Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001920.1 Hibiscus syriacus cultivar Beakdansim tig00003883_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: 51529
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Found at i:665 original size:19 final size:19
Alignment explanation
Indices: 641--677 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
631 CATCTTTCTA
641 AAAATTATAAAAAAAAATG
1 AAAATTATAAAAAAAAATG
660 AAAATTATAAAAAAAAAT
1 AAAATTATAAAAAAAAAT
678 ATTTATAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (19 bp):
AAAATTATAAAAAAAAATG
Found at i:1596 original size:17 final size:17
Alignment explanation
Indices: 1554--1601 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
1544 TTGAATAAAA
*
1554 TAATATATTTTATATTT
1 TAATATAATTTATATTT
* *
1571 GAATA-AATTTATTTTT
1 TAATATAATTTATATTT
*
1587 TAATATAATTAATAT
1 TAATATAATTTATAT
1602 ATATTGGGCA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TAATATAATTTATATTT
Found at i:4248 original size:7 final size:7
Alignment explanation
Indices: 4236--4272 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
4226 CAAACCGTTA
4236 ACCATTG
1 ACCATTG
*
4243 ATCATTG
1 ACCATTG
*
4250 ACCGTTG
1 ACCATTG
4257 ACCATTG
1 ACCATTG
4264 ACCATTG
1 ACCATTG
4271 AC
1 AC
4273 TGGCGTTGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (7 bp):
ACCATTG
Found at i:4255 original size:21 final size:21
Alignment explanation
Indices: 4229--4272 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4219 GAACTGGCAA
*
4229 ACCGTTAACCATTGATCATTG
1 ACCGTTAACCATTGACCATTG
*
4250 ACCGTTGACCATTGACCATTG
1 ACCGTTAACCATTGACCATTG
4271 AC
1 AC
4273 TGGCGTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (21 bp):
ACCGTTAACCATTGACCATTG
Found at i:5131 original size:27 final size:26
Alignment explanation
Indices: 5090--5273 Score: 107
Period size: 27 Copynumber: 7.6 Consensus size: 26
5080 TCACACCTTA
*
5090 ATGCATCCCTTCATGCATTTTTAGTT
1 ATGCATCCTTTCATGCATTTTTAGTT
*
5116 ATGACATCCTTTCATGC---CTTA---
1 ATG-CATCCTTTCATGCATTTTTAGTT
* *
5137 ATGCATTCGTTCATGCATTTTTAGTT
1 ATGCATCCTTTCATGCATTTTTAGTT
* *
5163 ATGTCATCCTTTCTTGC---CTTA---
1 ATG-CATCCTTTCATGCATTTTTAGTT
5184 ATGCATCCTTTCATGCATTTTTAGTT
1 ATGCATCCTTTCATGCATTTTTAGTT
* * *
5210 ATGAAATCATTTCATGC---CTTA---
1 ATG-CATCCTTTCATGCATTTTTAGTT
*
5231 ATGCATCCTTTCATGCATTTTTTGTT
1 ATGCATCCTTTCATGCATTTTTAGTT
*
5257 ATGGCATCATTTCATGC
1 AT-GCATCCTTTCATGC
5274 CTCAATGCAT
Statistics
Matches: 117, Mismatches: 19, Indels: 43
0.65 0.11 0.24
Matches are distributed among these distances:
20 34 0.29
21 9 0.08
23 8 0.07
24 9 0.08
26 11 0.09
27 46 0.39
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.46
Consensus pattern (26 bp):
ATGCATCCTTTCATGCATTTTTAGTT
Found at i:5136 original size:47 final size:47
Alignment explanation
Indices: 5067--5327 Score: 360
Period size: 47 Copynumber: 5.6 Consensus size: 47
5057 TTAATTTCAT
* ** *
5067 TTATGGCATCCTTTCACACCTTAATGCATCCCTTCATGCATTTTTAG
1 TTATGGCATCATTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* * *
5114 TTATGACATCCTTTCATGCCTTAATGCATTCGTTCATGCATTTTTAG
1 TTATGGCATCATTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* * * *
5161 TTATGTCATCCTTTCTTGCCTTAATGCATCCTTTCATGCATTTTTAG
1 TTATGGCATCATTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
** * *
5208 TTATGAAATCATTTCATGCCTTAATGCATCCTTTCATGCATTTTTTG
1 TTATGGCATCATTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* * *
5255 TTATGGCATCATTTCATGCCTCAATGCATCTGTTCATGGATTTTTAG
1 TTATGGCATCATTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
5302 TTATGGCATCATTTCATGCCTTAATG
1 TTATGGCATCATTTCATGCCTTAATG
5328 TATTTTTAGT
Statistics
Matches: 192, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 192 1.00
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (47 bp):
TTATGGCATCATTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
Found at i:5411 original size:45 final size:45
Alignment explanation
Indices: 5347--5476 Score: 242
Period size: 45 Copynumber: 2.9 Consensus size: 45
5337 TTATGGTATT
* *
5347 CTTTCATGCTTATAATGCACCCATATACATTATTATTTTGGCATC
1 CTTTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATC
5392 CTTTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATC
1 CTTTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATC
5437 CTTTCATGCCTATAATGCACCCATATGCATTATTATTTTG
1 CTTTCATGCCTATAATGCACCCATATGCATTATTATTTTG
5477 TTCATTCGTT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (45 bp):
CTTTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATC
Found at i:7309 original size:21 final size:22
Alignment explanation
Indices: 7272--7312 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
7262 ATATAAAATT
*
7272 TGTCCCTAAGTACCTATGAATA
1 TGTCCCGAAGTACCTATGAATA
7294 TGTCCCGAAG-ACCTATGAA
1 TGTCCCGAAGTACCTATGAA
7313 ACCCTCAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (22 bp):
TGTCCCGAAGTACCTATGAATA
Found at i:12302 original size:23 final size:23
Alignment explanation
Indices: 12275--12326 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
12265 TTGAGTGGCA
*
12275 TATGAAATTTGTCCCCAAGGACC
1 TATGAAATATGTCCCCAAGGACC
*
12298 TATG-AATATGTCCCGAAGGACC
1 TATGAAATATGTCCCCAAGGACC
12320 TATGAAA
1 TATGAAA
12327 CTCTTGACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (23 bp):
TATGAAATATGTCCCCAAGGACC
Found at i:13031 original size:36 final size:36
Alignment explanation
Indices: 12989--13058 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
12979 TAGTTCAAGA
*
12989 TGGTATCGATAC-ATTCCTTAAAGTATCGATACCCCT
1 TGGTATCAATACTATT-CTTAAAGTATCGATACCCCT
* *
13025 TGGTATCAATACTATTCTTCAGGTATCGATACCC
1 TGGTATCAATACTATTCTTAAAGTATCGATACCC
13059 TTTGAAGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 27 0.90
37 3 0.10
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.34
Consensus pattern (36 bp):
TGGTATCAATACTATTCTTAAAGTATCGATACCCCT
Found at i:17633 original size:27 final size:27
Alignment explanation
Indices: 17594--17656 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
17584 TGCCTTAATG
*
17594 CATCCCTTCATGCATTTTTAGTTATGC
1 CATCCTTTCATGCATTTTTAGTTATGC
* *
17621 CATCCTTTTATGCATTTTTAGTTATGT
1 CATCCTTTCATGCATTTTTAGTTATGC
17648 CATCCTTTC
1 CATCCTTTC
17657 TTGCCTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.17, C:0.24, G:0.10, T:0.49
Consensus pattern (27 bp):
CATCCTTTCATGCATTTTTAGTTATGC
Found at i:17673 original size:47 final size:47
Alignment explanation
Indices: 17621--17964 Score: 510
Period size: 47 Copynumber: 7.3 Consensus size: 47
17611 TTAGTTATGC
* * *
17621 CATCCTTTTATGCATTTTTAGTTATGTCATCCTTTCTTGCCTTAATG
1 CATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATG
* * * * * *
17668 CATCCTATCATGCATTCTTAGTTATGACATTCTTTAATGCCTTAATA
1 CATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATG
* *
17715 CATCCGTTCATGCA-TTTTAGTTATGGAATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATG
* *
17761 CATCCTTTCATGCAGTTTTAGTTATGGCATCCTTTAATGCCTTAATG
1 CATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATG
* * * *
17808 CATTCGTTCATGCATTTTTAGTTGTGGCATCCTTTCTTGCCTTAATG
1 CATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATG
*
17855 CATCCTTTCATGCATTTTTAGTTATGGCATCCTTTTATGCCTTAATG
1 CATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATG
*
17902 CATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATG
17949 CATCCTTTCATGCATT
1 CATCCTTTCATGCATT
17965 AATGCATCCT
Statistics
Matches: 263, Mismatches: 33, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
46 39 0.15
47 224 0.85
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATG
Found at i:17954 original size:114 final size:114
Alignment explanation
Indices: 17834--18078 Score: 418
Period size: 114 Copynumber: 2.1 Consensus size: 114
17824 TTTAGTTGTG
* * *
17834 GCATCCTTTCTTGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTTATGCCTTA
1 GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
* * * *
17899 ATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAAT
66 ATGCATCCATTCATGCATTTTTAGTTACGACATCCTTTAATGCCTTAAT
17948 GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
1 GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
*
18013 ATGCATCTATTCATGCATTTTTAGTTACGACATCCTTTAATGCCTTAAT
66 ATGCATCCATTCATGCATTTTTAGTTACGACATCCTTTAATGCCTTAAT
18062 GCATCCTTTCATGCATT
1 GCATCCTTTCATGCATT
18079 TTTAGTTATG
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 123 1.00
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.44
Consensus pattern (114 bp):
GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
