Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000402.1 Hibiscus syriacus cultivar Beakdansim tig00000738_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: 1701760
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:8222 original size:55 final size:55
Alignment explanation
Indices: 8138--8269 Score: 221
Period size: 55 Copynumber: 2.4 Consensus size: 55
8128 TCCACTAGAA
**
8138 AGCATGCACCAAATCTAATCTTTTTTATATTTTATTTTAATAACTTTATTACTCC
1 AGCATGCACCAAATCTAATCTTTTTTATATTTTATTTTAATAAAATTATTACTCC
8193 AGCATGCACCAAATCTAAGT-TTTTTTATATTTTATTTTAATAAAATTATTACTCC
1 AGCATGCACCAAATCTAA-TCTTTTTTATATTTTATTTTAATAAAATTATTACTCC
*
8248 GGCATGCACCAAATCTAATCTT
1 AGCATGCACCAAATCTAATCTT
8270 AATTCAGATT
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
54 1 0.01
55 70 0.97
56 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (55 bp):
AGCATGCACCAAATCTAATCTTTTTTATATTTTATTTTAATAAAATTATTACTCC
Found at i:13629 original size:54 final size:53
Alignment explanation
Indices: 13518--14148 Score: 510
Period size: 55 Copynumber: 12.0 Consensus size: 53
13508 ATACTTGAAA
* * *
13518 AATCTTCAAATAACGGGTCTGCTCCCT-TTCTTTCA-AGGAGTATA-AGACTCGAAC
1 AATCTTCAAA-AAC-GGTCCGCTCTCTATTCCTTCAGA-GAGTATAGA-ACTCGAAC
** *
13572 AATCCTT-AGCAACGGTCCGCTCTCTATCCCTTCAGAGAGTATAGAAACTCGAAC
1 AAT-CTTCAAAAACGGTCCGCTCTCTATTCCTTCAGAGAGTATAG-AACTCGAAC
* *
13626 AATCTTCATAAAACGGGT-C-CTCTTTATTCCTTC--AGAGTATAGAACTCGAAT
1 AATCTTCA-AAAAC-GGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
13677 AATCTTCATAAAACGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGATC
1 AATCTTCA-AAAACGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
13731 AA--TTCAACAAACGGGTCCACTCTCTATCCCTTCAGAGA-TATAGAACTCGAAC
1 AATCTTCAA-AAAC-GGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
13783 AA----C-----GGGTCCTCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCAAAAACGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * * * *
13827 AATCTTCATAAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAAC
1 AATCTTCA-AAAACG-GTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * * *
13882 AATCTTCAACAACGTGTCTGCTCCCTATTCATTCAG-GAGTATA-AGACTC-AACC
1 AATCTTCAAAAACG-GTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAA-C
* * * *
13935 AATCTTCAATAAACGTGTTCGTTCCCTATTCCTTCAGAGAGTATAGGACTCGAAC
1 AATCTTCAA-AAACG-GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * * * *
13990 AATCTTCAACAAACGGGTTCGCTCCCTATTCATTCAGGGAGTATAGAACTCAAAC
1 AATCTTCAA-AAAC-GGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
*
14045 AATCTTCATAAAATGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCG---
1 AATCTTCA-AAAACG-GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
14097 -ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAATATA-AGACTCGA
1 AATCTTCAA-AAACG-GTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGA
14149 TCTTCATAAA
Statistics
Matches: 488, Mismatches: 51, Indels: 78
0.79 0.08 0.13
Matches are distributed among these distances:
43 23 0.05
44 16 0.03
48 1 0.00
50 6 0.01
51 67 0.14
52 57 0.12
53 64 0.13
54 99 0.20
55 148 0.30
56 7 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (53 bp):
AATCTTCAAAAACGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
Found at i:13798 original size:43 final size:44
Alignment explanation
Indices: 13740--13828 Score: 153
Period size: 43 Copynumber: 2.0 Consensus size: 44
13730 CAATTCAACA
13740 AACGGGTCCACTCTCTATCCCTTCAGAGA-TATAGAACTCGAAC
1 AACGGGTCCACTCTCTATCCCTTCAGAGAGTATAGAACTCGAAC
* *
13783 AACGGGTCCTCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AACGGGTCCACTCTCTATCCCTTCAGAGAGTATAGAACTCGAAC
13827 AA
1 AA
13829 TCTTCATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 27 0.63
44 16 0.37
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (44 bp):
AACGGGTCCACTCTCTATCCCTTCAGAGAGTATAGAACTCGAAC
Found at i:14219 original size:37 final size:37
Alignment explanation
Indices: 14169--14245 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
14159 ATAAGTTTGA
*
14169 TTCACTACTCTTCCGTGAAGGTTTAAGATTGACTTGC
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGACTTGC
*
14206 TTCACTACTCTTCCGTTAAGGCTTAAGATTGACTTGC
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGACTTGC
14243 TTC
1 TTC
14246 GAAGGTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (37 bp):
TTCACTACTCTTCCGTGAAGGCTTAAGATTGACTTGC
Found at i:15526 original size:24 final size:26
Alignment explanation
Indices: 15499--15558 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 26
15489 CTCTCCTTTA
*
15499 TTTTTTCTTTTTTTCA-TTTTTC-TC
1 TTTTTTCTTTTTTCCATTTTTTCTTC
*
15523 TTTTTTC-ATTTTCCATTTTTTCTTC
1 TTTTTTCTTTTTTCCATTTTTTCTTC
15548 TTTTTTCTTTT
1 TTTTTTCTTTT
15559 CGTTTTTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 6 0.20
24 13 0.43
25 9 0.30
26 2 0.07
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTTCTTTTTTCCATTTTTTCTTC
Found at i:15542 original size:16 final size:15
Alignment explanation
Indices: 15500--15544 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
15490 TCTCCTTTAT
*
15500 TTTTTCTTTTTTTCA
1 TTTTCCTTTTTTTCA
*
15515 TTTTTCTCTTTTTTCA
1 TTTTCCT-TTTTTTCA
*
15531 TTTTCCATTTTTTC
1 TTTTCCTTTTTTTC
15545 TTCTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCCTTTTTTTCA
Found at i:15558 original size:7 final size:8
Alignment explanation
Indices: 15498--15544 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
15488 ACTCTCCTTT
15498 ATTTTTTC
1 ATTTTTTC
*
15506 TTTTTTTC
1 ATTTTTTC
15514 ATTTTTCTC
1 ATTTTT-TC
15523 -TTTTTTC
1 ATTTTTTC
*
15530 A-TTTTCC
1 ATTTTTTC
15537 ATTTTTTC
1 ATTTTTTC
15545 TTCTTTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
7 8 0.25
8 22 0.69
9 2 0.06
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTTC
Found at i:15558 original size:16 final size:15
Alignment explanation
Indices: 15500--15558 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
15490 TCTCCTTTAT
15500 TTTTTCTTTTTTTCA
1 TTTTTCTTTTTTTCA
15515 TTTTTCTCTTTTTTCA
1 TTTTTCT-TTTTTTCA
* *
15531 TTTTCCATTTTTTCTTCT
1 TTTTTC--TTTTT-TTCA
15549 TTTTTCTTTT
1 TTTTTCTTTT
15559 CGTTTTTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.19
16 17 0.46
17 4 0.11
18 9 0.24
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTTTTCA
Found at i:15559 original size:24 final size:23
Alignment explanation
Indices: 15509--15639 Score: 91
Period size: 22 Copynumber: 5.8 Consensus size: 23
15499 TTTTTTCTTT
15509 TTTTCA-TTTTTCTCTTTTTTCA
1 TTTTCATTTTTTCTCTTTTTTCA
15531 TTTTCCATTTTTTCTTCTTTTTTC-
1 TTTT-CATTTTTTC-TCTTTTTTCA
* *
15555 TTTTCGTTTTTTC-CATCATTTT--
1 TTTTCATTTTTTCTC-T-TTTTTCA
*
15577 TTTTCATTTTTT-TCTTTCTTC-
1 TTTTCATTTTTTCTCTTTTTTCA
* * *
15598 TTCTCATTTATTAT-TATTTTTCA
1 TTTTCATTTTTTCTCT-TTTTTCA
15621 TTTTTC-TTTTTTCTCTTTT
1 -TTTTCATTTTTTCTCTTTT
15640 ATTTCTTCTC
Statistics
Matches: 86, Mismatches: 11, Indels: 23
0.72 0.09 0.19
Matches are distributed among these distances:
20 3 0.03
21 13 0.15
22 23 0.27
23 23 0.27
24 15 0.17
25 9 0.10
ACGTcount: A:0.08, C:0.18, G:0.01, T:0.73
Consensus pattern (23 bp):
TTTTCATTTTTTCTCTTTTTTCA
Found at i:21043 original size:16 final size:16
Alignment explanation
Indices: 21024--21057 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
21014 ACTGTTAAAA
21024 TGTTCACCTGTCAAAC
1 TGTTCACCTGTCAAAC
21040 TGTTCACCTGTCAAAC
1 TGTTCACCTGTCAAAC
21056 TG
1 TG
21058 GGCTTCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (16 bp):
TGTTCACCTGTCAAAC
Found at i:25243 original size:51 final size:45
Alignment explanation
Indices: 25197--25287 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
25187 CCATGCTTTG
*
25197 TTATCCACAAAAAGAAATCCTAACCTCATGATATCTAATTCGCATGC
1 TTATCCA-AAAAAGAAA-CCTAACCGCATGATATCTAATTCGCATGC
* * *
25244 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATG
1 TTATCCAAAAAAGAAACCTAACCGCATGATATCTAATTCGCATG
25288 AATTTATTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 26 0.65
46 8 0.20
47 6 0.15
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (45 bp):
TTATCCAAAAAAGAAACCTAACCGCATGATATCTAATTCGCATGC
Found at i:31188 original size:16 final size:16
Alignment explanation
Indices: 31167--31209 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
31157 GATTAAGCGT
31167 TGAATGATTCAAATGC
1 TGAATGATTCAAATGC
31183 TGAATGATTCAAATGC
1 TGAATGATTCAAATGC
31199 TGAATGATTCA
1 TGAATGATTCA
31210 GAGGCTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (16 bp):
TGAATGATTCAAATGC
Found at i:34331 original size:40 final size:40
Alignment explanation
Indices: 34223--34332 Score: 175
Period size: 40 Copynumber: 2.8 Consensus size: 40
34213 AAACATACCT
** * *
34223 AAAATTTAATTTTTGTTTCATTTTAGTAGCCTGCCATTAA
1 AAAATTTAGCTTTTGTTTCATTTTAGTATCATGCCATTAA
*
34263 AAATTTTAGCTTTTGTTTCATTTTAGTATCATGCCATTAA
1 AAAATTTAGCTTTTGTTTCATTTTAGTATCATGCCATTAA
34303 AAAATTTAGCTTTTGTTTCATTTTAGTATC
1 AAAATTTAGCTTTTGTTTCATTTTAGTATC
34333 TCGTTCAGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (40 bp):
AAAATTTAGCTTTTGTTTCATTTTAGTATCATGCCATTAA
Found at i:34611 original size:25 final size:25
Alignment explanation
Indices: 34557--34620 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 25
34547 AGTTTACCTA
*
34557 ATTATTTTATTTTTGTTAAAATTTT
1 ATTATTTTATTTTTGTTAAAATATT
*
