Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1364
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: 118566
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Found at i:86 original size:32 final size:32
Alignment explanation
Indices: 31--425 Score: 609
Period size: 32 Copynumber: 12.3 Consensus size: 32
21 TCAAGCCCGC
31 GTGGCAAACCC-TTCCAAACGCCCACACAAGTCG
1 GTGGC-AACCCATTCCAAA-GCCCACACAAGTCG
64 GTGGCAACCCATTCCAAAGCCCACACCAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACA-CAAGTCG
97 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
129 GTGGCAAACCCATTCCAAAGCCCACACAAGTCG
1 GTGGC-AACCCATTCCAAAGCCCACACAAGTCG
162 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
*
194 GT-GCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
*
225 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
*
257 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
* *
289 GTGGCAACCCATTTCAAAACCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
321 GTGG-AA-CCATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
* *
351 GTGGCAACTCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
** ** *
383 GTGGCAACCCCATTTAAAAGCCCATGCAAGTCA
1 GTGGCAA-CCCATTCCAAAGCCCACACAAGTCG
416 GTGGCAACCC
1 GTGGCAACCC
426 TTTTCAAATC
Statistics
Matches: 344, Mismatches: 11, Indels: 15
0.93 0.03 0.04
Matches are distributed among these distances:
30 26 0.08
31 34 0.10
32 181 0.53
33 103 0.30
ACGTcount: A:0.32, C:0.35, G:0.18, T:0.14
Consensus pattern (32 bp):
GTGGCAACCCATTCCAAAGCCCACACAAGTCG
Found at i:431 original size:65 final size:64
Alignment explanation
Indices: 31--433 Score: 616
Period size: 65 Copynumber: 6.3 Consensus size: 64
21 TCAAGCCCGC
*
31 GTGGCAAACCC-TTCCAAACGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACCAAGT
1 GTGGC-AACCCATTTCAAA-GCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACA-CAAGT
95 CG
63 CG
*
97 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAAACCCATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC-AACCCATTCCAAAGCCCACACAAGTCG
* *
162 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGT-GCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCG
*
225 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCG
*
289 GTGGCAACCCATTTCAAAACCCACACAAGTCGGTGG-AA-CCATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCG
* ** ** *
351 GTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCAACCCCATTTAAAAGCCCATGCAAGTCA
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAA-CCCATTCCAAAGCCCACACAAGTCG
*
416 GTGGCAACCCTTTTCAAA
1 GTGGCAACCCATTTCAAA
434 TCACCATTTT
Statistics
Matches: 318, Mismatches: 13, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
62 57 0.18
63 63 0.20
64 66 0.21
65 100 0.31
66 32 0.10
ACGTcount: A:0.32, C:0.35, G:0.18, T:0.15
Consensus pattern (64 bp):
GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCG
Found at i:991 original size:20 final size:20
Alignment explanation
Indices: 963--1037 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
953 TCATACCCTG
963 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
983 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1003 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1023 ATGTATCGATACATT
1 ATGTATCGATACATT
1038 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1030 original size:40 final size:39
Alignment explanation
Indices: 963--1040 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
953 TCATACCCTG
* *
963 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1003 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1041 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:7754 original size:3 final size:3
Alignment explanation
Indices: 7746--7787 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
7736 GGGATTGCAT
7746 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
7788 GTAGTAGTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8373 original size:2 final size:2
Alignment explanation
Indices: 8366--8394 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8356 AAACTTAATC
8366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8395 CGACAGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8669 original size:41 final size:39
Alignment explanation
Indices: 8613--8715 Score: 152
Period size: 39 Copynumber: 2.5 Consensus size: 39
8603 TGACATTATG
8613 ATATAATATATGTTTGACATTTTCTTTGAATTTCCCTTATAAT
1 ATATAAT-T-TGTTTGACATTTTCTTTGAATTTCCC--ATAAT
* *
8656 ATATAATTTGTTTGACTTTTTCTTTGAATTTTCCATAAT
1 ATATAATTTGTTTGACATTTTCTTTGAATTTCCCATAAT
8695 ATATAATTTGTTTGACATTTT
1 ATATAATTTGTTTGACATTTT
8716 TTTTATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
39 25 0.44
41 24 0.42
42 1 0.02
43 7 0.12
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (39 bp):
ATATAATTTGTTTGACATTTTCTTTGAATTTCCCATAAT
Found at i:8717 original size:41 final size:41
Alignment explanation
Indices: 8613--8716 Score: 151
Period size: 41 Copynumber: 2.5 Consensus size: 41
8603 TGACATTATG
8613 ATATAATATATGTTTGACA-TTTTCTTTGAATTTCCCTTATAAT
1 ATATAAT-T-TGTTTGACATTTTTCTTTGAATTTCCC-TATAAT
*
8656 ATATAATTTGTTTGAC-TTTTTCTTTGAATTTTCC-ATAAT
1 ATATAATTTGTTTGACATTTTTCTTTGAATTTCCCTATAAT
8695 ATATAATTTGTTTGACATTTTT
1 ATATAATTTGTTTGACATTTTT
8717 TTTATTTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
39 21 0.36
40 5 0.09
41 24 0.41
42 1 0.02
43 7 0.12
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.55
Consensus pattern (41 bp):
ATATAATTTGTTTGACATTTTTCTTTGAATTTCCCTATAAT
Found at i:9242 original size:20 final size:20
Alignment explanation
Indices: 9214--9288 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
9204 TTTTACCCAG
9214 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
9234 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
9254 ATGTATCGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
9274 ATGTATCGATACATT
1 ATGTATCGATACATT
9289 ATGTTTTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:9270 original size:40 final size:39
Alignment explanation
Indices: 9214--9291 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
9204 TTTTACCCAG
9214 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCAATATATCGATACAT-TATGA
* *
9254 ATGTATCGATATATTTTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTTTTCAATATATCGATACATTATG
9292 TTTTTTTACC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (39 bp):
ATGTATCGATACATTTTTCAATATATCGATACATTATGA
Found at i:13057 original size:3 final size:3
Alignment explanation
Indices: 13049--13095 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
13039 ATTGAGATAA
*
13049 ATT ATT ATT ATT ATT ATT ATT -TT ATT TTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13096 TCACAACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:13384 original size:18 final size:17
Alignment explanation
Indices: 13362--13411 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
13352 TTTAAGTTAT
13362 ATTTAATATTTATATAA
1 ATTTAATATTTATATAA
13379 ATTTTAATATGTTA-AT-A
1 A-TTTAATAT-TTATATAA
13396 ATTT-ATATTT-TATAA
1 ATTTAATATTTATATAA
13411 A
1 A
13412 GTTTGAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 3 0.10
17 3 0.10
18 10 0.34
19 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
ATTTAATATTTATATAA
Found at i:14043 original size:3 final size:3
