.73
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (82 bp):
AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAAAAGATCA
ACATCAGCCCCAGTAGA
Found at i:42297 original size:3 final size:3
Alignment explanation
Indices: 42289--42389 Score: 195
Period size: 3 Copynumber: 34.0 Consensus size: 3
42279 ATTGATTTAT
42289 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42337 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42384 TTA TTA
1 TTA TTA
42390 AATATATTAA
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 95 0.98
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:45006 original size:6 final size:6
Alignment explanation
Indices: 44995--45089 Score: 100
Period size: 6 Copynumber: 15.8 Consensus size: 6
44985 AACACAAGGA
* * *
44995 GAAGAT GAAGAT AAAGAT GAAGAT GAAGAT AAAGAT GAAGAT AAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * * * *
45043 GAAGAT AAAGAT GATGAT TAAGAT AAAGAT GATGAT TAAGAT TAAGA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
45090 GAGTGTAAGC
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.54, C:0.00, G:0.25, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:51145 original size:2 final size:2
Alignment explanation
Indices: 51098--51133 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
51088 ATTAAATAAT
51098 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
51134 ATGTTAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54959 original size:32 final size:33
Alignment explanation
Indices: 54907--54983 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 33
54897 TAATGCTAAG
*
54907 AATTTATCGAGTGGGATTGAATAAAAA-ATTCA
1 AATTTATTGAGTGGGATTGAATAAAAATATTCA
54939 AATTTATTGAGTCGGG-TTGAATAAAAATATTCA
1 AATTTATTGAGT-GGGATTGAATAAAAATATTCA
*
54972 AATTAATTGAGT
1 AATTTATTGAGT
54984 TAATGAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
32 22 0.54
33 19 0.46
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (33 bp):
AATTTATTGAGTGGGATTGAATAAAAATATTCA
Found at i:54981 original size:33 final size:32
Alignment explanation
Indices: 54915--54983 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 32
54905 AGAATTTATC
*
54915 GAGTGGGATTGAATAAAAAATTCAAATTTATT
1 GAGTGGGATTGAATAAAAAATTCAAATTAATT
54947 GAGTCGGG-TTGAATAAAAATATTCAAATTAATT
1 GAGT-GGGATTGAATAAAAA-ATTCAAATTAATT
54980 GAGT
1 GAGT
54984 TAATGAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 15 0.44
33 19 0.56
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.33
Consensus pattern (32 bp):
GAGTGGGATTGAATAAAAAATTCAAATTAATT
Found at i:60883 original size:19 final size:19
Alignment explanation
Indices: 60859--60963 Score: 111
Period size: 19 Copynumber: 5.2 Consensus size: 19
60849 CGGTTTTGAA
60859 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
60878 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
60897 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
* *
60917 GAAAAACGATTTGTTGCGATAGTG
1 ---AAA--ATGTGTTGCGATAGTT
* *
60941 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
60960 AAAA
1 AAAA
60964 ATCCAAAATA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
19 53 0.72
20 2 0.03
21 3 0.04
23 3 0.04
24 1 0.01
25 12 0.16
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:61059 original size:17 final size:17
Alignment explanation
Indices: 61037--61075 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
61027 GTGTTGCGAT
*
61037 AGTGTAAAAGATTCTCA
1 AGTGTAAAAGATTCCCA
61054 AGTGTAAAAGATTCCCA
1 AGTGTAAAAGATTCCCA
61071 AGTGT
1 AGTGT
61076 TTGCAATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (17 bp):
AGTGTAAAAGATTCCCA
Found at i:62043 original size:19 final size:19
Alignment explanation
Indices: 61988--62073 Score: 64
Period size: 21 Copynumber: 4.3 Consensus size: 19
61978 TCGTTGCGAT
61988 TTTGGAAAATCGCAACGCGAA
1 TTTGGAAAATCGCAA--CGAA
* * ** *
62009 CTTCGACTATCACAACGAA
1 TTTGGAAAATCGCAACGAA
62028 TTTGGAAAATCGCAACGTGAA
1 TTTGGAAAATCGCAAC--GAA
* **
62049 CTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGAA
62068 TTTGGA
1 TTTGGA
62074 CTAACATAAA
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