34582 A-TATTTTGTTTTTGTTAAAATATT
1 ATTATTTTATTTTTGTTAAAATATT
34606 ATTATTTTAATTTTT
1 ATTATTTT-ATTTTT
34621 ATTCAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 22 0.65
25 7 0.21
26 5 0.15
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (25 bp):
ATTATTTTATTTTTGTTAAAATATT
Found at i:34960 original size:19 final size:18
Alignment explanation
Indices: 34905--34956 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
34895 TTTGGGCCAC
34905 ATTGTAAAAT-TATGATAA
1 ATTGTAAAATATAT-ATAA
* * *
34923 CTTGTAAGACAGTATATAA
1 ATTGTAAAATA-TATATAA
34942 ATTGTAAAATATATA
1 ATTGTAAAATATATA
34957 ATAATTAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
18 11 0.42
19 12 0.46
20 3 0.12
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.37
Consensus pattern (18 bp):
ATTGTAAAATATATATAA
Found at i:35987 original size:123 final size:122
Alignment explanation
Indices: 35760--36170 Score: 456
Period size: 123 Copynumber: 3.4 Consensus size: 122
35750 AACTTAGAAT
* * * * * * * *
35760 CTAAATTATCAGTTTTAGTTCGTTTTAGTATTTAAACTTT-TATTTCTTTAAAATTATATCTAAC
1 CTAAACTATAAGTTTTTGTCCGTTTTAGTACTTAAACTTTCAATTTTTTTAAAATCATA-CTAAC
* *
35824 ATTTAGTTTTTGTTTCATTTTAGTACTCCCAACTGTTAAAACTTTAACGCGTTTAGTAC
65 ATTTAGTTTTTGTTTCATTTTAGTAC-CCCCACTATTAAAACTTTAACGCGTTTAGTAC
* *
35883 CTAAACTATATGTTTTTGTCCGTTTTAGTAGTTAAACTTTCAATTTTTTTAAAATCATACATAAC
1 CTAAACTATAAGTTTTTGTCCGTTTTAGTACTTAAACTTTCAATTTTTTTAAAATCATAC-TAAC
* *
35948 ATTTAGTTTTTGTTTCATTTTAGCACCCCCACTATTAAAAATCTTAACGCGTTT-GTAC
65 ATTTAGTTTTTGTTTCATTTTAGTACCCCCACTATTAAAACT-TTAACGCGTTTAGTAC
* ** * * * *
36006 CTAAACTATAAGTTTTTATCTATTTTAGTACCTAAACTTCCAA-TTTTTTAAAACCATGCCTAAC
1 CTAAACTATAAGTTTTTGTCCGTTTTAGTACTTAAACTTTCAATTTTTTTAAAATCAT-ACTAAC
* * * *
36070 ATTTAGTTTTTATTTCATTTTAGTA-CCCCACTATGAAAACCTTAACGTGTTTAGTAC
65 ATTTAGTTTTTGTTTCATTTTAGTACCCCCACTATTAAAACTTTAACGCGTTTAGTAC
* * * * *
36127 CAAAACTATCAA-TTTTGGTTCG-TTTAGTACCTAAGCTTTCAATT
1 CTAAACTAT-AAGTTTTTGTCCGTTTTAGTACTTAAACTTTCAATT
36171 ATTATTTTTT
Statistics
Matches: 245, Mismatches: 36, Indels: 16
0.82 0.12 0.05
Matches are distributed among these distances:
120 28 0.11
121 31 0.13
122 42 0.17
123 89 0.36
124 55 0.22
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (122 bp):
CTAAACTATAAGTTTTTGTCCGTTTTAGTACTTAAACTTTCAATTTTTTTAAAATCATACTAACA
TTTAGTTTTTGTTTCATTTTAGTACCCCCACTATTAAAACTTTAACGCGTTTAGTAC
Found at i:44017 original size:44 final size:44
Alignment explanation
Indices: 43969--44057 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
43959 AAGCACGAAC
*
43969 CAAACAACCTTTGTGATAAAGAAATTATTAATATTCTCTAAGGA
1 CAAACAACCTTTGTGATAAAAAAATTATTAATATTCTCTAAGGA
44013 CAAACAACCTTTGTGATAAAAAAATTATTAATATTCTCTAAGGA
1 CAAACAACCTTTGTGATAAAAAAATTATTAATATTCTCTAAGGA
44057 C
1 C
44058 TTGAGTTCGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (44 bp):
CAAACAACCTTTGTGATAAAAAAATTATTAATATTCTCTAAGGA
Found at i:44173 original size:31 final size:30
Alignment explanation
Indices: 44083--44204 Score: 172
Period size: 30 Copynumber: 4.0 Consensus size: 30
44073 AAGGGTATGA
44083 GCCTTTAATGTCAAAAGATTGAAAGTTATC
1 GCCTTTAATGTCAAAAGATTGAAAGTTATC
* *
44113 GCCTTTAATATCAAAAGATTGAAAATTATC
1 GCCTTTAATGTCAAAAGATTGAAAGTTATC
* *
44143 ACCTTTAATGTTAAAAGATTTGAAAGTTATC
1 GCCTTTAATGTCAAAAGA-TTGAAAGTTATC
* *
44174 GCCTTTAATGTCAAAAAAATTAAAAGTTATC
1 GCCTTTAATGTC-AAAAGATTGAAAGTTATC
44205 TTTGAACAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
30 43 0.54
31 32 0.40
32 5 0.06
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (30 bp):
GCCTTTAATGTCAAAAGATTGAAAGTTATC
Found at i:45014 original size:4 final size:4
Alignment explanation
Indices: 45005--45033 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
44995 GGGTAGGGTA
45005 GGAG GGAG GGAG GGAG GGAG GGAG GGAG G
1 GGAG GGAG GGAG GGAG GGAG GGAG GGAG G
45034 TAGCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:52201 original size:12 final size:13
Alignment explanation
Indices: 52177--52208 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52167 TTTTATAATA
52177 TATCATATTTTAT
1 TATCATATTTTAT
52190 TATCAT-TTTTAT
1 TATCATATTTTAT
52202 TA-CATAT
1 TATCATAT
52209 AGTTATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 9 0.50
13 6 0.33
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (13 bp):
TATCATATTTTAT
Found at i:52208 original size:29 final size:29
Alignment explanation
Indices: 52153--52208 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
52143 TAACATGATT
* *
52153 TATTTTATTAATTTTTTTATAATATATCA
1 TATTTTATTAATATTTTTATAACATATCA
*
52182 TATTTTATT-ATCATTTTTATTACATAT
1 TATTTTATTAAT-ATTTTTATAACATAT
52209 AGTTATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (29 bp):
TATTTTATTAATATTTTTATAACATATCA
Found at i:54284 original size:23 final size:23
Alignment explanation
Indices: 54236--54304 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
54226 GAGTAGAGGG
* * *
54236 TTCTACGCGATCCTTTTGGGATAA
1 TTCTACGTGGTCC-TTTGGGACAA
54260 TTCTACGTGGTCCTTTGGGACAA
1 TTCTACGTGGTCCTTTGGGACAA
54283 TTCTACGTGGTCCTTTGGGACA
1 TTCTACGTGGTCCTTTGGGACA
54305 TTTTTATGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 31 0.74
24 11 0.26
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTCCTTTGGGACAA
Found at i:54430 original size:23 final size:23
Alignment explanation
Indices: 54260--54430 Score: 146
Period size: 23 Copynumber: 7.4 Consensus size: 23
54250 TTTGGGATAA
* * *
54260 TTCTACGTGGTCCTTTGGGACAA
1 TTCTATGTGGTCCTTCGGGACAT
* *
54283 TTCTACGTGGTCCTTTGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
* * *
54306 TTTTATGCT-ATCATTCGGGACAT
1 TTCTATG-TGGTCCTTCGGGACAT
* * **
54329 TTCTATGCGATCCTTCGAAACAT
1 TTCTATGTGGTCCTTCGGGACAT
* *
54352 ATCTATGTGGTCCTTCGAGACAT
1 TTCTATGTGGTCCTTCGGGACAT
*
54375 ATCTATGTGGTCCTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
* * * *
54398 ATCTATGTGGTCATTTGAGACAT
1 TTCTATGTGGTCCTTCGGGACAT
*
54421 TTCTACGTGG
1 TTCTATGTGG
54431 CACTTCAGTG
Statistics
Matches: 125, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
23 124 0.99
24 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAT
Found at i:57531 original size:40 final size:40
Alignment explanation
Indices: 57476--57554 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
57466 ATGTTACTAC
*
57476 TTGTATATATAGTGGATTTTGCTGTTTGATATAGAACTGT
1 TTGTATATATAGTGGATTTTGCCGTTTGATATAGAACTGT
57516 TTGTATATATAGTGGATTTTGCCGTTTGATATAGAACTG
1 TTGTATATATAGTGGATTTTGCCGTTTGATATAGAACTG
57555 AGCTTACAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (40 bp):
TTGTATATATAGTGGATTTTGCCGTTTGATATAGAACTGT
Found at i:63448 original size:20 final size:20
Alignment explanation
Indices: 63423--63467 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
63413 ATGGTTACCA
63423 AGGGATTTATGTTTTTTGAT
1 AGGGATTTATGTTTTTTGAT
63443 AGGGATTTATGTTTTTTGAT
1 AGGGATTTATGTTTTTTGAT
63463 AGGGA
1 AGGGA
63468 CGGATGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (20 bp):
AGGGATTTATGTTTTTTGAT
Found at i:63478 original size:21 final size:20
Alignment explanation
Indices: 63431--63478 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
63421 CAAGGGATTT
***
63431 ATGTTTTTTGATAGGGATTT
1 ATGTTTTTTGATAGGGACGG
63451 ATGTTTTTTGATAGGGACGG
1 ATGTTTTTTGATAGGGACGG
*
63471 ATGATTTT
1 ATGTTTTT
63479 GGCTCACTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.02, G:0.27, T:0.50
Consensus pattern (20 bp):
ATGTTTTTTGATAGGGACGG
Found at i:70033 original size:23 final size:23
Alignment explanation
Indices: 70007--70054 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
69997 TCATGACAGT
70007 GGCATGTCTCGTTCCTGGTCCGG
1 GGCATGTCTCGTTCCTGGTCCGG
70030 GGCATGTCTCGTTCCTGGTCCGG
1 GGCATGTCTCGTTCCTGGTCCGG
70053 GG
1 GG
70055 ATCAAGGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.04, C:0.29, G:0.38, T:0.29
Consensus pattern (23 bp):
GGCATGTCTCGTTCCTGGTCCGG
Found at i:72041 original size:11 final size:11
Alignment explanation
Indices: 72018--72049 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
72008 TGTAATTAAT
72018 TATTTATATATA
1 TATTTA-ATATA
72030 TATTTAATATA
1 TATTTAATATA
72041 TATTTAATA
1 TATTTAATA
72050 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:72053 original size:3 final size:3
Alignment explanation
Indices: 72045--72166 Score: 226
Period size: 3 Copynumber: 40.7 Consensus size: 3
72035 AATATATATT
*
72045 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
72093 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
72141 TAA TAA TAA TAA TAA CAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
72167 TGGATAAAAA
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 115 1.00
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:72732 original size:113 final size:113
Alignment explanation
Indices: 72487--73269 Score: 1369
Period size: 113 Copynumber: 7.0 Consensus size: 113
72477 AGAATTATGC
* * * * *
72487 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAATTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
72552 TATGAAC-TTCTCTGGGAATGCTGATCCATCAATTGATGAATTCATGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
*
72599 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
72664 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
72712 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