Alignment explanation
Indices: 14030--14075 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
14020 TAAAAATTTT
* *
14030 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
14076 ATGAAATGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:14170 original size:15 final size:15
Alignment explanation
Indices: 14150--14198 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
14140 ACATTTCATG
14150 CATGCATTTTCATTT
1 CATGCATTTTCATTT
14165 CATGCA-TTTCA---
1 CATGCATTTTCATTT
*
14176 CAT-AATTTTCATTT
1 CATGCATTTTCATTT
14190 CATGCATTT
1 CATGCATTT
14199 CGTTTCATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
10 1 0.04
11 8 0.30
14 8 0.30
15 10 0.37
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.49
Consensus pattern (15 bp):
CATGCATTTTCATTT
Found at i:14173 original size:40 final size:40
Alignment explanation
Indices: 14121--14287 Score: 126
Period size: 40 Copynumber: 4.0 Consensus size: 40
14111 TGCATGCATA
*
14121 ATTTCATACATTTCACGTAACATTTCATGCATGCATTTTC
1 ATTTCATGCATTTCACGTAACATTTCATGCATGCATTTTC
* * *
14161 ATTTCATGCATTTCACATAATTTTCATTTCATGCATTTC-GTTTC
1 ATTTCATGCATTTCACGTAA----CATTTCATGCA-TGCATTTTC
*
14205 A-TACATGCATTTCA--TAAACATTTCAAGATTCATGCATGCATTTTC
1 ATTTCATGCATTTCACGT-AACA--T-----TTCATGCATGCATTTTC
* *
14250 ATTTCATGCATTTCAGGTAACAATTCATGCATGCATTT
1 ATTTCATGCATTTCACGTAACATTTCATGCATGCATTT
14288 CACATAATTT
Statistics
Matches: 101, Mismatches: 9, Indels: 34
0.70 0.06 0.24
Matches are distributed among these distances:
38 2 0.02
40 34 0.34
41 1 0.01
42 2 0.02
43 12 0.12
44 18 0.18
45 15 0.15
46 12 0.12
47 4 0.04
48 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (40 bp):
ATTTCATGCATTTCACGTAACATTTCATGCATGCATTTTC
Found at i:14174 original size:14 final size:14
Alignment explanation
Indices: 14141--14333 Score: 66
Period size: 14 Copynumber: 14.9 Consensus size: 14
14131 TTTCACGTAA
*
14141 CATTTCA-TGCATG
1 CATTTCATTTCATG
14154 CATTTTCATTTCATG
1 CA-TTTCATTTCATG
14169 CATTTCA---CAT-
1 CATTTCATTTCATG
*
14179 AATTTTCATTTCATG
1 CA-TTTCATTTCATG
* *
14194 CATTTCGTTTCATA
1 CATTTCATTTCATG
*
14208 CA-TGCATTTCAT-
1 CATTTCATTTCATG
** *
14220 -A-AACATTTCAAG
1 CATTTCATTTCATG
*
14232 -A-TTCA-TGCATG
1 CATTTCATTTCATG
14243 CATTTTCATTTCATG
1 CA-TTTCATTTCATG
** *
14258 CATTTCAGGT-A-A
1 CATTTCATTTCATG
* *
14270 CAATTCA-TGCATG
1 CATTTCATTTCATG
14283 CATTTCA---CAT-
1 CATTTCATTTCATG
*
14293 AATTTTCATTTCATG
1 CA-TTTCATTTCATG
14308 CATTTCATTTCATG
1 CATTTCATTTCATG
*
14322 CA-TGCATTTCAT
1 CATTTCATTTCAT
14334 AAACATTTCA
Statistics
Matches: 135, Mismatches: 26, Indels: 38
0.68 0.13 0.19
Matches are distributed among these distances:
10 2 0.01
11 28 0.21
12 11 0.08
13 26 0.19
14 52 0.39
15 16 0.12
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.44
Consensus pattern (14 bp):
CATTTCATTTCATG
Found at i:14289 original size:114 final size:115
Alignment explanation
Indices: 14165--14375 Score: 379
Period size: 114 Copynumber: 1.8 Consensus size: 115
14155 ATTTTCATTT
*
14165 CATGCATTTCACATAATTTTCATTTCATGCATTTCGTTTCATACATGCATTTCATAAACATTTCA
1 CATGCATTTCACATAATTTTCATTTCATGCATTTCATTTCATACATGCATTTCATAAACATTTCA
14230 AGATTCATGCATGC-ATTTTCATTTCATGCATTTCAGGTAACAATTCATG
66 AGATTCATGCATGCAATTTTCATTTCATGCATTTCAGGTAACAATTCATG
*
14279 CATGCATTTCACATAATTTTCATTTCATGCATTTCATTTCATGCATGCATTTCATAAACATTTCA
1 CATGCATTTCACATAATTTTCATTTCATGCATTTCATTTCATACATGCATTTCATAAACATTTCA
*
14344 AGCTTCATGCATGCAAATTTTCATTTCATGCA
66 AGATTCATGCATGC-AATTTTCATTTCATGCA
14376 ACATGCAAAT
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
114 76 0.83
116 16 0.17
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (115 bp):
CATGCATTTCACATAATTTTCATTTCATGCATTTCATTTCATACATGCATTTCATAAACATTTCA
AGATTCATGCATGCAATTTTCATTTCATGCATTTCAGGTAACAATTCATG
Found at i:14307 original size:25 final size:25
Alignment explanation
Indices: 14244--14314 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
14234 TCATGCATGC
**
14244 ATTTTCATTTCATGCATTTCAGGTA
1 ATTTTCATTTCATGCATTTCACATA
** *
14269 ACAATTCA-TGCATGCATTTCACATA
1 A-TTTTCATTTCATGCATTTCACATA
14294 ATTTTCATTTCATGCATTTCA
1 ATTTTCATTTCATGCATTTCA
14315 TTTCATGCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
24 4 0.11
25 28 0.78
26 4 0.11
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.44
Consensus pattern (25 bp):
ATTTTCATTTCATGCATTTCACATA
Found at i:14647 original size:27 final size:26
Alignment explanation
Indices: 14593--14652 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
14583 AAAAAAGGGG
14593 AAAAAACGTGAAAGCAATTCGAACAA
1 AAAAAACGTGAAAGCAATTCGAACAA
14619 AAAAAACGTGAAAGCAATTCGAACAA
1 AAAAAACGTGAAAGCAATTCGAACAA
14645 AAAGAAAC
1 AAA-AAAC
14653 AAAAGGTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 29 0.88
27 4 0.12
ACGTcount: A:0.60, C:0.15, G:0.15, T:0.10
Consensus pattern (26 bp):
AAAAAACGTGAAAGCAATTCGAACAA
Found at i:14664 original size:32 final size:30
Alignment explanation
Indices: 14595--14667 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 30
14585 AAAAGGGGAA
14595 AAAACGTGAAAGCAATTCGAACAAAAAAAAC
1 AAAA-GTGAAAGCAATTCGAACAAAAAAAAC
14626 ----GTGAAAGCAATTCGAACAAAAAGAAAC
1 AAAAGTGAAAGCAATTCGAACAAAAA-AAAC
14653 AAAAGGTGAAAGCAA
1 AAAA-GTGAAAGCAA
14668 AAATCCAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
26 22 0.61
27 4 0.11
32 10 0.28
ACGTcount: A:0.59, C:0.14, G:0.18, T:0.10
Consensus pattern (30 bp):
AAAAGTGAAAGCAATTCGAACAAAAAAAAC
Found at i:15169 original size:74 final size:74
Alignment explanation
Indices: 15083--15223 Score: 194
Period size: 74 Copynumber: 1.9 Consensus size: 74
15073 ACAATCCCCA
* * *
15083 AACACAGTAACTCCGGCAAACAGCAAACAGC-TCCGAGCAGCTTGCAACTAAGGCAGCTCCAGCT
1 AACACAGCAACTCCAGCAAACAGCAAACAGCTTCC-AGCAGCTTGCAACTAAGGCAACTCCAGCT
15147 CCAGCAATCG
65 CCAGCAATCG
* ** **
15157 AACACAGCAACTCCAGTAAACAGCAAGTAGCTTCCAGCAGCTTGCAACTCGGGCAACTCCAGCTC
1 AACACAGCAACTCCAGCAAACAGCAAACAGCTTCCAGCAGCTTGCAACTAAGGCAACTCCAGCTC
15222 CA
66 CA
15224 CTAACACGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 55 0.95
75 3 0.05
ACGTcount: A:0.33, C:0.34, G:0.19, T:0.13
Consensus pattern (74 bp):
AACACAGCAACTCCAGCAAACAGCAAACAGCTTCCAGCAGCTTGCAACTAAGGCAACTCCAGCTC
CAGCAATCG
Found at i:18370 original size:16 final size:16
Alignment explanation
Indices: 18331--18374 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
18321 TCATTTTTTG
* *
18331 TTCGAATCAATTCAAA
1 TTCGAATTATTTCAAA
18347 TTCGAATTATTTCAAA
1 TTCGAATTATTTCAAA
**
18363 TTTTAATTATTT
1 TTCGAATTATTT
18375 TCGAGTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (16 bp):
TTCGAATTATTTCAAA
Found at i:18939 original size:6 final size:6
Alignment explanation
Indices: 18928--18958 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
18918 ATATATTTTT
18928 AATATA AATATA AATATCA AATATA AATATA
1 AATATA AATATA AATAT-A AATATA AATATA
18959 TCTGACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:18951 original size:13 final size:12
Alignment explanation
Indices: 18928--18958 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
18918 ATATATTTTT
18928 AATATAAATATA
1 AATATAAATATA
18940 AATATCAAATATA
1 AATAT-AAATATA
18953 AATATA
1 AATATA
18959 TCTGACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATAAATATA
Found at i:21599 original size:26 final size:25