19 23 0.47
21 26 0.53
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (19 bp):
TTTGGAAAATCGCAACGAA
Found at i:62043 original size:40 final size:40
Alignment explanation
Indices: 61988--62073 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
61978 TCGTTGCGAT
61988 TTTGGAAAATCGCAACGCGAACTTCGACTATCACAACGAA
1 TTTGGAAAATCGCAACGCGAACTTCGACTATCACAACGAA
* * *
62028 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGCGAACTTCGACTATCACAACGAA
62068 TTTGGA
1 TTTGGA
62074 CTAACATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (40 bp):
TTTGGAAAATCGCAACGCGAACTTCGACTATCACAACGAA
Found at i:62054 original size:21 final size:20
Alignment explanation
Indices: 61989--62065 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 20
61979 CGTTGCGATT
61989 TTGGAAAATCGCAACGCGAAC
1 TTGGAAAATCGCAACG-GAAC
* ** * *
62010 TTCGACTATCACAAC-GAAT
1 TTGGAAAATCGCAACGGAAC
62029 TTGGAAAATCGCAACGTGAAC
1 TTGGAAAATCGCAACG-GAAC
**
62050 TTGGACTATCGCAACG
1 TTGGAAAATCGCAACG
62066 AATTTGGACT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 14 0.33
21 28 0.67
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
TTGGAAAATCGCAACGGAAC
Found at i:62074 original size:19 final size:19
Alignment explanation
Indices: 62013--62076 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
62003 CGCGAACTTC
*
62013 GACTATCACAACGAATTTG
1 GACTATCGCAACGAATTTG
** *
62032 GAAAATCGCAACGTGAACTTG
1 GACTATCGCAAC--GAATTTG
62053 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTG
62072 GACTA
1 GACTA
62077 ACATAAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
19 20 0.56
21 16 0.44
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (19 bp):
GACTATCGCAACGAATTTG
Found at i:62958 original size:17 final size:17
Alignment explanation
Indices: 62936--62991 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
62926 TATTTTTTAT
*
62936 TATTATATTTGTATAAA
1 TATTATATTTATATAAA
*
62953 TATTAT-TTTTTATTAAA
1 TATTATATTTATA-TAAA
* *
62970 -ATAATATTTATATAAT
1 TATTATATTTATATAAA
62986 TATTAT
1 TATTAT
62992 TTATTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TATTATATTTATATAAA
Found at i:62988 original size:30 final size:28
Alignment explanation
Indices: 62954--63021 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 28
62944 TTGTATAAAT
*
62954 ATTATTTTTTATTAAAATAATATTTATATA
1 ATTATTTTTTATTAAAATAA-ATTAAT-TA
* * *
62984 ATTATTATTTATTTAAATTAATTAATTA
1 ATTATTTTTTATTAAAATAAATTAATTA
63012 ATTATTTTTT
1 ATTATTTTTT
63022 GTACTAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 11 0.33
29 5 0.15
30 17 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTATTTTTTATTAAAATAAATTAATTA
Found at i:63199 original size:17 final size:17
Alignment explanation
Indices: 63162--63200 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
63152 TATTATTTTT
* *
63162 AATTTATATTTATAATG
1 AATTTATATTAATAATA
*
63179 AATTTATATTAATTATA
1 AATTTATATTAATAATA
63196 AATTT
1 AATTT
63201 TTATAATGCA
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:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTATATTAATAATA
Found at i:64825 original size:21 final size:21
Alignment explanation
Indices: 64799--64864 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
64789 TCTTCGCAGT
*
64799 GTTACATTCCTATCCCTCAGG
1 GTTACATTCCTAGCCCTCAGG
*
64820 GTTACATTCCTAGCCTGTCA-G
1 GTTACATTCCTAGCC-CTCAGG
* *
64841 GTTACATGCCTAGCCCACAGG
1 GTTACATTCCTAGCCCTCAGG
64862 GTT
1 GTT
64865 TTATGACACC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 2 0.05
21 33 0.87
22 3 0.08
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
GTTACATTCCTAGCCCTCAGG
Found at i:65541 original size:14 final size:14
Alignment explanation
Indices: 65522--65548 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65512 TATCCTTAAC
65522 ATATACATTAAAAT
1 ATATACATTAAAAT
65536 ATATACATTAAAA
1 ATATACATTAAAA
65549 CCAACTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATACATTAAAAT
Found at i:65719 original size:63 final size:64
Alignment explanation
Indices: 65615--65744 Score: 190
Period size: 63 Copynumber: 2.0 Consensus size: 64
65605 TTTCATGCAC
* * *