72777 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
72825 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
72890 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
72938 AAAAGGTTGAACAAATT-TT-TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
73001 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
73049 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
73114 TATGAACCTTT-TCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAA-CTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
*
73162 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
73227 TATGAACCTTT-TCTGGAAAAGCTAATCTATCAAATGATAGATT
66 TATGAA-CTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATT
73270 TGAATCTTTG
Statistics
Matches: 651, Mismatches: 16, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
111 108 0.17
112 72 0.11
113 467 0.72
114 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
Found at i:73039 original size:337 final size:339
Alignment explanation
Indices: 72487--73269 Score: 1369
Period size: 337 Copynumber: 2.3 Consensus size: 339
72477 AGAATTATGC
* * * * *
72487 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAATTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
72552 TATGAAC-TTCTCTGGGAATGCTGATCCATCAATTGATGAATTCATGTAAAAGGTTGAACAAGTT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
72616 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
72681 AAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
196 AAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
72746 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTTCTCTGGAAAAGCTGATCCATCAA
261 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTT-TCTGGAAAAGCTGATCCATCAA
72810 ATGATGGATTCAGGT
325 ATGATGGATTCAGGT
72825 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
72890 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
72955 -TT-TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
73018 AAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
196 AAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
73083 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTTCTGGAAAAGCTGATCCATCAAA
261 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTTCTGGAAAAGCTGATCCATCAAA
73148 TGATGGATTCAGGT
326 TGATGGATTCAGGT
*
73162 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
73227 TATGAACCTTT-TCTGGAAAAGCTAATCTATCAAATGATAGATT
66 TATGAA-CTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATT
73270 TGAATCTTTG
Statistics
Matches: 426, Mismatches: 16, Indels: 7
0.95 0.04 0.02
Matches are distributed among these distances:
337 298 0.70
338 77 0.18
339 51 0.12
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (339 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTTCTGGAAAAGCTGATCCATCAAA
TGATGGATTCAGGT
Found at i:74145 original size:84 final size:84
Alignment explanation
Indices: 73979--74790 Score: 1513
Period size: 84 Copynumber: 9.7 Consensus size: 84
73969 GTAATTCCTA
*
73979 CCAACCCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CAAATTCA-TCTTCC
1 CCAA-CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT-ATTCTTCC
*
74042 AAACTCAATGATTGGTTCTGT
64 AAATTCAATGATTGGTTCTGT
74063 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
74128 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
74147 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
74212 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
*
74231 CCAACCAGATCAGATAACTCAAAG-ACACTTCCAGAAGATGCTATTGAGCACATTATCCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
74295 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
74314 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
74379 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
74398 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
74463 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
* *
74482 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCATATTATTCTTCTAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
74547 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
*
74566 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGAGCACATTATTCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
74631 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
*
74650 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCATATTATTCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
74715 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
*
74734 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACACATTAT
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
74791 ATTTGTTCCA
Statistics
Matches: 712, Mismatches: 13, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
83 127 0.18
84 585 0.82
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (84 bp):
CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
ATTCAATGATTGGTTCTGT
Found at i:75955 original size:12 final size:12
Alignment explanation
Indices: 75938--76003 Score: 84
Period size: 12 Copynumber: 5.8 Consensus size: 12
75928 TTGACCCCCT
75938 TTTTTTCTTTTC
1 TTTTTTCTTTTC
* *
75950 TTTTTTCTATTA
1 TTTTTTCTTTTC
75962 TTTTTTCTTTT-
1 TTTTTTCTTTTC
75973 TTTTTTCTTTTC
1 TTTTTTCTTTTC
*
75985 -TTTCT-TTTTC
1 TTTTTTCTTTTC
75995 TTTTTTCTT
1 TTTTTTCTT
76004 CAAGCATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
10 5 0.11
11 19 0.41
12 22 0.48
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:75974 original size:26 final size:25
Alignment explanation
Indices: 75937--76004 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
75927 CTTGACCCCC
75937 TTTTTTTC--TTTTCTT-TTTTCTAT
1 TTTTTTTCTTTTTTCTTCTTTTCT-T
*
75960 TATTTTTTCTTTTTTTTTTCTTTTCTT
1 T-TTTTTTC-TTTTTTCTTCTTTTCTT
*
75987 TCTTTTTCTTTTTTCTTC
1 TTTTTTTCTTTTTTCTTC
76005 AAGCATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 1 0.03
24 7 0.19
25 9 0.24
26 6 0.16
27 8 0.22
28 6 0.16
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTTTTCTTTTTTCTTCTTTTCTT
Found at i:75983 original size:35 final size:33
Alignment explanation
Indices: 75937--76003 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 33
75927 CTTGACCCCC
*
75937 TTTTTTTCTTTTCTTTTTTCTATTATTTTTTCTTT
1 TTTTTTTCTTTTCTTTCTT-T-TTATTTTTTCTTT
*
75972 TTTTTTTCTTTTCTTTCTTTTTCTTTTTTCTT
1 TTTTTTTCTTTTCTTTCTTTTTATTTTTTCTT
76004 CAAGCATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 11 0.37
34 1 0.03
35 18 0.60
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (33 bp):
TTTTTTTCTTTTCTTTCTTTTTATTTTTTCTTT
Found at i:86667 original size:6 final size:7
Alignment explanation
Indices: 86648--86672 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
86638 TAAATATATG
86648 AATTTTT
1 AATTTTT
86655 AATTTTT
1 AATTTTT
86662 AATTTTT
1 AATTTTT
86669 AATT
1 AATT
86673 AATAGAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:88856 original size:3 final size:3
Alignment explanation
Indices: 88774--88840 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
88764 TTAATATATT
* *
88774 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
88822 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
88841 TAAAAAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:89016 original size:84 final size:84
Alignment explanation
Indices: 88875--89502 Score: 1188
Period size: 84 Copynumber: 7.5 Consensus size: 84
88865 AAAAATTAGT
88875 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
*
88940 GAATAATATGCTCAATAGC
66 GAATAATGTGCTCAATAGC
88959 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
89024 GAATAATGTGCTCAATAGC
66 GAATAATGTGCTCAATAGC
89043 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
89108 GAATAATGTGCTCAATAGC
66 GAATAATGTGCTCAATAGC
89127 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
*
89192 GGATAATGTGCTCAATAGC
66 GAATAATGTGCTCAATAGC
89211 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
89276 GAATAATGTGCTCAATAGC
66 GAATAATGTGCTCAATAGC
89295 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
89360 GAATAATGTGCTCAATAGC
66 GAATAATGTGCTCAATAGC
*
89379 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAGTTTGGAA
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
*
89444 G-ATGAATTTG-TCAATAGC
66 GAAT-AATGTGCTCAATAGC
89462 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGGTTGG
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GGTTGG
89503 TAGGAATTAC
Statistics
Matches: 537, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
83 44 0.08
84 493 0.92
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.35
Consensus pattern (84 bp):
ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGAA
GAATAATGTGCTCAATAGC
Found at i:90407 original size:113 final size:113
Alignment explanation
Indices: 90204--90875 Score: 1152
Period size: 113 Copynumber: 6.0 Consensus size: 113
90194 CAAAGATTCA
* * *
90204 AATCTATCATTTGATAGATTAGCTTTTCCAGA-AAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAA-GTTCATAATGAGAAGAACTCATCTGAAG
*
90268 AAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
90317 AATCCATCATTTGATGGATCAGCTTTTCCAGA-AAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAA-GTTCATAATGAGAAGAACTCATCTGAAG
90381 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