Alignment explanation
Indices: 21538--21604 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 25
21528 ATATTCAGAG
*
21538 GAAAA-TTACAAATTACATATTTCT
1 GAAAATTTACAACTTACATATTTCT
*
21562 GAAAATACTACAACTTACATATTTCT
1 GAAAAT-TTACAACTTACATATTTCT
21588 GCAAAATTTACAACTTA
1 G-AAAATTTACAACTTA
21605 AGATCCAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 5 0.14
26 27 0.73
27 5 0.14
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.34
Consensus pattern (25 bp):
GAAAATTTACAACTTACATATTTCT
Found at i:30023 original size:5 final size:5
Alignment explanation
Indices: 30000--30059 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
29990 TAAAATTACT
* * * *
30000 TTTAA TTTAA GTTAT TTTAA TTTATT TTTAAA TCTTAA ATTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTA-A TTT-AA T-TTAA TTTAA TTTAA
30048 TTTAA TTTAA TT
1 TTTAA TTTAA TT
30060 ATTTTAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
5 35 0.80
6 6 0.14
7 3 0.07
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:30046 original size:28 final size:26
Alignment explanation
Indices: 29999--30069 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 26
29989 TTAAAATTAC
* *
29999 TTTTAATTTAAGTTATTTTAATTTAT
1 TTTTAATTTAAATTAATTTAATTTAT
30025 TTTTAAATCTTAAATTAATTTAATTTAAT
1 TTTT-AAT-TTAAATTAATTTAATTT-AT
*
30054 TTAATTATTTTAAATT
1 TT--TTAATTTAAATT
30070 TTAAGATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 4 0.11
27 3 0.08
28 15 0.41
29 11 0.30
30 2 0.05
31 2 0.05
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (26 bp):
TTTTAATTTAAATTAATTTAATTTAT
Found at i:30158 original size:21 final size:19
Alignment explanation
Indices: 30141--30193 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 19
30131 TTTTTTATAT
30141 TTAATCATTTTAAATTTAGA
1 TTAATCATTTTAAATTTA-A
30161 -T--T-ATTTTAAATTTAAA
1 TTAATCATTTTAAATTT-AA
30177 TTAATCAATTTTAAATT
1 TTAATC-ATTTTAAATT
30194 ATTAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 11
0.71 0.00 0.29
Matches are distributed among these distances:
16 12 0.44
17 3 0.11
19 2 0.07
21 10 0.37
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (19 bp):
TTAATCATTTTAAATTTAA
Found at i:30166 original size:16 final size:16
Alignment explanation
Indices: 29976--30179 Score: 90
Period size: 15 Copynumber: 12.3 Consensus size: 16
29966 AATTATTTTT
29976 AATT-TTTTAAAATTTAA
1 AATTATTTT-AAATTT-A
29993 AATTACTTTT-AATTTA
1 AATTA-TTTTAAATTTA
*
30009 AGTTATTTT-AATTT-
1 AATTATTTTAAATTTA
30023 -A-T-TTTTAAATCTTA
1 AATTATTTTAAAT-TTA
*
30037 AATTAATTT-AATTTAA
1 AATTATTTTAAATTT-A
30053 TTTAATTATTTTAAATTTTA
1 ---AATTATTTTAAA-TTTA
*
30073 AGATTATATT-AA-TTA
1 A-ATTATTTTAAATTTA
30088 AATTTAATATTTAAATTTA
1 AA-TT-AT-TTTAAATTTA
*
30107 GAATAATCAAATTTTACATTTA
1 -AAT--T---ATTTTAAATTTA
*
30129 AATT-TTTTATATTT-
1 AATTATTTTAAATTTA
*
30143 AATCATTTTAAATTTA
1 AATTATTTTAAATTTA
*
30159 GATTATTTTAAATTTA
1 AATTATTTTAAATTTA
30175 AATTA
1 AATTA
30180 ATCAATTTTA
Statistics
Matches: 147, Mismatches: 13, Indels: 55
0.68 0.06 0.26
Matches are distributed among these distances:
11 4 0.03
12 4 0.03
13 2 0.01
14 4 0.03
15 36 0.24
16 30 0.20
17 17 0.12
18 9 0.06
19 17 0.12
20 5 0.03
21 7 0.05
22 9 0.06
23 3 0.02
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
AATTATTTTAAATTTA
Found at i:30191 original size:15 final size:15
Alignment explanation
Indices: 30171--30221 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
30161 TTATTTTAAA
30171 TTTAAATTAATCAAT
1 TTTAAATTAATCAAT
* *
30186 TTTAAATTATTAAAT
1 TTTAAATTAATCAAT
* *
30201 TTT--TTTAATCAAA
1 TTTAAATTAATCAAT
30214 TTTAAATT
1 TTTAAATT
30222 TAAATAAATT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
13 9 0.33
15 18 0.67
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAAATTAATCAAT
Found at i:30215 original size:37 final size:36
Alignment explanation
Indices: 30141--30215 Score: 82
Period size: 37 Copynumber: 2.1 Consensus size: 36
30131 TTTTTTATAT
* *
30141 TTAATCATTTTAAATTTAGATTATTTTAAATTTAAA
1 TTAATCATTTTAAATTTAAATTATTTTAAATTCAAA
*
30177 TTAATCAATTTTAAATTATTAAATT-TTTTTAA-TCAAA
1 TTAATC-ATTTTAAA-T-TTAAATTATTTTAAATTCAAA
30214 TT
1 TT
30216 TAAATTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
36 6 0.18
37 14 0.42
38 7 0.21
39 6 0.18
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (36 bp):
TTAATCATTTTAAATTTAAATTATTTTAAATTCAAA
Found at i:30346 original size:22 final size:21
Alignment explanation
Indices: 30316--30358 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
30306 TTATATAAAT
*
30316 ATTAATAAATTAATAATTTAA
1 ATTAATAAATTAATAAATTAA
*
30337 ATTATATAAATTTATAAATTAA
1 ATTA-ATAAATTAATAAATTAA
30359 GAATTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAATAAATTAATAAATTAA
Found at i:30356 original size:30 final size:32
Alignment explanation
Indices: 30306--30364 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
30296 CATTTTATAT
*
30306 TTATATAAATATTAATAAATTAATAATTTAAA
1 TTATATAAATATTAATAAATTAAGAATTTAAA
30338 TTATATAAAT-TT-ATAAATTAAGAATTT
1 TTATATAAATATTAATAAATTAAGAATTT
30365 TATATCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 14 0.54
31 2 0.08
32 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (32 bp):
TTATATAAATATTAATAAATTAAGAATTTAAA
Found at i:34101 original size:3 final size:3
Alignment explanation
Indices: 34093--34118 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
34083 ACCAAAACCA
34093 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
34119 AAGAGCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34625 original size:2 final size:2
Alignment explanation
Indices: 34620--34648 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34610 TGCGTGTGTG
34620 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34649 TATGCAGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42264 original size:22 final size:22
Alignment explanation
Indices: 42236--42278 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
42226 AAATTAATAA
42236 TTTATTT-TCTTTTTTTATTTCC
1 TTTATTTAT-TTTTTTTATTTCC
42258 TTTATTTATTTTTTTTATTTC
1 TTTATTTATTTTTTTTATTTC
42279 TGAATCTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTATTTATTTTTTTTATTTCC
Found at i:42274 original size:13 final size:13
Alignment explanation
Indices: 42235--42277 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
42225 GAAATTAATA
42235 ATTTATTTTCTTTT
1 ATTTATTTT-TTTT
**
42249 -TTTATTTCCTTT
1 ATTTATTTTTTTT
42261 ATTTATTTTTTTT
1 ATTTATTTTTTTT
42274 ATTT
1 ATTT
42278 CTGAATCTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 3 0.12
13 21 0.88
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (13 bp):
ATTTATTTTTTTT
Found at i:42486 original size:22 final size:22
Alignment explanation
Indices: 42458--42585 Score: 97
Period size: 22 Copynumber: 5.7 Consensus size: 22
42448 ATCAAGTTAA
42458 TTTAAATTAATTAATTTTAATT
1 TTTAAATTAATTAATTTTAATT
* * *
42480 TTTAAATT--TTTA-TATATTT
1 TTTAAATTAATTAATTTTAATT
42499 TTTAAATTTAAATT-ATTTTAA-T
1 TTTAAA-TT-AATTAATTTTAATT
*
42521 TTTAAATTAATTAAATTTAATAT
1 TTTAAATTAATTAATTTTAAT-T
*
42544 TTT-AATTAATTAAATTTAAATTAT
1 TTTAAATTAATT-AATTTTAA-T-T
42568 TTTAAATTTAAATTAATT
1 TTTAAA-TT-AATTAATT
42586 AAATTTAACA
Statistics
Matches: 85, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
19 11 0.13
20 9 0.11