65615 ACAACCAACTTATCACTTCACATTTATTCAATTTGTCCATAACATTTTATCTAATATATTCA-A
1 ACAACCAAATGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCTAATATATTCATA
* * * *
65678 ACAACCAAATGATCACTTCACATTTATTCAATTTATTCATAATATTTTATCTTATTTATTCATA
1 ACAACCAAATGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCTAATATATTCATA
65742 ACA
1 ACA
65745 TTTTATCCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
63 55 0.93
64 4 0.07
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.42
Consensus pattern (64 bp):
ACAACCAAATGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCTAATATATTCATA
Found at i:65734 original size:23 final size:23
Alignment explanation
Indices: 65700--65760 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
65690 TCACTTCACA
* *
65700 TTTATTCAATTTATTCATAATAT
1 TTTATCCAATTTATTCATAACAT
**
65723 TTTATCTTATTTATTCATAACAT
1 TTTATCCAATTTATTCATAACAT
65746 TTTATCCAATTTATT
1 TTTATCCAATTTATT
65761 GAAACTTCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTATCCAATTTATTCATAACAT
Found at i:66165 original size:116 final size:116
Alignment explanation
Indices: 65807--66697 Score: 1484
Period size: 116 Copynumber: 7.7 Consensus size: 116
65797 ATCCAATTTC
* *
65807 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTTACAAAATAATGGAAGGTGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* * *
65872 GGACCGCGCTTTCACCACTTTGGGTACTGACATGAATAGTG-CCCCAAGGG
66 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGG
65922 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGC-CCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
65986 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGG
66 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGG
** *
66037 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATTAAATAATGGAAGGCACCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
*
66102 GGAACGC-CCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCTGAGGG
66 GGAACGCGCC-TTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGG
* *
66153 ACATGAGGGACATAATAGGGCAATGATAACATATTCTATGACAAAATAATGGAAGGCGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
*
66218 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCTGAGGG
66 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGG
*
66269 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCCCTCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCC-CCC
* * *
66334 GGGAACGTGGCTTCACCACTTTGGGCACTGACATGAATAGTGCCCCCGAGGG
65 GGGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGG
*
66386 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATAATGGAAGGCGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* * * *
66451 GGAACGCGCCATCACCACTTTGGGTTA-AGATATGAATAGTGCCCCCAAGGG
66 GGAACGCGCCTTCACCACTTTGGG-TACTGACATGAATAGTGCCCCCGAGGG
* * *
66502 GCATGAGTGACGTAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCACCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* *
66567 GGAACGCGCCTTCACCACTTTGGGTTCTGACATGAATAGTGCTCCCGAGGG
66 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGG
66618 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
*
66683 GGAACGCACCTTCAC
66 GGAACGCGCCTTCAC
66698 GTGAATAGTA
Statistics
Matches: 726, Mismatches: 43, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
114 46 0.06
115 121 0.17
116 446 0.61
117 113 0.16
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (116 bp):
ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGG
Found at i:66450 original size:349 final size:346
Alignment explanation
Indices: 65807--66697 Score: 1473
Period size: 349 Copynumber: 2.6 Consensus size: 346
65797 ATCCAATTTC
* *
65807 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTTACAAAATAATGGAAGGTGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* * *
65872 GGACCGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCAAGGGACATGAGTGACATAA
66 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCGAGGGACATGAGTGACATAA
65937 TAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAG-GCCCCCCCGGGAACGCGCCTTCAC
131 TAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGCG-CCCCCCGGGAACGCGCCTTCAC