90430 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
90495 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
90543 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
90608 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
90656 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
90721 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * *
90769 AATTCATCAATTGATGGATCAGCATTCCCAGAG-AAGTTCATAATGAGAAGAATTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
90833 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
90876 GCATAATTCT
Statistics
Matches: 540, Mismatches: 18, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
112 69 0.13
113 468 0.87
114 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:91203 original size:3 final size:3
Alignment explanation
Indices: 91197--91303 Score: 169
Period size: 3 Copynumber: 35.7 Consensus size: 3
91187 TTTTTATCCA
*
91197 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
91245 TAT TAT TAC TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
91293 TAT TAT TAT TA
1 TAT TAT TAT TA
91304 AATATATATT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:91315 original size:11 final size:11
Alignment explanation
Indices: 91299--91323 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
91289 TTATTATTAT
91299 TATTAAATATA
1 TATTAAATATA
91310 TATTAAATATA
1 TATTAAATATA
91321 TAT
1 TAT
91324 AAAAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TATTAAATATA
Found at i:91829 original size:16 final size:15
Alignment explanation
Indices: 91810--91839 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
91800 GAGAGAACCG
91810 GAGAAAGAAAAAAACA
1 GAGAAA-AAAAAAACA
91826 GAGAAAAAAAAAAC
1 GAGAAAAAAAAAAC
91840 TACTAACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.77, C:0.07, G:0.17, T:0.00
Consensus pattern (15 bp):
GAGAAAAAAAAAACA
Found at i:101209 original size:7 final size:7
Alignment explanation
Indices: 101199--101236 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
101189 ACCCAAACTA
*
101199 TAAACCT
1 TAAACCC
*
101206 TAAATCC
1 TAAACCC
101213 TAAACCC
1 TAAACCC
101220 TAAACCC
1 TAAACCC
101227 TAAACCC
1 TAAACCC
101234 TAA
1 TAA
101237 CTAAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:101217 original size:21 final size:21
Alignment explanation
Indices: 101187--101236 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
101177 ACCCTACCTC
* *
101187 AAACCC-AAACTATAAACCTT
1 AAACCCTAAACCATAAACCCT
* *
101207 AAATCCTAAACCCTAAACCCT
1 AAACCCTAAACCATAAACCCT
101228 AAACCCTAA
1 AAACCCTAA
101237 CTAAAAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCCTAAACCATAAACCCT
Found at i:103982 original size:18 final size:18
Alignment explanation
Indices: 103959--104007 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
103949 CAACCCCTCC
*
103959 ACAAGTGTCACCCCTAAT
1 ACAAGTGCCACCCCTAAT
* *
103977 ACAAGTGCCACTCTTAAT
1 ACAAGTGCCACCCCTAAT
103995 ACAAGTGCCACCC
1 ACAAGTGCCACCC
104008 TGGGACTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.20
Consensus pattern (18 bp):
ACAAGTGCCACCCCTAAT
Found at i:105315 original size:45 final size:43
Alignment explanation
Indices: 105266--105373 Score: 137
Period size: 45 Copynumber: 2.5 Consensus size: 43
105256 TTTCTTGTAG
105266 AAAAATAATATTTTAAATAACACCAAATATTAACATTT-CAGGTA
1 AAAAATAATATTTTAAATAACACC-AATATTAACATTTACA-GTA
* ** * *
105310 TAAAAATAACATTTTAAATAACGTCAATATTAATATTTACATTA
1 -AAAAATAATATTTTAAATAACACCAATATTAACATTTACAGTA
105354 AAAAATAATATTTTAAATAA
1 AAAAATAATATTTTAAATAA
105374 TATTTTACTA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 19 0.34
44 14 0.25
45 23 0.41
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (43 bp):
AAAAATAATATTTTAAATAACACCAATATTAACATTTACAGTA
Found at i:105371 original size:12 final size:12
Alignment explanation
Indices: 105356--105380 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
105346 TTACATTAAA
105356 AAATAATATTTT
1 AAATAATATTTT
105368 AAATAATATTTT
1 AAATAATATTTT
105380 A
1 A
105381 CTAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:107183 original size:95 final size:96
Alignment explanation
Indices: 106988--107184 Score: 360
Period size: 95 Copynumber: 2.1 Consensus size: 96
106978 CTGGGCTGAG
*
106988 GTATAAGTATTGTTCATACAATACTGATACTGCTCGTCGAGAGTTGGGCAAAAATTCAAAAGGTT
1 GTATCAGTATTGTTCATACAATACTGATACTGCTCGTCGAGAGTTGGGCAAAAATTCAAAAGGTT
*
107053 TGTGAGAAGAGTATCGATACCCCTTCAAGGG
66 TGTGAGAAGAGTATCGATACCCCTTCAAGGA
107084 GTATCAGTATTGTTCATACAATACTGATACTGCTCGTCGAGAGTTGGGC-AAAATTCAAAAGGTT
1 GTATCAGTATTGTTCATACAATACTGATACTGCTCGTCGAGAGTTGGGCAAAAATTCAAAAGGTT
*
107148 TGTGAGGAGAGTATCGATACCCCTTCAAGGA
66 TGTGAGAAGAGTATCGATACCCCTTCAAGGA
107179 GTATCA
1 GTATCA
107185 ATACTACTCA
Statistics
Matches: 98, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
95 50 0.51
96 48 0.49
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (96 bp):
GTATCAGTATTGTTCATACAATACTGATACTGCTCGTCGAGAGTTGGGCAAAAATTCAAAAGGTT
TGTGAGAAGAGTATCGATACCCCTTCAAGGA
Found at i:107267 original size:18 final size:19
Alignment explanation
Indices: 107244--107293 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
107234 GGCAATTTTG
*
107244 GTATCGATACTCATGG-GA
1 GTATCGATACTCAGGGAGA
*
107262 GTATCGATACTGAGGGTAGA
1 GTATCGATACTCAGGG-AGA
107282 GTATCGATACTC
1 GTATCGATACTC
107294 CCAGTAGGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 14 0.52
20 13 0.48
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (19 bp):
GTATCGATACTCAGGGAGA
Found at i:107387 original size:20 final size:20
Alignment explanation
Indices: 107361--107417 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
107351 TGATACACAT
*
107361 GAGAGTATCGATACTGT-GG
1 GAGAGTATCGATACTGTCAG
* *
107380 GTAGAGTATCAATACTCTCAG
1 G-AGAGTATCGATACTGTCAG
107401 GAGAAGTATCGATACTG
1 GAG-AGTATCGATACTG
107418 AGGCTTTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.03
20 16 0.53
21 13 0.43
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (20 bp):
GAGAGTATCGATACTGTCAG
Found at i:109349 original size:14 final size:14
Alignment explanation
Indices: 109311--109353 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
109301 TAGATTATAT
* * *
109311 GTTCGTTTATATTT
1 GTTCATTTATGTTC
109325 GTTCATTTATGTTC
1 GTTCATTTATGTTC
109339 GTTCATTTATGTTC
1 GTTCATTTATGTTC
109353 G
1 G
109354 AACAGAGGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:109734 original size:16 final size:16
Alignment explanation
Indices: 109709--109740 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
109699 AAATTTTTTT
109709 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
109725 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
109741 CTTATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.56
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:109899 original size:31 final size:32
Alignment explanation
Indices: 109855--109925 Score: 126
Period size: 31 Copynumber: 2.2 Consensus size: 32
109845 GATAATAACT
*
109855 AATACTATCACCTTTCTTCTTATATGGCCAAC
1 AATACGATCACCTTTCTTCTTATATGGCCAAC
109887 AATACGAT-ACCTTTCTTCTTATATGGCCAAC
1 AATACGATCACCTTTCTTCTTATATGGCCAAC
109918 AATACGAT
1 AATACGAT
109926 TATTTGGAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 31 0.82
32 7 0.18
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (32 bp):
AATACGATCACCTTTCTTCTTATATGGCCAAC
Found at i:111965 original size:49 final size:49
Alignment explanation
Indices: 111893--111992 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
111883 AAAGACACTT
111893 TTTTATGTGGTTAAAGAGAGTGTCAGACGGATGAAGATACAACGAAATG
1 TTTTATGTGGTTAAAGAGAGTGTCAGACGGATGAAGATACAACGAAATG
*
111942 TTTTATGTGGTTAAAGAGAGTGTCATACGGATGAAGATACAACGAAATG
1 TTTTATGTGGTTAAAGAGAGTGTCAGACGGATGAAGATACAACGAAATG
111991 TT
1 TT
111993 AAATTGCAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.29
Consensus pattern (49 bp):
TTTTATGTGGTTAAAGAGAGTGTCAGACGGATGAAGATACAACGAAATG
Found at i:119056 original size:19 final size:19
Alignment explanation
Indices: 119023--119059 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
119013 ATGACCAATA
**
119023 AAATCGCAATGCGATCTCT
1 AAATCGCAACACGATCTCT
119042 AAATCGCAACACGATCTC
1 AAATCGCAACACGATCTC
119060 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCGCAACACGATCTCT
Found at i:120065 original size:24 final size:24
Alignment explanation
Indices: 120008--120067 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
119998 TAGTCAGTAT
120008 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
120032 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
120056 TCGAATTTTGAT
1 TCGAAATTTGAT
120068 GATGTTTAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:122501 original size:41 final size:40
Alignment explanation
Indices: 122401--122505 Score: 102
Period size: 41 Copynumber: 2.6 Consensus size: 40
122391 TGAATGGTGG
* * * *
122401 GAGGACCTCTTCAACGATGACAGGGCCTCTTGAACGGTGGA
1 GAGG-CCTCTTGAAAGATGACAGGGCCTCTTGAACGATAGA
* ** ** *
122442 GGGGAATCTTGAGGGATGATAGGGGCCTCTTGAACGATAGA
1 GAGGCCTCTTGAAAGATGACA-GGGCCTCTTGAACGATAGA
122483 GAGGCCTCTTGAAAGATGACAGG
1 GAGGCCTCTTGAAAGATGACAGG
122506 TGAGTCGGCT
Statistics
Matches: 48, Mismatches: 15, Indels: 3
0.73 0.23 0.05
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.20
Consensus pattern (40 bp):