21 8 0.09
22 24 0.28
23 15 0.18
24 6 0.07
25 2 0.02
26 6 0.07
27 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAAATTAATTAATTTTAATT
Found at i:42519 original size:16 final size:16
Alignment explanation
Indices: 42498--42598 Score: 98
Period size: 16 Copynumber: 6.0 Consensus size: 16
42488 TTTATATATT
42498 TTTTAAATTTAAATTA
1 TTTTAAATTTAAATTA
*
42514 TTTTAATTTTAAATTA
1 TTTTAAATTTAAATTA
*
42530 -ATTAAATTTAATATTTTAA
1 TTTTAAATTTAA-A--TT-A
42549 TTAATTAAATTTAAATTA
1 TT--TTAAATTTAAATTA
42567 TTTTAAATTTAAATTA
1 TTTTAAATTTAAATTA
*
42583 -ATTAAATTTAACATTA
1 TTTTAAATTTAA-ATTA
42599 CGATAAATTA
Statistics
Matches: 72, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
15 19 0.26
16 34 0.47
18 5 0.07
19 3 0.04
21 1 0.01
22 10 0.14
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:42545 original size:7 final size:6
Alignment explanation
Indices: 42499--42593 Score: 54
Period size: 6 Copynumber: 17.8 Consensus size: 6
42489 TTATATATTT
* *
42499 TTTAAA TTTAAA -TT-AT TTTAAT TTTAAA -TT-AA -TTAAA TTTAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
* *
42543 TTTTAA -TT-AA -TTAAA TTTAAA -TT-AT TTTAAA TTTAAA -TT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
42584 -TTAAA TTTAA
1 TTTAAA TTTAA
42594 CATTACGATA
Statistics
Matches: 73, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
4 14 0.19
5 20 0.27
6 34 0.47
7 5 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:42582 original size:31 final size:33
Alignment explanation
Indices: 42536--42598 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 33
42526 ATTAATTAAA
*
42536 TTTAATATTTTAATTAATTAAATTTAA-ATTAT
1 TTTAATATTTAAATTAATTAAATTTAACATTAT
42568 TTTAA-ATTTAAATTAATTAAATTTAACATTA
1 TTTAATATTTAAATTAATTAAATTTAACATTA
42599 CGATAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 20 0.69
32 9 0.31
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (33 bp):
TTTAATATTTAAATTAATTAAATTTAACATTAT
Found at i:42608 original size:53 final size:53
Alignment explanation
Indices: 42500--42617 Score: 173
Period size: 53 Copynumber: 2.2 Consensus size: 53
42490 TATATATTTT
* * ** *
42500 TTAAATTTAAATTATTTTAATTTTAAATTAATTAAATTTAATATTTTAATTAA
1 TTAAATTTAAATTATTTTAAATTTAAATTAATTAAATTTAACATTACAATAAA
*
42553 TTAAATTTAAATTATTTTAAATTTAAATTAATTAAATTTAACATTACGATAAA
1 TTAAATTTAAATTATTTTAAATTTAAATTAATTAAATTTAACATTACAATAAA
*
42606 TTAATTTTAAAT
1 TTAAATTTAAAT
42618 AAATTAGGTA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (53 bp):
TTAAATTTAAATTATTTTAAATTTAAATTAATTAAATTTAACATTACAATAAA
Found at i:42688 original size:16 final size:16
Alignment explanation
Indices: 42650--42715 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
42640 TTATTATCTT
42650 TTTTA-ATTTAAATTA
1 TTTTAGATTTAAATTA
* * *
42665 TTTCAGATTTATATTG
1 TTTTAGATTTAAATTA
42681 TTTTAGA-TTAAATTA
1 TTTTAGATTTAAATTA
*
42696 TTTTAAATTTAAATTA
1 TTTTAGATTTAAATTA
42712 TTTT
1 TTTT
42716 TAAATTTGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
15 16 0.38
16 26 0.62
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTAGATTTAAATTA
Found at i:42706 original size:31 final size:31
Alignment explanation
Indices: 42657--42715 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
42647 CTTTTTTAAT
* * *
42657 TTAAATTATTTCAGATTTATATTGTTTTAGA
1 TTAAATTATTTCAAATTTAAATTATTTTAGA
*
42688 TTAAATTATTTTAAATTTAAATTATTTT
1 TTAAATTATTTCAAATTTAAATTATTTT
42716 TAAATTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (31 bp):
TTAAATTATTTCAAATTTAAATTATTTTAGA
Found at i:42875 original size:29 final size:28
Alignment explanation
Indices: 42817--42880 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
42807 AATTGATAAG
*
42817 TATATTTTAAAATTTTTTATATTTTTAT
1 TATATTTTAAAATTTTTTATATTTTAAT
42845 TATATTTTAATAATTTATTT-T-TTATTAAT
1 TATATTTTAA-AATTT-TTTATATT-TTAAT
42874 TATATTT
1 TATATTT
42881 GTATCTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 12 0.38
29 17 0.53
30 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TATATTTTAAAATTTTTTATATTTTAAT
Found at i:43180 original size:16 final size:15
Alignment explanation
Indices: 43167--43224 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
43157 TATATATTTT
43167 TAATAATATTTATTA
1 TAATAATATTTATTA
43182 TATATAATATTTATT-
1 TA-ATAATATTTATTA
* *
43197 TAATATTAAATTTATTT
1 TAATA--ATATTTATTA
43214 TAA-AATATTTA
1 TAATAATATTTA
43225 AAATCTTGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 9 0.24
15 4 0.11
16 21 0.57
17 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATAATATTTATTA
Found at i:43891 original size:15 final size:15
Alignment explanation
Indices: 43871--43901 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
43861 AAACTAACTG
43871 TTTAATGATGTATTA
1 TTTAATGATGTATTA
43886 TTTAATGATGTATTA
1 TTTAATGATGTATTA
43901 T
1 T
43902 CACATTCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (15 bp):
TTTAATGATGTATTA
Found at i:46051 original size:21 final size:20
Alignment explanation
Indices: 46011--46052 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
46001 TACTCAATTT
*
46011 TTTTAAAGTTTTTCCATATA
1 TTTTAAAGTTTATCCATATA
46031 TTTTAAAGATTATATCC-TATA
1 TTTTAAAG-TT-TATCCATATA
46052 T
1 T
46053 CCACAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 7 0.37
22 4 0.21
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTTAAAGTTTATCCATATA
Found at i:46541 original size:62 final size:62
Alignment explanation
Indices: 46442--46566 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
46432 CGAGTAGACC
*
46442 ATCAAAGCCTTGTAGAGTGGGAAAGCATCTTTTTTTAACAAGCATTCTTTCCTTCACTCTAT
1 ATCAAAGCCTTGTAGAGTGGGAAAGCATCTTTGTTTAACAAGCATTCTTTCCTTCACTCTAT
*
46504 ATCAAAGCCTTGTAGAGTGGGAAAGCATCTTTGTTTAACAGGCATTCTTTCCTTCACTCTAT
1 ATCAAAGCCTTGTAGAGTGGGAAAGCATCTTTGTTTAACAAGCATTCTTTCCTTCACTCTAT
46566 A
1 A
46567 GAGCAATGCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (62 bp):
ATCAAAGCCTTGTAGAGTGGGAAAGCATCTTTGTTTAACAAGCATTCTTTCCTTCACTCTAT
Found at i:55312 original size:2 final size:2
Alignment explanation
Indices: 55305--55345 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
55295 TGAAGGGAAA
* *
55305 AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG GG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
55346 AAGGTCTACT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55500 original size:4 final size:4
Alignment explanation
Indices: 55483--55552 Score: 52
Period size: 4 Copynumber: 16.8 Consensus size: 4
55473 CTCATTTCTA
* * *
55483 TTAT TTAT TCAT TTAT TTATT TTAT TTGT TT-T TTAAT TTTT TTAT TTAAT
1 TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTAT TT-AT TTAT TTAT TT-AT
* *
55533 TCAT TTAA TTATT TTAT TTA
1 TTAT TTAT TTA-T TTAT TTA
55553 ATTTCTTCTG
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
3 3 0.06
4 36 0.69
5 13 0.25
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:55506 original size:9 final size:9
Alignment explanation
Indices: 55494--55552 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
55484 TATTTATTCA
55494 TTTATTTAT
1 TTTATTTAT
*
55503 TTTATTTGT
1 TTTATTTAT
*
55512 TTT-TTAAT
1 TTTATTTAT
55520 TTT-TTTAT
1 TTTATTTAT
* *
55528 TTAATTCA-
1 TTTATTTAT
*
55536 TTTAATTAT
1 TTTATTTAT
55545 TTTATTTA
1 TTTATTTA
55553 ATTTCTTCTG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