*
66001 CACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAA
195 CACTTTGGGCACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAA
* ** *
66066 CATATTCTCTGATTAAATAATGGAAGGCACCCCCCGGGAACGC-CCTTTCACCACTTTGGG-TAC
260 CATATTCTCTAACAAAATAATGGAAGGCACCCCCCGGGAACGCGCC-ATCACCACTTTGGGTTA-
* **
66129 TGACATGAATAGTGCCCCTGAGGG
323 AGACATGAATAGTGCCCCCAAGGG
* *
66153 ACATGAGGGACATAATAGGGCAATGATAACATATTCTATGACAAAATAATGGAAGGCGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
66218 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCTGAGGGACATGAGTGACATA
66 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCC-GAGGGACATGAGTGACATA
* *
66283 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCCCTCCCGGGAACGTGGCTTC
130 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA-GCGCCC-CCCGGGAACGCGCCTTC
66348 ACCACTTTGGGCACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGAT
193 ACCACTTTGGGCACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGAT
*
66413 AACATATTCTCTAACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCATCACCACTTTGGGTTA
258 AACATATTCTCTAACAAAATAATGGAAGGCACCCCCCGGGAACGCGCCATCACCACTTTGGGTTA
*
66478 AGATATGAATAGTGCCCCCAAGGG
323 AGACATGAATAGTGCCCCCAAGGG
* * *
66502 GCATGAGTGACGTAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCACCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
*
66567 GGAACGCGCCTTCACCACTTTGGGTTCTGACATGAATAGTGCTCCCGAGGGACATGAGTGACATA
66 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGC-CCCGAGGGACATGAGTGACATA
*
66632 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCACCTTCA
130 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA-GCGCCCCCCGGGAACGCGCCTTCA
66697 C
194 C
66698 GTGAATAGTA
Statistics
Matches: 509, Mismatches: 29, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
346 104 0.20
347 58 0.11
348 20 0.04
349 320 0.63
350 7 0.01
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (346 bp):
ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCGAGGGACATGAGTGACATAA
TAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGCGCCCCCCGGGAACGCGCCTTCACC
ACTTTGGGCACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAAC
ATATTCTCTAACAAAATAATGGAAGGCACCCCCCGGGAACGCGCCATCACCACTTTGGGTTAAGA
CATGAATAGTGCCCCCAAGGG
Found at i:69896 original size:26 final size:28
Alignment explanation
Indices: 69851--69911 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
69841 TATTTATATA
* *
69851 AATTATTTATATTGTAATTTTATAAAAT
1 AATTAATTATATTGTAATTTAATAAAAT
* *
69879 GATTAATTATATT-T-ATTTAATATAAT
1 AATTAATTATATTGTAATTTAATAAAAT
69905 AATTAAT
1 AATTAAT
69912 ATTTTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 16 0.57
27 1 0.04
28 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (28 bp):
AATTAATTATATTGTAATTTAATAAAAT
Found at i:70615 original size:61 final size:60
Alignment explanation
Indices: 70509--70625 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 60
70499 AAAATACCAG
* * * *
70509 CGTGACATCTGACTCAGCAGAACCTAGGTAAAGCGCATCCCCGGGGATGCGCCTTTCATA
1 CGTGACATCCGACTCAGCAAAACCCAGGAAAAGCGCATCCCCGGGGATGCGCCTTTCATA
* * *
70569 CGTGGCATCCGACTCAGCAAAAACCCAGGAAAAGCGCGTCCTCGGGGATGCGCCTTT
1 CGTGACATCCGACTCAGC-AAAACCCAGGAAAAGCGCATCCCCGGGGATGCGCCTTT
70626 GTGCCACCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 16 0.33
61 33 0.67
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.18
Consensus pattern (60 bp):
CGTGACATCCGACTCAGCAAAACCCAGGAAAAGCGCATCCCCGGGGATGCGCCTTTCATA
Found at i:71864 original size:22 final size:22
Alignment explanation
Indices: 71833--71885 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
71823 GATTTTTTTT
* *
71833 ATGAATAGTGATGAACAATACC
1 ATGAACAGTGATAAACAATACC
* *
71855 ATGAACAGTGATAAACAGTACT
1 ATGAACAGTGATAAACAATACC
*
71877 GTGAACAGT
1 ATGAACAGT
71886 ATATCGATGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (22 bp):
ATGAACAGTGATAAACAATACC
Found at i:72620 original size:57 final size:57
Alignment explanation
Indices: 72528--72645 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 57
72518 TGCTAACCCG
* * **
72528 TATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATAGTCCC-A