GAGGCCTCTTGAAAGATGACAGGGCCTCTTGAACGATAGA
Found at i:122998 original size:20 final size:20
Alignment explanation
Indices: 122973--123016 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
122963 AATAGTTTCT
122973 GAAACTTAAAATCACAACAC
1 GAAACTTAAAATCACAACAC
* *
122993 GAAACTTAAAATCGCAACTC
1 GAAACTTAAAATCACAACAC
123013 GAAA
1 GAAA
123017 ATGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.23, G:0.09, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATCACAACAC
Found at i:123026 original size:20 final size:20
Alignment explanation
Indices: 123003--123051 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
122993 GAAACTTAAA
*
123003 ATCGCAACTCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
123023 ATCGAAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
123043 ATCGCAACG
1 ATCGCAACG
123052 GGATAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:123089 original size:19 final size:20
Alignment explanation
Indices: 123056--123094 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
123046 GCAACGGGAT
*
123056 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
*
123075 AATCGCAACGTGAAACTAAA
1 AATCGCAACGCGAAACTAAA
123095 TTCGCGTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:123131 original size:14 final size:14
Alignment explanation
Indices: 123112--123144 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
123102 TACGATTTTC
123112 ATTTTCGCATTGCG
1 ATTTTCGCATTGCG
*
123126 ATTTTCGCGTTGCG
1 ATTTTCGCATTGCG
123140 ATTTT
1 ATTTT
123145 TATTTCGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTTCGCATTGCG
Found at i:123156 original size:33 final size:34
Alignment explanation
Indices: 123095--123174 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 34
123085 TGAAACTAAA
*
123095 TTCGCGTTACGATTTTCATTTTCGCATTGCGATT
1 TTCGCGTTGCGATTTTCATTTTCGCATTGCGATT
*
123129 TTCGCGTTGCGATTTTTA-TTTCGCATTGCGATT
1 TTCGCGTTGCGATTTTCATTTTCGCATTGCGATT
* *
123162 ATCCCGTTGCGAT
1 TTCGCGTTGCGAT
123175 AGTCAAATTC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 26 0.62
34 16 0.38
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (34 bp):
TTCGCGTTGCGATTTTCATTTTCGCATTGCGATT
Found at i:123597 original size:38 final size:40
Alignment explanation
Indices: 123521--123603 Score: 134
Period size: 38 Copynumber: 2.1 Consensus size: 40
123511 TACCTCACCA
123521 CGTAAAGTAGATACCTCGTCACACCATGCACCATTGTCATCG
1 CGTAAAGTAGATACCTCGT-ACA-CATGCACCATTGTCATCG
123563 CGTAAAGTAGATACCTCGT-CA-ATGCACCATTGTCATCG
1 CGTAAAGTAGATACCTCGTACACATGCACCATTGTCATCG
123601 CGT
1 CGT
123604 CCGACCTCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
38 20 0.49
40 2 0.05
42 19 0.46
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (40 bp):
CGTAAAGTAGATACCTCGTACACATGCACCATTGTCATCG
Found at i:125165 original size:20 final size:20
Alignment explanation
Indices: 125142--125241 Score: 94
Period size: 20 Copynumber: 5.0 Consensus size: 20
125132 TCTGAAACTT
* *
125142 AAAATTGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
**
125162 AAAATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
** **
125182 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
125202 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
125221 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
125241 A
1 A
125242 CTATCACAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
19 14 0.21
20 54 0.79
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:125243 original size:59 final size:60
Alignment explanation
Indices: 125148--125267 Score: 179
Period size: 59 Copynumber: 2.0 Consensus size: 60
125138 ACTTAAAATT
* ** *
125148 GCAACACGAAAATGAAAATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATC
1 GCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCACAACGCGAATTTGACTATC
* *
125208 GCAACGCG-AAATGAAAATCGCAACACGAAAATGACTATCACAATGCGAATTTGACTATC
1 GCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCACAACGCGAATTTGACTATC
125267 G
1 G
125268 TTGTGATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
59 47 0.87
60 7 0.13
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (60 bp):
GCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCACAACGCGAATTTGACTATC
Found at i:125758 original size:20 final size:20
Alignment explanation
Indices: 125735--125838 Score: 86
Period size: 20 Copynumber: 5.2 Consensus size: 20
125725 AAATCGAAAC
125735 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
125755 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
* * * *
125775 GTGAT-TTACATATTCGCGTT
1 GCGATAGT-CAGAATCGCGTT
* * * * *
125795 ACGAT-TTACATATTCGCATT
1 GCGATAGT-CAGAATCGCGTT
*
125815 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
125835 GCGA
1 GCGA
125839 ATCTAGAAAC
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.01
20 68 0.97
21 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:125876 original size:20 final size:19
Alignment explanation
Indices: 125853--125898 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
125843 AGAAACTGAT
* *
125853 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
125873 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
125892 TTGCGAT
1 TTGCGAT
125899 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:125888 original size:19 final size:19
Alignment explanation
Indices: 125864--125900 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
125854 TGCGATACTG
*
125864 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
125883 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
125901 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:140371 original size:11 final size:11
Alignment explanation
Indices: 140351--140390 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
140341 TTGAGCTTGA
*
140351 AATATGTATTT
1 AATATATATTT
140362 AATATATATTT
1 AATATATATTT
140373 ATATATAATATTT
1 A-ATAT-ATATTT
140386 AATAT
1 AATAT
140391 TTAATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 11 0.42
12 8 0.31
13 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:140388 original size:7 final size:7
Alignment explanation
Indices: 140367--140399 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
140357 TATTTAATAT
140367 ATATTT-
1 ATATTTA
*
140373 ATATATA
1 ATATTTA
140380 ATATTTA
1 ATATTTA
140387 ATATTTA
1 ATATTTA
140394 ATATTT
1 ATATTT
140400 TCAGTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATATTTA
Found at i:140395 original size:14 final size:13
Alignment explanation
Indices: 140357--140399 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
140347 TTGAAATATG
140357 TATTTA-ATAT-A
1 TATTTATATATAA
140368 TATTTATATATAA
1 TATTTATATATAA
*
140381 TATTTAATATTTAA
1 TATTT-ATATATAA
140395 TATTT
1 TATTT
140400 TCAGTTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 6 0.21
12 4 0.14
13 6 0.21
14 12 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTTATATATAA
Found at i:146781 original size:43 final size:43
Alignment explanation
Indices: 146687--146789 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 43
146677 ATCTCTTGGC
* * * *
146687 ATCTCTCGGCGTCTTCAACACATAATGTCCATGCATGAAATGG
1 ATCTCTCGGCGTCTTCAACAAAAAATGTCCATACATGAAATAG
* *
146730 AT-TGCTCGGCGTCTTCAACAAAAAAATTTCCATACATTAAA-AG
1 ATCT-CTCGGCGTCTTCAAC-AAAAAATGTCCATACATGAAATAG
*
146773 ATCTCTCGGCATCTTCA
1 ATCTCTCGGCGTCTTCA
146790 TTGAAAAACT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
42 1 0.02
43 32 0.64
44 17 0.34
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (43 bp):
ATCTCTCGGCGTCTTCAACAAAAAATGTCCATACATGAAATAG
Found at i:148451 original size:552 final size:549
Alignment explanation
Indices: 147331--148754 Score: 2250
Period size: 552 Copynumber: 2.6 Consensus size: 549
147321 TCAAATTGGC
* *
147331 TTGA-TCCCTAAACCCTAAACTATATATAAACAAAATTAAATCAAATGTAATCT-TGACACAAAC
1 TTGACTCCCTAAACCCTAAACTCTATATAAACAAAATTAAATCGAATGTAATCTAT-ACACAAAC
* *
147394 TAAATTGATCTGAAATGTTCCAACTTAAATCTAATAT-GAATGATCCGTTTGTCGCCCCTACTTC
65 TAAATTGATCTGAAATGATCCAACTTAAATCTAAT-TCGAATGATCCGTTTGTCACCCCTACTTC
* * **** * * * * *** *
147458 TACTTA-AACCTAAAAGC-AT-TTTA-TAACA-TATACTCTTAATAAATAAAGAAAATA-ATTAT
129 TACGTATAA-TTATTTTCTTTATTTATTAAGAGTATA-TGTT-AT-AA-AATGATTTTAGGTT-T
* *
147517 ACGTAGAAGTAGGGGTGACAAACGGATCATTCGAATTAGATTTAAGTTGGATCATTTCAGATCAA
188 AAGTAGAAGTAGGGGTGACAAACGGATCATTCGTATTAGATTTAAGTTGGATCATTTCAGATCAA
* *
147582 TTTAGTTTGTGTCTAGATTACATTCGATCTAATTTTGTTCATATAAAGTTTAGGATTTAGGGTTT
253 TTTAGTTTGTGTCTAGATTACATTCGATTTAATTTTGTTCATATAAGGTTTAGGATTTA--G---
147647 AGAGTTTAACCATAGGCTTTTAAAGTATAACTATTAACACGTTATATTTTATATAGATATAAAAA
313 -G-GTTTAACCATAGGCTTTTAAAGTATAACTATTAACACGTTATATTTTATATAGATATAAAAA
147712 ATAAACACGAAGAAACACAGAATTACTGAAATGTCGATATCACCAAATCTGATAATACTTTATAC
376 ATAAACACGAAGAAACACAGAATTACTGAAATGTCGATATCACCAAATCTGATAATACTTTATAC
*
147777 TTTACCCATAGGCTATCGAGTAGTGACCCACTTAATTGCTGAAAGTTTTCAACCCTTAAAAAATT
441 TTTACCCATAGGCTACCGAGTAGTGACCCACTTAATTGCTGAAAGTTTTCAACCCTTAAAAAATT
147842 AACCGATTCGTATTGACCCGAACAAAAAATTAACCGATCTAATA
506 AACCGATTCGTATTGACCCGAACAAAAAATTAACCGATCTAATA
* *
147886 TTGACT---T-AACCCTAAACCCTATATAAACAAAATTAAATCGAATATAATCTATACACAAACT
1 TTGACTCCCTAAACCCTAAACTCTATATAAACAAAATTAAATCGAATGTAATCTATACACAAACT
147947 AAATTGATCTGAAATGATCCAACTTAAATCTAATTCGAATGATCCGTTTGTCACCCCTACTTCTA