8 17 0.45
9 21 0.55
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTATTTAT
Found at i:56945 original size:2 final size:2
Alignment explanation
Indices: 56934--57030 Score: 106
Period size: 2 Copynumber: 49.0 Consensus size: 2
56924 CTTTGGTATC
*
56934 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
56975 GT AT AT AT AT TT GT AT AT AT AT AT AT GT AT CT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
57017 GT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT
57031 GTACTTTCTA
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
1 1 0.01
2 77 0.99
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (2 bp):
AT
Found at i:57409 original size:3 final size:3
Alignment explanation
Indices: 57403--57441 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
57393 TTAAACTTAT
57403 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
57442 CTAAAGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:59545 original size:27 final size:27
Alignment explanation
Indices: 59507--59567 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
59497 TTAAAGTCAA
* *
59507 AAAGGCCTTGCATCGTATGAAGACTAG
1 AAAGGCATTGCACCGTATGAAGACTAG
*
59534 AAAGGCATTGCACCGTCTGAAGACTAG
1 AAAGGCATTGCACCGTATGAAGACTAG
59561 AAAGGCA
1 AAAGGCA
59568 GTAGGCCTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (27 bp):
AAAGGCATTGCACCGTATGAAGACTAG
Found at i:59791 original size:21 final size:21
Alignment explanation
Indices: 59774--59819 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
59764 TATTTTAAGT
59774 ATTTTA-ATTTAAAGTTTAAA
1 ATTTTATATTTAAAGTTTAAA
*
59794 ATTTTATATTTAAATATTTAAA
1 ATTTTATATTTAAA-GTTTAAA
59816 ATTT
1 ATTT
59820 AAACGGATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 7 0.30
22 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTTTATATTTAAAGTTTAAA
Found at i:59819 original size:7 final size:7
Alignment explanation
Indices: 59779--59822 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
59769 TAAGTATTTT
59779 AATTTAA
1 AATTTAA
*
59786 AGTTTAA
1 AATTTAA
*
59793 AATTTTA
1 AATTTAA
*
59800 TATTTAA
1 AATTTAA
59807 ATATTTAA
1 A-ATTTAA
59815 AATTTAA
1 AATTTAA
59822 A
1 A
59823 CGGATGAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (7 bp):
AATTTAA
Found at i:59859 original size:21 final size:20
Alignment explanation
Indices: 59829--59870 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
59819 TAAACGGATG
* *
59829 AAAAAAATAAAATAATGTTA
1 AAAAAAATAAAAAAAGGTTA
59849 AAAATAAATAAAAAAAGGTTA
1 AAAA-AAATAAAAAAAGGTTA
59870 A
1 A
59871 TAGATGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (20 bp):
AAAAAAATAAAAAAAGGTTA
Found at i:64280 original size:20 final size:21
Alignment explanation
Indices: 64257--64304 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
64247 AAATAAAGTA
*
64257 TTTTATTATAA-AATTTATAT
1 TTTTAATATAATAATTTATAT
*
64277 TTTTAAAATATAATTATTTATAT
1 TTTT--AATATAATAATTTATAT
64300 TTTTA
1 TTTTA
64305 GAAAACTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 4 0.17
21 1 0.04
22 6 0.26
23 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAATATAATAATTTATAT
Found at i:64325 original size:25 final size:23
Alignment explanation
Indices: 64263--64327 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
64253 AGTATTTTAT
64263 TATAA-AATTTATATTTTTAAAA
1 TATAATAATTTATATTTTTAAAA
*
64285 TATAATTATTTATATTTTTAGAAAA
1 TATAATAATTTATATTTTT--AAAA
*
64310 CTATTATAATTT-TATTTT
1 -TATAATAATTTATATTTT
64328 ATTAATTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.14
23 12 0.33
25 10 0.28
26 9 0.25
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TATAATAATTTATATTTTTAAAA
Found at i:65849 original size:2 final size:2
Alignment explanation
Indices: 65802--65838 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
65792 GTTTTGGTCC
65802 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
65839 CAACAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:70711 original size:22 final size:23
Alignment explanation
Indices: 70669--70711 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
70659 AAACGCAATA
*
70669 TAAAACTTAAAATTGACTAAAAT
1 TAAAACTTAAAATTAACTAAAAT
*
70692 TAAAA-TTAAAATTAATTAAA
1 TAAAACTTAAAATTAACTAAA
70712 TAAAAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAACTTAAAATTAACTAAAAT
Found at i:71242 original size:21 final size:19
Alignment explanation
Indices: 71212--71252 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
71202 TATTTTTATT
*
71212 TAAATTTAATTATAAAATATA
1 TAAATATAA-TATAAAA-ATA
71233 TAAATATAATATAAAAATA
1 TAAATATAATATAAAAATA
71252 T
1 T
71253 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAATATAATATAAAAATA
Found at i:71536 original size:33 final size:32
Alignment explanation
Indices: 71484--71545 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
71474 TTAAAATACG
*
71484 ATATAATATAAATAAATTAATATTTTATAATTT
1 ATATAATATAAATAAATTAA-AATTTATAATTT
* **
71517 ATATAATATTAATGTATTAAAATTTATAA
1 ATATAATATAAATAAATTAAAATTTATAA
71546 ATATAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 8 0.32
33 17 0.68
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
ATATAATATAAATAAATTAAAATTTATAATTT
Found at i:71540 original size:25 final size:25
Alignment explanation
Indices: 71495--71549 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
71485 TATAATATAA
* *
71495 ATAA-ATTAATATTTTATAATTTAT
1 ATAATATTAATATATTAAAATTTAT
*
71519 ATAATATTAATGTATTAAAATTTAT
1 ATAATATTAATATATTAAAATTTAT
71544 A-AATAT
1 ATAATAT
71550 AAAAAAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
ATAATATTAATATATTAAAATTTAT
Found at i:72157 original size:28 final size:28
Alignment explanation
Indices: 72103--72174 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
72093 AATATCTATC
*
72103 ATATTATAAGATAAGACATTTAAATATT
1 ATATTATAAGATAAGAAATTTAAATATT
* *
72131 ATGTTATAAGATAAGAAACTTT-GATATT
1 ATATTATAAGATAAGAAA-TTTAAATATT
* *
72159 ATATCATAAAATAAGA
1 ATATTATAAGATAAGA
72175 TGCTCTAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 34 0.92
29 3 0.08
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (28 bp):
ATATTATAAGATAAGAAATTTAAATATT
Found at i:72864 original size:37 final size:37
Alignment explanation
Indices: 72770--72870 Score: 111
Period size: 37 Copynumber: 2.7 Consensus size: 37
72760 CAAAAGCTCA
*
72770 TTTTATTATTTAAAATAAT-ATTAAATTTTAAAAATAT
1 TTTTATTATTT-AAATAATAATTAAATTTAAAAAATAT
*
72807 TTTTA-TA-TTAATATTTATAATTAAATTTAAATAAAT-T
1 TTTTATTATTTAA-A-TAATAATTAAATTTAAA-AAATAT
*
72844 TTTTATTATTTAAATAATAATTTAATT
1 TTTTATTATTTAAATAATAATTAAATT
72871 CAGATCAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
34 2 0.04
35 3 0.06
36 5 0.09
37 33 0.61
38 7 0.13
39 4 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (37 bp):
TTTTATTATTTAAATAATAATTAAATTTAAAAAATAT
Found at i:73266 original size:21 final size:21
Alignment explanation
Indices: 73240--73281 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
73230 CTCGATTTGA
73240 TTTTTT-TAATTATATAATATT
1 TTTTTTATAATTATAT-ATATT
*
73261 TTTTTTATATTTATATATATT
1 TTTTTTATAATTATATATATT
73282 ATGATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTTATAATTATATATATT
Found at i:73274 original size:22 final size:19
Alignment explanation
Indices: 73240--73281 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