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATA-TCCCAA
* *
72585 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATCCCAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATATCCCAA
72642 TATG
1 TATG
72646 CAGCCTGCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 4 0.07
57 50 0.93
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (57 bp):
TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATATCCCAA
Found at i:81842 original size:20 final size:20
Alignment explanation
Indices: 81817--81863 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
81807 AACTGGTCAA
81817 CGGTTCGGGTCAGGTCAACT
1 CGGTTCGGGTCAGGTCAACT
* **
81837 CGGTTCAGGTTGGGTCAACT
1 CGGTTCGGGTCAGGTCAACT
*
81857 CAGTTCG
1 CGGTTCG
81864 TTTCGGTTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.15, C:0.23, G:0.34, T:0.28
Consensus pattern (20 bp):
CGGTTCGGGTCAGGTCAACT
Found at i:92252 original size:3 final size:3
Alignment explanation
Indices: 92244--92304 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
92234 TATAATTGAC
* *
92244 AAT AAT AAT AAT AGT AAGT AAT AAT AAT -AT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
92289 -AT AA- GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
92305 GTTAATAGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:92266 original size:33 final size:32
Alignment explanation
Indices: 92152--92304 Score: 95
Period size: 33 Copynumber: 4.8 Consensus size: 32
92142 ACAGTAATGG
* * *
92152 TAATAATATTATAATGTTATAATAATAGT-ATAA
1 TAATAATAATATAA-GTAATAATAATA-TAACAA
* *
92185 TAAT--TAATAATAA--AATGATAACTAAAACAA
1 TAATAATAAT-ATAAGTAATAATAA-TATAACAA
* * * *
92215 T-ATAGTAACATATGTAATATATAAT-TGACAA
1 TAATAATAATATAAGTAATA-ATAATATAACAA
*
92246 TAATAATAATAGTAAGTAATAATAATATAATAA
1 TAATAATAATA-TAAGTAATAATAATATAACAA
*
92279 TAATAGTAATATAAGATAATAATAAT
1 TAATAATAATATAAG-TAATAATAAT
92305 GTTAATAGCA
Statistics
Matches: 92, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
29 8 0.09
30 9 0.10
31 11 0.12
32 24 0.26
33 40 0.43
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.35
Consensus pattern (32 bp):
TAATAATAATATAAGTAATAATAATATAACAA
Found at i:92278 original size:11 final size:11
Alignment explanation
Indices: 92152--92304 Score: 73
Period size: 11 Copynumber: 13.6 Consensus size: 11
92142 ACAGTAATGG
*
92152 TAATAATATTA
1 TAATAATATAA
**
92163 TAATGTTATAA
1 TAATAATATAA
*
92174 TAATAGTATAA
1 TAATAATATAA
*
92185 TAATTA-ATAA
1 TAATAATATAA
92195 TAA-AATGATAA
1 TAATAAT-ATAA
* *
92206 CTAAAACAATATAG
1 -T--AATAATATAA
* *
92220 TAACATATGTAA
1 TAATA-ATATAA
*
92232 TATATAAT-TGA
1 TA-ATAATATAA
*
92243 CAATAATAATAA
1 TAATAAT-ATAA
* *
92255 TAGTAA-GTAA
1 TAATAATATAA
92265 TAATAATATAA
1 TAATAATATAA
92276 TAATAATAGTAA
1 TAATAATA-TAA
*
92288 T-ATAAGATAA
1 TAATAATATAA
92298 TAATAAT
1 TAATAAT
92305 GTTAATAGCA
Statistics
Matches: 107, Mismatches: 22, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
9 1 0.01
10 24 0.22
11 52 0.49
12 19 0.18
13 3 0.03
14 5 0.05
15 3 0.03
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.35
Consensus pattern (11 bp):
TAATAATATAA
Found at i:92298 original size:30 final size:27
Alignment explanation
Indices: 92245--92302 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 27
92235 ATAATTGACA
*
92245 ATAATAATAATAGTAAGTAATAATAAT
1 ATAATAATAATAGTAAATAATAATAAT
92272 ATAATAATAATAGTAATATAAGATAATAAT
1 ATAATAATAATAGTAA-AT-A-ATAATAAT
92302 A
1 A
92303 ATGTTAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 16 0.59
28 1 0.04
29 1 0.04
30 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (27 bp):
ATAATAATAATAGTAAATAATAATAAT
Found at i:94458 original size:17 final size:16
Alignment explanation
Indices: 94423--94470 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
94413 GCTTTAATCA
94423 TTTTTCAAAACTTCATTT
1 TTTTTCAAAAC--CATTT
94441 TTTTTCAAAACCAGTTT
1 TTTTTCAAAACCA-TTT
*
94458 TGCTTTCAAAACC
1 T-TTTTCAAAACC
94471 TAATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 2 0.07
17 4 0.15
18 21 0.78
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (16 bp):
TTTTTCAAAACCATTT
Done.