66 AAATTGATCTGAAATGATCCAACTTAAATCTAATTCGAATGATCCGTTTGTCACCCCTACTTCTA
148012 CGTATAATTATTTTCTTTATTTATTAAGAGTATATGTTATAAAATGATTTTAGGTTTAAGTAGAA
131 CGTATAATTATTTTCTTTATTTATTAAGAGTATATGTTATAAAATGATTTTAGGTTTAAGTAGAA
148077 GTAGGGGTGACAAACGGATCATTCGTATTAGATTTAAGTTGGATCATTTCAGATCAATTTAGTTT
196 GTAGGGGTGACAAACGGATCATTCGTATTAGATTTAAGTTGGATCATTTCAGATCAATTTAGTTT
* *
148142 GTGTCTAGATTACATTTGATTTAATTTTGTTTATATAAGGTTTAGGATTTAGGGTTTAACCATAG
261 GTGTCTAGATTACATTCGATTTAATTTTGTTCATATAAGGTTTAGGATTTAGGGTTTAACCATAG
148207 GCTTTTAAAGTATAACTATTAACACGTTATATTTTATATAGATATAAAAAATAAACACGAAGAAA
326 GCTTTTAAAGTATAACTATTAACACGTTATATTTTATATAGATATAAAAAATAAACACGAAGAAA
148272 CACAGAATTACTGAAATGTCGATATCACCAAATCTGATAATACTTTATACTTTACCCATAGGCTA
391 CACAGAATTACTGAAATGTCGATATCACCAAATCTGATAATACTTTATACTTTACCCATAGGCTA
148337 CCGAGTAGTGACCCACTTAATTGCTGAAAGTTTTCAACCCTTAAAAAATTAACCGATTCGTATTG
456 CCGAGTAGTGACCCACTTAATTGCTGAAAGTTTTCAACCCTTAAAAAATTAACCGATTCGTATTG
148402 ACCCGAACAAAAAATTAACCGATCTAATA
521 ACCCGAACAAAAAATTAACCGATCTAATA
* *
148431 TTGACTTAACCCTAAACCCTAAACTCTATATGAACAAAATTAAATCGAATGTAATCTAGACACAA
1 TTGAC-T--CCCTAAACCCTAAACTCTATATAAACAAAATTAAATCGAATGTAATCTATACACAA
148496 ACTAAATTGATCTGAAATGATCCAACTTAAATCTAATTCGAATGATCCGTTTGTCA-CCC--CTT
63 ACTAAATTGATCTGAAATGATCCAACTTAAATCTAATTCGAATGATCCGTTTGTCACCCCTACTT
148558 CTACGTATAATTATTTTCTTTATTTATTAAGAGTATATGTTATAAAATGATTTTAGGTTTAAGTA
128 CTACGTATAATTATTTTCTTTATTTATTAAGAGTATATGTTATAAAATGATTTTAGGTTTAAGTA
148623 GAAGTAGGGGTGACAAACGGATCATTCGTATTAGATTTAAGTTGGATCATTTCAGATCAATTTAG
193 GAAGTAGGGGTGACAAACGGATCATTCGTATTAGATTTAAGTTGGATCATTTCAGATCAATTTAG
* * * * * * *
148688 TTTGTGTCTAGACTACATTCGATTTAATTTTGTTCATACAGGGTTTAGAACTTAGGATTTAGCCA
258 TTTGTGTCTAGATTACATTCGATTTAATTTTGTTCATATAAGGTTTAGGATTTAGGGTTTAACCA
148753 TA
323 TA
148755 TTAGGGTTTA
Statistics
Matches: 813, Mismatches: 40, Indels: 38
0.91 0.04 0.04
Matches are distributed among these distances:
545 240 0.30
546 2 0.00
549 191 0.23
550 1 0.00
551 5 0.01
552 343 0.42
553 9 0.01
554 6 0.01
555 11 0.01
556 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (549 bp):
TTGACTCCCTAAACCCTAAACTCTATATAAACAAAATTAAATCGAATGTAATCTATACACAAACT
AAATTGATCTGAAATGATCCAACTTAAATCTAATTCGAATGATCCGTTTGTCACCCCTACTTCTA
CGTATAATTATTTTCTTTATTTATTAAGAGTATATGTTATAAAATGATTTTAGGTTTAAGTAGAA
GTAGGGGTGACAAACGGATCATTCGTATTAGATTTAAGTTGGATCATTTCAGATCAATTTAGTTT
GTGTCTAGATTACATTCGATTTAATTTTGTTCATATAAGGTTTAGGATTTAGGGTTTAACCATAG
GCTTTTAAAGTATAACTATTAACACGTTATATTTTATATAGATATAAAAAATAAACACGAAGAAA
CACAGAATTACTGAAATGTCGATATCACCAAATCTGATAATACTTTATACTTTACCCATAGGCTA
CCGAGTAGTGACCCACTTAATTGCTGAAAGTTTTCAACCCTTAAAAAATTAACCGATTCGTATTG
ACCCGAACAAAAAATTAACCGATCTAATA
Found at i:150599 original size:30 final size:29
Alignment explanation
Indices: 150425--150830 Score: 170
Period size: 30 Copynumber: 13.5 Consensus size: 29
150415 TATTCTTACA
*
150425 ATATTTTAAAATTAAAA-AAAAATTAAATAT
1 ATATTTT-AAGTTAAAATAAAAA-TAAATAT
* **
150455 AT-TTCTATAGTTAGGATAAAAATAAA-AT
1 ATATTTTA-AGTTAAAATAAAAATAAATAT
* * * * *
150483 TTATTTCTTAA-TTAAAATTAGAATTACATAC
1 ATA-TT-TTAAGTTAAAA-TAAAAATAAATAT
* * *
150514 ACTTTTTTAAATTAAAATTAAAAA-GAATAT
1 A-TATTTTAAGTTAAAA-TAAAAATAAATAT
** *
150544 ATATTTTTAAGTTAAGGTAAGAATAAGATAT
1 ATA-TTTTAAGTTAAAATAAAAATAA-ATAT
150575 ATATTTTAAGTTAAAATAAAAATAAATA-
1 ATATTTTAAGTTAAAATAAAAATAAATAT
* ** *
150603 ATATTTAATAATTTAAGGTGAAAATAGAATAT
1 ATATTT--TAAGTTAAAATAAAAATA-AATAT
* * ** *
150635 AT-TTAATAATTTAAGTTAATAATATAATAT
1 ATATT-TTAAGTTAAAATAAAAATA-AATAT
*
150665 ATATGTAATAAG-TAAAGATAAAAATAAA-AT
1 ATAT-T-TTAAGTTAAA-ATAAAAATAAATAT
*
150695 ATATTTTTAAAAGTTAAGATAAGAACA-AAATAT
1 ATA-TTTT--AAGTTAAAATAA-AA-ATAAATAT
* * * *
150728 ATTTTTTAAGTTAAGATAAGACT-AATAT
1 ATATTTTAAGTTAAAATAAAAATAAATAT
* *
150756 ATATTTTTAGTTAAAATAAGAATAAA-AT
1 ATATTTTAAGTTAAAATAAAAATAAATAT
* *
150784 ATACTTAATAAGTTCAAATAAAAATAAAATAT
1 ATA-TT-TTAAGTTAAAATAAAAAT-AAATAT
*
150816 ATTTTTTAATGTTAA
1 ATATTTTAA-GTTAA
150831 GATCTGAATT
Statistics
Matches: 285, Mismatches: 57, Indels: 67
0.70 0.14 0.16
Matches are distributed among these distances:
28 39 0.14
29 31 0.11
30 126 0.44
31 52 0.18
32 32 0.11
33 5 0.02
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (29 bp):
ATATTTTAAGTTAAAATAAAAATAAATAT
Found at i:150796 original size:58 final size:58
Alignment explanation
Indices: 150542--150821 Score: 224
Period size: 58 Copynumber: 4.7 Consensus size: 58
150532 TAAAAAGAAT
* * * * *
150542 ATATATTT-TTAAGTTAAGGTAAGAATAAGATATATATTTTAAGTTAAAATAAAAAT-AA
1 ATATATTTAATAAGTTAAGATAAAAATAA-A-ATATATTTTTAGTTAAAATAAGAATAAA
* * * * * * ** *
150600 ATAATATTTAATAATTTAAGGTGAAAATAGAATATATTTAATAATTTAAGTTAATAATATAA
1 AT-ATATTTAATAAGTTAAGATAAAAATAAAATATATTT--TTAGTTAAAATAAGAATA-AA
* * * *
150662 TATATATGTAATAAGTAAAGATAAAAATAAAATATATTTTTAAAAGTTAAGATAAGAACAAA
1 -ATATATTTAATAAGTTAAGATAAAAATAAAATATATTTTT---AGTTAAAATAAGAATAAA
** * * *
150724 ATATATTTTTTAAGTTAAGATAAGACTAATATATATTTTTAGTTAAAATAAGAATAAA
1 ATATATTTAATAAGTTAAGATAAAAATAAAATATATTTTTAGTTAAAATAAGAATAAA
*
150782 ATATACTTAATAAGTTCAA-ATAAAAATAAAATATATTTTT
1 ATATATTTAATAAGTT-AAGATAAAAATAAAATATATTTTT
150822 TAATGTTAAG
Statistics
Matches: 176, Mismatches: 35, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
58 57 0.32
59 9 0.05
60 29 0.16
61 33 0.19
62 34 0.19
63 14 0.08
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (58 bp):
ATATATTTAATAAGTTAAGATAAAAATAAAATATATTTTTAGTTAAAATAAGAATAAA
Found at i:150815 original size:151 final size:150
Alignment explanation
Indices: 150532--150817 Score: 319
Period size: 151 Copynumber: 1.9 Consensus size: 150
150522 AAATTAAAAT
* * * *
150532 TAAAAAGAATATATATTTTTAAGTTAAGGTAAGAATAAGATATATATTTTAAGTTAAAATAAAAA
1 TAAAAAGAAAATATATTTTTAAGTTAAGATAAGAACAAAATATATATTTTAAGTTAAAATAAAAA
* ** * * * * * *
150597 TAAATAATATTTAATAATTTAAGGTGAAAATAGAATATATTTAATAATTTAAGTTAATAATATAA
66 TAAATAATATTT-ATAAGTTAAAATGAAAATAAAATATACTTAATAATTCAAGATAAAAATAAAA
150662 TATATATGTAATAAGTAAAGA
130 TATATATGTAATAAGTAAAGA
* * * *
150683 TAAAAATAAAATATATTTTTAAAAGTTAAGATAAGAACAAAATATATTTTTTAAGTTAAGATAAG
1 TAAAAAGAAAATATATTTTT--AAGTTAAGATAAGAACAAAATATATATTTTAAGTTAAAATAAA
* *
150748 ACT-AATATATATTT-TTAGTTAAAAT-AAGAATAAAATATACTTAATAAGTTCAA-ATAAAAAT
64 AATAAATA-ATATTTATAAGTTAAAATGAA-AATAAAATATACTTAATAA-TTCAAGATAAAAAT
150809 AAAATATAT
126 AAAATATAT
150818 TTTTTAATGT
Statistics
Matches: 111, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
150 2 0.02
151 56 0.50
152 8 0.07
153 45 0.41
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.36
Consensus pattern (150 bp):
TAAAAAGAAAATATATTTTTAAGTTAAGATAAGAACAAAATATATATTTTAAGTTAAAATAAAAA
TAAATAATATTTATAAGTTAAAATGAAAATAAAATATACTTAATAATTCAAGATAAAAATAAAAT
ATATATGTAATAAGTAAAGA
Found at i:151841 original size:24 final size:24
Alignment explanation
Indices: 151794--151841 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
151784 AGAGGTTGAG
* *
151794 AAGGAGAAAGTGATGACATTGGAA
1 AAGGAGAAACTGATGACATAGGAA
151818 AAGGAGAAGACTGATG-CATAGGAA
1 AAGGAGAA-ACTGATGACATAGGAA
151842 TATGGACATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.46, C:0.06, G:0.33, T:0.15
Consensus pattern (24 bp):
AAGGAGAAACTGATGACATAGGAA
Found at i:157911 original size:18 final size:18
Alignment explanation
Indices: 157888--157931 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
157878 TTGATATTGA
157888 ATATATTTATTAAT-AGTT
1 ATATATTTA-TAATAAGTT
*
157906 ATATATATATAATAAGTT
1 ATATATTTATAATAAGTT
157924 ATA-ATTTA
1 ATATATTTA
157932 ATAGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATATATTTATAATAAGTT
Found at i:158065 original size:2 final size:2
Alignment explanation
Indices: 158058--158083 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
158048 TTATAATTTA
158058 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
158084 TTATTTATTC
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:160932 original size:31 final size:30
Alignment explanation
Indices: 160861--160932 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
160851 CTAAAGTTTA
*
160861 TTTTTTAATTTAATTACTTAACTTTCAAAT
1 TTTTTTAATTTAATCACTTAACTTTCAAAT
* ** *
160891 TACTCCTAATTTAATCACTCTAACTTTCAAGT
1 T-TTTTTAATTTAATCACT-TAACTTTCAAAT
160923 TTTTTTAATT
1 TTTTTTAATT
160933 ATATTAATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
30 1 0.03
31 19 0.59
32 12 0.38
ACGTcount: A:0.31, C:0.15, G:0.01, T:0.53
Consensus pattern (30 bp):
TTTTTTAATTTAATCACTTAACTTTCAAAT
Found at i:162211 original size:31 final size:31
Alignment explanation
Indices: 162176--162237 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
162166 ATGTTCCAAA
162176 CTCATATTTTTATTTTAAAAAATTAAAGGTC
1 CTCATATTTTTATTTTAAAAAATTAAAGGTC
162207 CTCATATTTTTATTTTAAAAAATTAAAGGTC
1 CTCATATTTTTATTTTAAAAAATTAAAGGTC
162238 GTCTAAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (31 bp):
CTCATATTTTTATTTTAAAAAATTAAAGGTC
Found at i:164265 original size:40 final size:40
Alignment explanation
Indices: 164194--164269 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
164184 ATGAACAAAA
* **
164194 CACATCATACGAGTTTAAAGCACTCGCCTTACAATATTTT
1 CACATCATACGAGTTTAAACCACTCAACTTACAATATTTT
** *
164234 CACATCATGTGAGTTTAAACCATTCAACTTACAATA
1 CACATCATACGAGTTTAAACCACTCAACTTACAATA