73230 CTCGATTTGA
73240 TTTTTTTAATTATATAATAT
1 TTTTTTTAATTATAT-ATAT
73260 TTTTTTTATATTTATATATAT
1 TTTTTTTA-A-TTATATATAT
73281 T
1 T
73282 ATGATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 6 0.30
22 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTTAATTATATATAT
Found at i:73749 original size:32 final size:32
Alignment explanation
Indices: 73659--73749 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 32
73649 AAATAAAAAG
*
73659 TATAACATGATATGAAAA-A-ATAATACGAATA
1 TATAACAT-ATATAAAAATATATAATACGAATA
* *
73690 TATAA-ATTTATCAAAATTTATATAATACGAAT-
1 TATAACATATAT-AAAA-ATATATAATACGAATA
73722 TATTAACATATATAAAAATATATAATAC
1 TA-TAACATATATAAAAATATATAATAC
73750 TTTAAACTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
29 3 0.06
30 5 0.10
31 5 0.10
32 13 0.27
33 18 0.37
34 5 0.10
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (32 bp):
TATAACATATATAAAAATATATAATACGAATA
Found at i:74259 original size:14 final size:14
Alignment explanation
Indices: 74235--74279 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
74225 TATTAAATAT
*
74235 TATATTAATATTTA
1 TATAATAATATTTA
*
74249 TTTAATAATATTTA
1 TATAATAATATTTA
*
74263 TATGA-AATATTTA
1 TATAATAATATTTA
74276 TATA
1 TATA
74280 TTTGATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
TATAATAATATTTA
Found at i:74600 original size:2 final size:2
Alignment explanation
Indices: 74593--74628 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
74583 GTCTCTTAAG
74593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74629 TGAGACTAAA
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):
AT
Found at i:74697 original size:19 final size:19
Alignment explanation
Indices: 74673--74760 Score: 71
Period size: 19 Copynumber: 4.8 Consensus size: 19
74663 AATATTATAG
74673 TTATTTTAATTTTATAATA
1 TTATTTTAATTTTATAATA
*
74692 TTA-TTTGA-TTTATAATA
1 TTATTTTAATTTTATAATA
*
74709 TTAAATTTAATTTTATAAT-
1 TT-ATTTTAATTTTATAATA
* *
74728 TT-TTATGTAAATTTAT-TTA
1 TTATT-T-TAATTTTATAATA
74747 TT-TTTTAATTTTAT
1 TTATTTTAATTTTAT
74761 TGAGAAATTA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
17 20 0.35
18 8 0.14
19 21 0.37
20 8 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTTTAATTTTATAATA
Found at i:74703 original size:23 final size:23
Alignment explanation
Indices: 74651--74732 Score: 64
Period size: 25 Copynumber: 3.5 Consensus size: 23
74641 TCATGTTTTT
74651 TTTTAAATTTTTAATATTATAGTTA
1 TTTT-AATTTTTAATATTATA-TTA
74676 TTTTAATTTTATAATATTAT-TTGA
1 TTTTAATTTT-TAATATTATATT-A
* *
74700 TTTATAATATTAAAT-TTA-ATT-
1 TTT-TAATTTTTAATATTATATTA
*
74721 TTATAATTTTTA
1 TTTTAATTTTTA
74733 TGTAAATTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
20 7 0.15
21 2 0.04
23 7 0.15
24 13 0.27
25 19 0.40
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTAATTTTTAATATTATATTA
Found at i:74707 original size:25 final size:24
Alignment explanation
Indices: 74652--74732 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
74642 CATGTTTTTT
74652 TTTA-AATTTTTAATATTATAGTTA
1 TTTATAATTTTTAATATTATA-TTA
74676 TTT-TAATTTTATAATATTAT-TTGA
1 TTTATAATTTT-TAATATTATATT-A
* *
74700 TTTATAA-TATTAA-ATT-TAAT-
1 TTTATAATTTTTAATATTATATTA
74720 TTTATAATTTTTA
1 TTTATAATTTTTA
74733 TGTAAATTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
20 7 0.15
21 5 0.10
22 4 0.08
23 5 0.10
24 15 0.31
25 12 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTATAATTTTTAATATTATATTA
Found at i:74981 original size:2 final size:2
Alignment explanation
Indices: 74976--75001 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
74966 ATAGTTTGGA
74976 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
75002 GAAAGTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75876 original size:20 final size:17
Alignment explanation
Indices: 75827--75884 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 17
75817 AAATGATTAC
*
75827 TTATTTTATTTAATATAA
1 TTATATTATTTAA-ATAA
75845 TTATATTAATTTAAATAA
1 TTATATT-ATTTAAATAA
75863 TGTATTAATTATTTAAATAA
1 T-TA-T-ATTATTTAAATAA
75883 TT
1 TT
75885 TTTTATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 11 0.31
19 9 0.26
20 12 0.34
21 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTATATTATTTAAATAA
Found at i:78948 original size:33 final size:33
Alignment explanation
Indices: 78910--78975 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
78900 GATTCATGCA
78910 ATAAATTTGAAGTTCGAATCTATACATTATGTG
1 ATAAATTTGAAGTTCGAATCTATACATTATGTG
78943 ATAAATTTGAAGTTCGAATCTATACATTATGTG
1 ATAAATTTGAAGTTCGAATCTATACATTATGTG
78976 TGAAAGTCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (33 bp):
ATAAATTTGAAGTTCGAATCTATACATTATGTG
Found at i:79009 original size:2 final size:2
Alignment explanation
Indices: 79002--79026 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
78992 CAACTTGCAT
79002 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
79027 TAAAGAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:79206 original size:23 final size:21
Alignment explanation
Indices: 79180--79223 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
79170 TTAAAAATAT
79180 TAAAATTTATTATTGAATTTAAA
1 TAAAATTTATTATT--ATTTAAA
*
79203 TAAAATTTTTTATTATTTAAA
1 TAAAATTTATTATTATTTAAA
79224 CAGTATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
23 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TAAAATTTATTATTATTTAAA
Found at i:79430 original size:21 final size:21
Alignment explanation
Indices: 79404--79446 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
79394 TTCATTTTAC
79404 TTTCATTCTTTTATAATTAAT
1 TTTCATTCTTTTATAATTAAT
79425 TTTCATTCTTTTATAATTAAT
1 TTTCATTCTTTTATAATTAAT
79446 T
1 T
79447 CTTGAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTCATTCTTTTATAATTAAT
Found at i:79613 original size:17 final size:17
Alignment explanation
Indices: 79587--79631 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
79577 TTGGATTAAA
*
79587 AAATAAATATTAAATAT
1 AAATATATATTAAATAT
*
79604 AAATATATATTTAATAT
1 AAATATATATTAAATAT
79621 AAA-ATAT-TTAA
1 AAATATATATTAA
79632 TTTATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 3 0.12
16 4 0.16
17 18 0.72
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATATATTAAATAT
Found at i:79644 original size:19 final size:19
Alignment explanation
Indices: 79622--79659 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
79612 ATTTAATATA
79622 AAATATTTA-ATTTATTTTT
1 AAAT-TTTATATTTATTTTT
*
79641 AAATTTTATTTTTATTTTT
1 AAATTTTATATTTATTTTT
79660 TTATGCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
AAATTTTATATTTATTTTT
Found at i:80271 original size:14 final size:15
Alignment explanation
Indices: 80249--80279 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
80239 TTATTTATGT
80249 TTAATTATAAAAATA
1 TTAATTATAAAAATA
80264 TTAA-TATAAAAATA
1 TTAATTATAAAAATA
80278 TT
1 TT
80280 TTTAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAATTATAAAAATA
Found at i:80338 original size:33 final size:33
Alignment explanation
Indices: 80289--80383 Score: 83
Period size: 33 Copynumber: 2.9 Consensus size: 33
80279 TTTTAATATT
*
80289 ATTT-AATAAA-ATAAATAATAATTTAAATTTAA
1 ATTTAAATAAATA-AAATAATAATTAAAATTTAA
* * *
80321 ATTTAAATAAATAAAATAA-AATAAATCAAATCAA
1 ATTTAAATAAATAAAATAATAATTAA--AATTTAA