164270 ATTTAACAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.32
Consensus pattern (40 bp):
CACATCATACGAGTTTAAACCACTCAACTTACAATATTTT
Found at i:164943 original size:12 final size:13
Alignment explanation
Indices: 164928--164956 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
164918 TCTCTCAAAA
164928 AAGAT-ATTTTTT
1 AAGATAATTTTTT
164940 AAGATAATTTTTT
1 AAGATAATTTTTT
164953 AAGA
1 AAGA
164957 GGTTGATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (13 bp):
AAGATAATTTTTT
Found at i:165006 original size:21 final size:21
Alignment explanation
Indices: 164980--165022 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
164970 AATACGTGTA
* *
164980 TAAATTATATATTTTTTATTT
1 TAAATTATAAATATTTTATTT
*
165001 TAAATTTTAAATATTTTATTT
1 TAAATTATAAATATTTTATTT
165022 T
1 T
165023 TTTAAAATAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TAAATTATAAATATTTTATTT
Found at i:171693 original size:24 final size:24
Alignment explanation
Indices: 171661--171717 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
171651 TCTTCTCCTC
*
171661 AAATCCACCTTCAAGATCTTCACA
1 AAATTCACCTTCAAGATCTTCACA
171685 AAATTCACCTTCAAGATCTTCACA
1 AAATTCACCTTCAAGATCTTCACA
171709 AAATTCACC
1 AAATTCACC
171718 ACAATCCCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.39, C:0.32, G:0.04, T:0.26
Consensus pattern (24 bp):
AAATTCACCTTCAAGATCTTCACA
Found at i:173773 original size:16 final size:17
Alignment explanation
Indices: 173742--173775 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
173732 TGTATTTAAT
173742 TTATTTAAGCATTTTAC
1 TTATTTAAGCATTTTAC
*
173759 TTATTTAA-TATTTTAC
1 TTATTTAAGCATTTTAC
173775 T
1 T
173776 AATATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (17 bp):
TTATTTAAGCATTTTAC
Found at i:176025 original size:26 final size:24
Alignment explanation
Indices: 175954--176025 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
175944 TTATATTTGT
175954 ATTTACTTTATTTTGTTAAATTATA
1 ATTTACTTTATTTTGTTAAATT-TA
*
175979 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
176001 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
176026 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:179459 original size:14 final size:12
Alignment explanation
Indices: 179424--179451 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
179414 AATAAGTATA
179424 ATAAAAAAATTT
1 ATAAAAAAATTT
179436 ATAAAAAAATTT
1 ATAAAAAAATTT
179448 ATAA
1 ATAA
179452 CGAAAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAAAAATTT
Found at i:183869 original size:10 final size:10
Alignment explanation
Indices: 183854--183879 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
183844 AATATAGATT
183854 GTTCATGTTC
1 GTTCATGTTC
183864 GTTCATGTTC
1 GTTCATGTTC
183874 GTTCAT
1 GTTCAT
183880 TTAAATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.50
Consensus pattern (10 bp):
GTTCATGTTC
Found at i:184125 original size:14 final size:14
Alignment explanation
Indices: 184106--184156 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
184096 CCCTTTGTTC
184106 GAACATAAATGAAT
1 GAACATAAATGAAT
**
184120 GAACATAAATGAGC
1 GAACATAAATGAAT
184134 GAACATAAATGAAT
1 GAACATAAATGAAT
184148 GAACATAAA
1 GAACATAAA
184157 CGAACATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.57, C:0.10, G:0.16, T:0.18
Consensus pattern (14 bp):
GAACATAAATGAAT
Found at i:190249 original size:23 final size:23
Alignment explanation
Indices: 190229--190273 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
190219 TGAGATTCTC
190229 ATGGGAATGAAATTCACATTCCT
1 ATGGGAATGAAATTCACATTCCT
*
190252 ATGGGAATGGAATTCACATTCC
1 ATGGGAATGAAATTCACATTCC
190274 CCCGTTTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (23 bp):
ATGGGAATGAAATTCACATTCCT
Found at i:195209 original size:22 final size:22
Alignment explanation
Indices: 195160--195219 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
195150 AGTATTCACG
*
195160 ATGGTACCGATAC-T-CCTCCT
1 ATGGTATCGATACTTCCCTCCT
195180 -TGGATATCGATACTTCCCTCCT
1 ATGG-TATCGATACTTCCCTCCT
*
195202 ATGGTATCAATACTTCCC
1 ATGGTATCGATACTTCCC
195220 CGAGTATCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.09
20 8 0.24
21 1 0.03
22 19 0.56
23 3 0.09
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.33
Consensus pattern (22 bp):
ATGGTATCGATACTTCCCTCCT
Found at i:197587 original size:14 final size:13
Alignment explanation
Indices: 197565--197594 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
197555 GTATAATTTA
197565 AAATTTTAAAAAT
1 AAATTTTAAAAAT
197578 AAATTATTAAAAAT
1 AAATT-TTAAAAAT
197592 AAA
1 AAA
197595 ATACTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:202063 original size:28 final size:29
Alignment explanation
Indices: 202030--202086 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
202020 TTTTATATTA
* *
202030 TAGGGG-CAAACTTGAATTTATAAAATTT
1 TAGGGGACAAACTTAAACTTATAAAATTT
*
202058 TAGGGGACAAATTTAAACTTATAAAATTT
1 TAGGGGACAAACTTAAACTTATAAAATTT
202087 CATTGGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (29 bp):
TAGGGGACAAACTTAAACTTATAAAATTT
Found at i:203876 original size:22 final size:22
Alignment explanation
Indices: 203851--203901 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
203841 CACCACAGCT
*
203851 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
203873 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
203895 CGTAGAA
1 CGTAGAA
203902 TTTTGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:203902 original size:22 final size:22
Alignment explanation
Indices: 203859--203903 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
203849 CTCGTATAAA
203859 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
203881 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
203903 T
1 T
203904 TTGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:204237 original size:29 final size:29
Alignment explanation
Indices: 204195--204266 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
204185 TTTTCTGCAT
**
204195 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
204224 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
204253 ATTCATGTCATGTA
1 ATTCATGTCATGTA
204267 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:204687 original size:68 final size:67
Alignment explanation
Indices: 204570--204720 Score: 207
Period size: 68 Copynumber: 2.3 Consensus size: 67
204560 TTTTTCTCAT
* * *
204570 GGGGGAATCGGTT-CCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGAT
1 GGGGGTATCGGTTCCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGAT
204634 GA
66 GA
* *
204636 GGGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCG
1 GGGGGTATCGGTTCCCCCCCCT-GGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACG
*
204700 TTGA
64 ATGA
*
204704 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
204721 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 12 0.16
67 8 0.11
68 54 0.72
69 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.26
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGAT
GA
Found at i:204730 original size:21 final size:21
Alignment explanation
Indices: 204700--204742 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
204690 ATCATATTCG
* *
204700 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
204721 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
204742 T
1 T
204743 AACCCAGAAA
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:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:210784 original size:22 final size:22
Alignment explanation
Indices: 210759--210809 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
210749 CACCACAGCT
*
210759 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
210781 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
210803 CGTAGAA
1 CGTAGAA
210810 TTTTGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:210810 original size:22 final size:22
Alignment explanation
Indices: 210767--210811 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
210757 CTCGTATAAA
210767 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
210789 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
210811 T
1 T
210812 TTGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:211145 original size:29 final size:29
Alignment explanation
Indices: 211103--211174 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
211093 TTTTCTGCAT
**
211103 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
211132 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
211161 ATTCATGTCATGTA
1 ATTCATGTCATGTA
211175 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:211615 original size:67 final size:65
Alignment explanation
Indices: 211479--211626 Score: 199
Period size: 67 Copynumber: 2.2 Consensus size: 65
211469 TTTTCTCATG
* * * *
211479 GGGGAATCGGTTCCCCCCCTGGGGTATCGATTCCCTTAAGCAATCTGGAATTCATATACGATGAG
1 GGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCTTAAGCAATCTGGAAATCATATACGATGAA
* * *
211544 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCGTT
1 GGGGTATCGGTTCCCCCCCT-GGGGTACCGATT-CCCT-TAAGCAATCTGGAAATCATATACGAT
211608 GAA
63 GAA
211611 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
211627 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 19 0.26
66 11 0.15
67 42 0.58
68 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (65 bp):
GGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCTTAAGCAATCTGGAAATCATATACGATGAA
Found at i:211636 original size:21 final size:21
Alignment explanation
Indices: 211606--211648 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
211596 ATCATATTCG
* *
211606 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
211627 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
211648 T
1 T
211649 AACCCAGAAA
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:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:211637 original size:67 final size:66
Alignment explanation
Indices: 211479--211648 Score: 186
Period size: 67 Copynumber: 2.6 Consensus size: 66
211469 TTTTCTCATG
* * *
211479 GGGGAATCGGTTCCCCCCCT-GGGGTATCGATT-CCCTTAAGCAATCTGGAATTCATATACGATG
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATG
*
211542 AG
65 AA
* * *
211544 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGAT
211608 GAA
64 GAA
* *
211611 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
211649 AACCCAGAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
65 25 0.27
66 11 0.12
67 54 0.59
68 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATGA
A
Found at i:220560 original size:16 final size:16
Alignment explanation
Indices: 220539--220571 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
220529 TTCCTTGAGC
220539 TTCCTTGAAGCTAGCT
1 TTCCTTGAAGCTAGCT
220555 TTCCTTGAAGCTAGCT
1 TTCCTTGAAGCTAGCT
220571 T
1 T
220572 CACTCCAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (16 bp):
TTCCTTGAAGCTAGCT
Found at i:225634 original size:23 final size:22
Alignment explanation
Indices: 225584--225630 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
225574 GTACCATGTC
225584 TTTATTTAATTAAAATCTAGTT
1 TTTATTTAATTAAAATCTAGTT
225606 TTTATTTAA-TACAAATCTAGTT
1 TTTATTTAATTA-AAATCTAGTT
225628 TTT
1 TTT
225631 TATTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTATTTAATTAAAATCTAGTT
Found at i:231704 original size:3 final size:3
Alignment explanation
Indices: 231696--231723 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
231686 GAATTGGGTT
231696 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
231724 CTCTAAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:232143 original size:60 final size:60
Alignment explanation
Indices: 232031--232143 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
232021 TAGGGATCAA
* *
232031 TTTAGAATGAGATTCATAGTTTATGGATGAAATTGAAATATTCAAAAGTTTAAGAACTAC
1 TTTAGAATGAGAATCATAGTTTATGGATGAAATTGAAATATTCAAAACTTTAAGAACTAC
*
232091 TTTAGAATGAGAAAT-ATAGTTTGA-GTATGAAATTAGAAAGT-TT-AAAACTTTAA
1 TTTAGAATGAG-AATCATAGTTT-ATGGATGAAATT-GAAA-TATTCAAAACTTTAA
232144 TGACTAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
60 36 0.78
61 9 0.20
62 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (60 bp):
TTTAGAATGAGAATCATAGTTTATGGATGAAATTGAAATATTCAAAACTTTAAGAACTAC
Found at i:250287 original size:12 final size:12
Alignment explanation
Indices: 250270--250328 Score: 68
Period size: 12 Copynumber: 4.9 Consensus size: 12
250260 CAAAACTCAA
250270 AACAGAATTCAG
1 AACAGAATTCAG
250282 AACAG-ATATCAG
1 AACAGAAT-TCAG
*
250294 AACAGAATCCA-
1 AACAGAATTCAG
*
250305 AATCAGAAATCAG
1 AA-CAGAATTCAG
250318 AACAGAATTCA
1 AACAGAATTCA
250329 TGTCATGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 4 0.10
12 31 0.79
13 4 0.10
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.15
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:250364 original size:24 final size:24
Alignment explanation
Indices: 250270--250364 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 24
250260 CAAAACTCAA
* *
250270 AACAGAATTC-AGAACAGATATCAG
1 AACAGAATTCAAG-TCAGAAATCAG
* *
250294 AACAGAATCCAAATCAGAAATCAG
1 AACAGAATTCAAGTCAGAAATCAG
* *
250318 AACAGAATTCATGTCATG-TATCAG
1 AACAGAATTCAAGTCA-GAAATCAG
* *
250342 AACATAATTCAAGTCGGAAATCA
1 AACAGAATTCAAGTCAGAAATCA
250365 AATAAAATAT
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
23 1 0.02
24 53 0.95
25 2 0.04
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (24 bp):
AACAGAATTCAAGTCAGAAATCAG
Found at i:267395 original size:16 final size:16
Alignment explanation
Indices: 267371--267401 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
267361 GGGAATTTAT
267371 ATTTGATTTCGTTGTA
1 ATTTGATTTCGTTGTA
*
267387 ATTTTATTTCGTTGT
1 ATTTGATTTCGTTGT
267402 GTTTGGAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.16, T:0.61
Consensus pattern (16 bp):
ATTTGATTTCGTTGTA
Found at i:270904 original size:23 final size:23
Alignment explanation
Indices: 270845--270894 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
270835 AAAAAATAGA
270845 AAAC-TACCA-AAAGACAGAGAT
1 AAACATACCACAAAGACAGAGAT
* *
270866 AAACATACCACAAAGATAGAGTT
1 AAACATACCACAAAGACAGAGAT
270889 AAACAT
1 AAACAT
270895 GTCATAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.16
22 5 0.20
23 16 0.64
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.14
Consensus pattern (23 bp):
AAACATACCACAAAGACAGAGAT
Found at i:273775 original size:20 final size:19
Alignment explanation
Indices: 273739--273776 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
273729 ATTTCGGTTG
*
273739 GGGCAAGCCAGTGTATGGT
1 GGGCAAGCCAATGTATGGT
273758 GGGCAAGCCAATGTTATGG
1 GGGCAAGCCAATG-TATGG
273777 ATGGAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.24, C:0.16, G:0.39, T:0.21
Consensus pattern (19 bp):
GGGCAAGCCAATGTATGGT
Found at i:274367 original size:20 final size:20
Alignment explanation
Indices: 274342--274391 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
274332 GACCAACAAA
274342 TTCGCAACGCAAACTCCAAT
1 TTCGCAACGCAAACTCCAAT
* ***
274362 TTCGCAACCCAGTTTCCAAT
1 TTCGCAACGCAAACTCCAAT
274382 TTCGCAACGC
1 TTCGCAACGC
274392 GAATCTATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.36, G:0.12, T:0.24
Consensus pattern (20 bp):
TTCGCAACGCAAACTCCAAT
Found at i:274406 original size:20 final size:20
Alignment explanation
Indices: 274383--274431 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
274373 GTTTCCAATT
*
274383 TCGCAACGCGAATCTATAAA
1 TCGCAACACGAATCTATAAA
* *
274403 TCGCAACACGAATTTGTAAA
1 TCGCAACACGAATCTATAAA
274423 TCGCAACAC
1 TCGCAACAC
274432 AGAAGTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (20 bp):
TCGCAACACGAATCTATAAA
Found at i:274446 original size:20 final size:19
Alignment explanation
Indices: 274423--274561 Score: 120
Period size: 20 Copynumber: 7.0 Consensus size: 19
274413 AATTTGTAAA
274423 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
274443 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
274463 TCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
****
274483 TCGCGTTGCGAATTTGT-AAA-
1 TCGCAACACGAA---GTCAAAT
*
274503 TCGCAACACAAAGTCAAAT
1 TCGCAACACGAAGTCAAAT
274522 TCGCAACACGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
274542 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACG-AAGTCAAAT
274562 GTTTTTACGC
Statistics
Matches: 95, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
17 2 0.02
18 3 0.03
19 14 0.15
20 69 0.73
21 5 0.05
22 2 0.02
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:274447 original size:40 final size:39
Alignment explanation
Indices: 274403--274532 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 39
274393 AATCTATAAA
274403 TCGCAACACGAATTTGTAAATCGCAACACAGAAGTCAAAT
1 TCGCAACACGAATTTGTAAATCGCAACACA-AAGTCAAAT
* *
274443 TCGCAACGCG-A-TAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACGAATTTGT-AAA-TCGCAACAC-AAAGTCAAAT
****
274483 TCGCGTTGCGAATTTGTAAATCGCAACACAAAGTCAAAT
1 TCGCAACACGAATTTGTAAATCGCAACACAAAGTCAAAT
274522 TCGCAACACGA
1 TCGCAACACGA
274533 TAGTCAAATT
Statistics
Matches: 75, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
38 3 0.04
39 21 0.28
40 43 0.57
41 5 0.07
42 3 0.04
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (39 bp):
TCGCAACACGAATTTGTAAATCGCAACACAAAGTCAAAT
Found at i:274543 original size:79 final size:80
Alignment explanation
Indices: 274411--274561 Score: 268
Period size: 79 Copynumber: 1.9 Consensus size: 80
274401 AATCGCAACA
*
274411 CGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAA
1 CGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACGATAGTCAAATTCGCAACACAAAA
274476 GTCAAATTCGCGTTG
66 GTCAAATTCGCGTTG
* *
274491 CGAATTTGTAAATCGCAACACA-AAGTCAAATTCGCAACACGATAGTCAAATTCGCAACGCGAAA
1 CGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACGATAGTCAAATTCGCAACACAAAA
274555 GTCAAAT
66 GTCAAAT
274562 GTTTTTACGC
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
79 46 0.68
80 22 0.32
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (80 bp):
CGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACGATAGTCAAATTCGCAACACAAAA
GTCAAATTCGCGTTG
Found at i:278001 original size:20 final size:20
Alignment explanation
Indices: 277976--278013 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
277966 AAATAATGTA
*
277976 CAACGCGATAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
277996 CAACGCGAAAGTCAAATT
1 CAACGCGAAAGTCAAATT
278014 TGGTTTGCGA
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:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Done.