*
80355 ATTTAAAT-AATAAACTAA-AATTAAAATTT
1 ATTTAAATAAATAAAATAATAATTAAAATTT
80384 TTTTGGACCC
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
31 3 0.06
32 8 0.16
33 26 0.51
34 14 0.27
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (33 bp):
ATTTAAATAAATAAAATAATAATTAAAATTTAA
Found at i:80517 original size:13 final size:14
Alignment explanation
Indices: 80500--80538 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
80490 TTAAATATTA
80500 AATAAAAATTAAAT
1 AATAAAAATTAAAT
*
80514 -ATAAAAATTAATT
1 AATAAAAATTAAAT
80527 AATAAAATATTA
1 AATAAAA-ATTA
80539 TATTTAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 12 0.55
14 6 0.27
15 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAAAAATTAAAT
Found at i:81504 original size:56 final size:56
Alignment explanation
Indices: 81418--81527 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 56
81408 AAAGAGTTAA
*
81418 GAGTAATATAGTAATGTATATTATTTGTAAAACTTGAAATTTTTGTTATGTTTTAG
1 GAGTAATATAGTAATGTATATTATTTGTAAAACTTGAAATTTTTATTATGTTTTAG
*
81474 GAGTAATATAGTAATGTATATTATTTGTAAAGCTTGAAATTTTTATTATGTTTT
1 GAGTAATATAGTAATGTATATTATTTGTAAAACTTGAAATTTTTATTATGTTTT
81528 TTTAGTAGTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (56 bp):
GAGTAATATAGTAATGTATATTATTTGTAAAACTTGAAATTTTTATTATGTTTTAG
Found at i:87597 original size:17 final size:17
Alignment explanation
Indices: 87575--87626 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
87565 AAAAACTTGA
87575 ACATACCCGTATTGAAC
1 ACATACCCGTATTGAAC
* *
87592 ACATACCCGTGTCGAAC
1 ACATACCCGTATTGAAC
* *
87609 ACATACCCATATTTAAC
1 ACATACCCGTATTGAAC
87626 A
1 A
87627 TTTACACCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.37, C:0.31, G:0.10, T:0.23
Consensus pattern (17 bp):
ACATACCCGTATTGAAC
Found at i:89224 original size:17 final size:18
Alignment explanation
Indices: 89188--89229 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
89178 ATTATTATTT
*
89188 ATTTAAATATTTTTTATA
1 ATTTAAATATTTTATATA
*
89206 ATTTAAA-ATTTTATGTA
1 ATTTAAATATTTTATATA
89223 A-TTAAAT
1 ATTTAAAT
89230 TTAAAGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 9 0.43
18 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTAAATATTTTATATA
Found at i:89322 original size:23 final size:24
Alignment explanation
Indices: 89294--89338 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
89284 GATACGATAT
*
89294 AAATATAATATG-AAAAATAATTA
1 AAATATAATACGAAAAAATAATTA
89317 AAATATAATACGAAAAAATAAT
1 AAATATAATACGAAAAAATAAT
89339 ATTACATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (24 bp):
AAATATAATACGAAAAAATAATTA
Found at i:90099 original size:22 final size:22
Alignment explanation
Indices: 90048--90107 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
90038 CATGGACATG
*
90048 ATATAAAAATCAATTAAAATGTA
1 ATATAAAAAT-AATAAAAATGTA
90071 ATA-AAAAATAATAAAATATG-A
1 ATATAAAAATAATAAAA-ATGTA
90092 ATATAAAAAT-ATAAAA
1 ATATAAAAATAATAAAA
90108 GATAATTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 16 0.47
22 15 0.44
23 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (22 bp):
ATATAAAAATAATAAAAATGTA
Found at i:91283 original size:17 final size:18
Alignment explanation
Indices: 91241--91288 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
91231 TAAATAATAA
91241 TTATTT-ATTTAAATATT
1 TTATTTAATTTAAATATT
91258 TT-TTGTAATTTAAA-ATT
1 TTATT-TAATTTAAATATT
91275 TTATTTAA-TTAAAT
1 TTATTTAATTTAAAT
91289 TTAAAGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.26
17 11 0.41
18 9 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATTTAATTTAAATATT
Found at i:92284 original size:17 final size:17
Alignment explanation
Indices: 92262--92297 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
92252 AACACATAAA
92262 TTTTTTTCATTCCTTTC
1 TTTTTTTCATTCCTTTC
* *
92279 TTTTTTTCTTTCTTTTC
1 TTTTTTTCATTCCTTTC
92296 TT
1 TT
92298 CCTTTTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTCATTCCTTTC
Found at i:92302 original size:21 final size:21
Alignment explanation
Indices: 92278--92317 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
92268 TCATTCCTTT
*
92278 CTTTTT-TTCTTTCTTTTCTTC
1 CTTTTTCTCCTTT-TTTTCTTC
92299 CTTTTTCTCCTTTTTTTCT
1 CTTTTTCTCCTTTTTTTCT
92318 CTCCCTGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (21 bp):
CTTTTTCTCCTTTTTTTCTTC
Found at i:93263 original size:24 final size:22
Alignment explanation
Indices: 93231--93279 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
93221 ATTACTATAT
93231 TATAAATAAAAGAATATATCAATA
1 TATAAAT-AAAGAA-ATATCAATA
* * *
93255 TATATATAATGAAATATTAATA
1 TATAAATAAAGAAATATCAATA
93277 TAT
1 TAT
93280 TAAAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 11 0.50
23 5 0.23
24 6 0.27
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (22 bp):
TATAAATAAAGAAATATCAATA
Found at i:93481 original size:18 final size:17
Alignment explanation
Indices: 93451--93502 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
93441 CAAACACGAA
*
93451 AAAATTTTA-AATATTAT
1 AAAATATTATAATATT-T
93468 AAAATATTATAATATTT
1 AAAATATTATAATATTT
* *
93485 AAATTAATATACATATTT
1 AAAATATTATA-ATATTT
93503 TAATCAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
AAAATATTATAATATTT
Found at i:93500 original size:26 final size:29
Alignment explanation
Indices: 93471--93525 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
93461 ATATTATAAA
93471 ATATTATAAT-AT-TTA-AATTAATATAC
1 ATATTATAATAATGTTATAATTAATATAC
*
93497 ATATTTTAATCAATGTTATAATTAATATA
1 ATATTATAAT-AATGTTATAATTAATATA
93526 TATTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 9 0.38
28 2 0.08
29 3 0.12
30 10 0.42
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (29 bp):
ATATTATAATAATGTTATAATTAATATAC
Found at i:95322 original size:20 final size:21
Alignment explanation
Indices: 95281--95322 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
95271 TATTTTTATT
95281 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
*
95302 TAAATATTAATTAAAAAATAT
1 TAAAT-TTAATTATAAAATAT
95323 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:95834 original size:114 final size:114
Alignment explanation
Indices: 95689--95911 Score: 261
Period size: 114 Copynumber: 2.0 Consensus size: 114
95679 TTATATAAAT
* ** * * *
95689 TTTGATATAGTAACAATTCATATTTTATAGATTTTGGGAATGTATT-TGTGTTGTGTTATATTTT
1 TTTGATATAGTAACAATTCATATTATATAGATTTTAAGAATATATTCT-TATTATGTTATATTTT
* *
95753 AATTATTTTATACATATCATATTTCTATAATCGTGTTTAAAATTATCAAG
65 AATTATTTTATACATATCATATTTATATAATCGTGTCTAAAATTATCAAG
* * * * *
95803 TTTGATA-AGTTAATAATTTATATTATGTAGATTTTAATAATATATTCTTATTATGTTGTATTTT
1 TTTGATATAG-TAACAATTCATATTATATAGATTTTAAGAATATATTCTTATTATGTTATATTTT
** * *
95867 AATTATTTTATATGTGTTATATTTATATAATCGTGTCTAAAATTA
65 AATTATTTTATACATATCATATTTATATAATCGTGTCTAAAATTA
95912 GTAAATCTAA
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
113 2 0.02
114 87 0.97
115 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (114 bp):
TTTGATATAGTAACAATTCATATTATATAGATTTTAAGAATATATTCTTATTATGTTATATTTTA
ATTATTTTATACATATCATATTTATATAATCGTGTCTAAAATTATCAAG
Found at i:96028 original size:2 final size:2
Alignment explanation
Indices: 96021--96063 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
96011 CCCACTTCGC
*
96021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96063 A
1 A
96064 ATTTCAACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:96939 original size:26 final size:26
Alignment explanation
Indices: 96916--96967 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
96906 TTAAATCATA
*
96916 AATCATCATTAAATTATAAGATCACT
1 AATCATCATTAAATTAAAAGATCACT
96942 AATCATCATTAAATTAAAAGATCACT
1 AATCATCATTAAATTAAAAGATCACT
96968 TTAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (26 bp):
AATCATCATTAAATTAAAAGATCACT
Found at i:97358 original size:18 final size:21
Alignment explanation
Indices: 97311--97350 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
97301 ATATTTTATT
97311 TAAA-TTTAATTATAAAAATA
1 TAAATTTTAATTATAAAAATA
97331 TAAATTTTAA-TATAAAAATA
1 TAAATTTTAATTATAAAAATA
97351 ATTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTTAATTATAAAAATA
Found at i:97384 original size:18 final size:18
Alignment explanation
Indices: 97351--97385 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
97341 TATAAAAATA
**
97351 ATTTTTAAATTTTTTAAT
1 ATTTTTAAATAATTTAAT
97369 ATTTTTAAATAATTTAA
1 ATTTTTAAATAATTTAA
97386 ATATAAAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTAAATAATTTAAT
Found at i:97388 original size:19 final size:18
Alignment explanation
Indices: 97346--97389 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
97336 TTTAATATAA
*
97346 AAATAATTTTTAAATTTTT
1 AAAT-ATTTTTAAATATTT
*
97365 TAATATTTTTAAATAATTT
1 AAATATTTTTAAAT-ATTT
97384 AAATAT
1 AAATAT
97390 AAAATCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATATTTTTAAATATTT
Found at i:97698 original size:30 final size:32
Alignment explanation
Indices: 97659--97722 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 32
97649 ATTATAAACA
*
97659 TAATATAT-AACTATTAAATATG-TTAAAATTT
1 TAATATATAAAC-ATAAAATATGATTAAAATTT
97690 TAAT-TATAAACATAAAATATGTATTAAAATTT
1 TAATATATAAACATAAAATATG-ATTAAAATTT
97722 T
1 T
97723 GTTTAATTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 12 0.41
31 7 0.24
32 10 0.34
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (32 bp):
TAATATATAAACATAAAATATGATTAAAATTT
Found at i:98011 original size:22 final size:23
Alignment explanation
Indices: 97970--98012 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
97960 AAGTGACTTA
97970 AAATAATATTTTTATATTAAAAT
1 AAATAATATTTTTATATTAAAAT
97993 AAAT-ATATATTTTAT-TTAAA
1 AAATAATAT-TTTTATATTAAA
98013 TTTAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATAATATTTTTATATTAAAAT
Found at i:98040 original size:22 final size:21
Alignment explanation
Indices: 98009--98049 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
97999 ATATTTTATT
* *
98009 TAAATTTAATTTTAAAATATA
1 TAAATTTAATATAAAAATATA
98030 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
98050 ATTTTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTTAATATAAAAATATA
Found at i:98101 original size:18 final size:18
Alignment explanation
Indices: 98063--98118 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
98053 TTTAATAAGA
*
98063 TAAATAATGATTTAAATT
1 TAAATAATGAATTAAATT
98081 TAAATGAATGAATTAAA-T
1 TAAAT-AATGAATTAAATT
*
98099 TAAAT-TTGAATCTAAATT
1 TAAATAATGAAT-TAAATT
98117 TA
1 TA
98119 TAAATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 5 0.15
17 4 0.12
18 14 0.42
19 10 0.30
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (18 bp):
TAAATAATGAATTAAATT
Found at i:98390 original size:21 final size:21
Alignment explanation
Indices: 98361--98403 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
98351 TTTCTTTCGT
98361 CGGGGTCAACTCAGGCAACTG
1 CGGGGTCAACTCAGGCAACTG
* * *
98382 CGGGTTCAAGTCTGGCAACTG
1 CGGGGTCAACTCAGGCAACTG
98403 C
1 C
98404 CGAAGGACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.19
Consensus pattern (21 bp):
CGGGGTCAACTCAGGCAACTG
Found at i:98532 original size:12 final size:11
Alignment explanation
Indices: 98502--98569 Score: 50
Period size: 12 Copynumber: 5.9 Consensus size: 11
98492 TAATTATTTA
98502 AAATATAATTAT
1 AAATAT-ATTAT
98514 AATATATATTATT
1 AA-ATATATTA-T
*
98527 AAATATATTAA
1 AAATATATTAT
98538 AAAT-TATTAAT
1 AAATATATT-AT
*
98549 ATAA-ATATAAT
1 A-AATATATTAT
*
98560 AAATAAATTA
1 AAATATATTA
98570 AACGTGTTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
10 6 0.13
11 13 0.29
12 19 0.42
13 7 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAATATATTAT
Found at i:104247 original size:19 final size:18
Alignment explanation
Indices: 104204--104239 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
104194 AAATCTATAT
* *
104204 TTCTTATAAAAATTTTCA
1 TTCTCATAAAAATTTTAA
104222 TTCTCATAAAAATTTTAA
1 TTCTCATAAAAATTTTAA
104240 ATTTTCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (18 bp):
TTCTCATAAAAATTTTAA
Found at i:104260 original size:25 final size:25
Alignment explanation
Indices: 104213--104261 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
104203 TTTCTTATAA
*
104213 AAATTTTCATTCTCATAAAAATTTT
1 AAATTTTCATTCCCATAAAAATTTT
* *
104238 AAATTTTCATTCCCGTAAGAATTT
1 AAATTTTCATTCCCATAAAAATTT
104262 CCTTTCTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.45
Consensus pattern (25 bp):
AAATTTTCATTCCCATAAAAATTTT
Found at i:104751 original size:2 final size:2
Alignment explanation
Indices: 104744--104774 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
104734 CTGTCAACCC
104744 AT AT 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 AT AT A
104775 AATGAGTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:107258 original size:16 final size:16
Alignment explanation
Indices: 107237--107271 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
107227 TTGAAGTATC
107237 CGATGTCACCCATGTT
1 CGATGTCACCCATGTT
107253 CGATGTCACCCATGTT
1 CGATGTCACCCATGTT
107269 CGA
1 CGA
107272 CGCATCCGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (16 bp):
CGATGTCACCCATGTT
Found at i:110927 original size:2 final size:2
Alignment explanation
Indices: 110920--110954 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
110910 TTTGGTATGT
110920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
110955 TTAATTTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:113734 original size:20 final size:20
Alignment explanation
Indices: 113706--113743 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
113696 TATCAATTAC
*
113706 AAGTTGATAATTAAAAAACT
1 AAGTCGATAATTAAAAAACT
113726 AAGTCGATAATTAAAAAA
1 AAGTCGATAATTAAAAAA
113744 AATTATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (20 bp):
AAGTCGATAATTAAAAAACT
Found at i:113893 original size:12 final size:12
Alignment explanation
Indices: 113872--113908 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
113862 TTTTTTACAT
113872 AAATTAAATAAA
1 AAATTAAATAAA
*
113884 AAATTGAATAAA
1 AAATTAAATAAA
113896 AAATTAAATAAA
1 AAATTAAATAAA
113908 A
1 A
113909 TAAACAGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AAATTAAATAAA
Found at i:117215 original size:2 final size:2
Alignment explanation
Indices: 117208--117257 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
117198 TACTTCAAGG
* * *
117208 TA TA TA TA TA TA T- TA TA AA TA TA AA GA TA -A 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
*
117248 TA TA AA TA TA
1 TA TA TA TA TA
117258 ACTATAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (2 bp):
TA
Done.