ATGCATCCATTCATGCATTTTTAGTTACGACATCCTTTAATGCCTTAAT
Found at i:17955 original size:161 final size:162
Alignment explanation
Indices: 17787--18109 Score: 533
Period size: 161 Copynumber: 2.0 Consensus size: 162
17777 TTTAGTTATG
* * * *
17787 GCATCCTTTAATGCCTTAATGCATTCGTTCATGCATTTTTAGTTGTGGCATCCTTTCTTGCCTTA
1 GCATCCTTTAATGCATTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
* * *
17852 ATGCATCCT-TTCATGCATTTTTAGTTATGGCATCCTTTTATGCCTTAATGCATCCGTTCATGCA
66 ATGCAT-CTATTCATGCATTTTTAGTTACGACATCCTTTAATGCCTTAATGCATCCGTTCATGCA
17916 TTTTTAGTTATGGCATCCTTTCATGCCT-TAAT
130 TTTTTAGTTATGGCATCCTTTCATGCCTATAAT
* *
17948 GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
1 GCATCCTTTAATGCATTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
*
18013 ATGCATCTATTCATGCATTTTTAGTTACGACATCCTTTAATGCCTTAATGCATCCTTTCATGCAT
66 ATGCATCTATTCATGCATTTTTAGTTACGACATCCTTTAATGCCTTAATGCATCCGTTCATGCAT
18078 TTTTAGTTATGGCATCCTTTCATGCCTATAAT
131 TTTTAGTTATGGCATCCTTTCATGCCTATAAT
18110 ACACCAATAT
Statistics
Matches: 150, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
160 2 0.01
161 144 0.96
162 4 0.03
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (162 bp):
GCATCCTTTAATGCATTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
ATGCATCTATTCATGCATTTTTAGTTACGACATCCTTTAATGCCTTAATGCATCCGTTCATGCAT
TTTTAGTTATGGCATCCTTTCATGCCTATAAT
Found at i:17970 original size:67 final size:67
Alignment explanation
Indices: 17881--18031 Score: 259
Period size: 67 Copynumber: 2.3 Consensus size: 67
17871 TTTAGTTATG
* *
17881 GCATCCTTTTATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
1 GCATCCTTTCATGCATTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
17946 AT
66 AT
*
17948 GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
1 GCATCCTTTCATGCATTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
18013 AT
66 AT
18015 GCAT-CTATTCATGCATT
1 GCATCCT-TTCATGCATT
18032 TTTAGTTACG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
66 2 0.03
67 78 0.98
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.43
Consensus pattern (67 bp):
GCATCCTTTCATGCATTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
AT
Found at i:17999 original size:47 final size:47
Alignment explanation
Indices: 17948--18202 Score: 272
Period size: 47 Copynumber: 5.5 Consensus size: 47
17938 ATGCCTTAAT
*
17948 GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
*
17995 GCATCCTTTCATGCCTTAATGCAT-CTATTCATGCATTTTTAGTTACG
1 GCATCCTTTCATGCCTTAATGCATCCT-TTCATGCATTTTTAGTTATG
* *
18042 ACATCCTTTAATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
* ** * * *
18089 GCATCCTTTCATGCCTATAATACA-CCAAT-ATGCATTATTA-TTTTA
1 GCATCCTTTCATGCCT-TAATGCATCCTTTCATGCATTTTTAGTTATG
* ** ** *
18134 GCATCCTTTCATACCTATAATGCA-CCCAT-ATGCATTAATA-TTTTG
1 GCATCCTTTCATGCCT-TAATGCATCCTTTCATGCATTTTTAGTTATG
*
18179 GCATTCTTTCATGCCTATAATGCA
1 GCATCCTTTCATGCCT-TAATGCA
18203 CCCATATGCA
Statistics
Matches: 185, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
45 65 0.35
46 12 0.06
47 100 0.54
48 8 0.04
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.42
Consensus pattern (47 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
Found at i:18008 original size:141 final size:136
Alignment explanation
Indices: 17621--17981 Score: 424
Period size: 140 Copynumber: 2.6 Consensus size: 136
17611 TTAGTTATGC
* * * * **
17621 CATCCTTTTATGCATTTTTAGTTATGTCATCCTTTCTTGCCTTAATGCATCC-TATCATGCATTC
1 CATCCGTTCATGCAGTTTTAGTTATGGCATCCTTTAATGCCTTAATGCATCCGT-TCATGCA-T-
* * * * *
17685 TTAGTTATGACATTCTTTAATGCCTTAATACATCCGTTCATGCATTTTAGTTATGGAATCCTTTC
63 TTA--TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGAATCCTTTC
17750 ATGCCTTAATG
126 ATGCCTTAATG
* *
17761 CATCCTTTCATGCAGTTTTAGTTATGGCATCCTTTAATGCCTTAATGCATTCGTTCATGCATTTT
1 CATCCGTTCATGCAGTTTTAGTTATGGCATCCTTTAATGCCTTAATGCATCCGTTCATGCA--TT
* * * *
17826 TAGTTGTGGCATCCTTTCTTGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTT
64 TA--TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA-TTTTAGTTATGGAATCCTTTC
17891 ATGCCTTAATG
126 ATGCCTTAATG
* * *
17902 CATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA-TTA
1 CATCCGTTCATGCAGTTTTAGTTATGGCATCCTTTAATGCCTTAATGCATCCGTTCATGCATTTA
17966 -AT-GCATCCTTTCATGC
66 TATGGCATCCTTTCATGC
17982 ATTTTTAGTT
Statistics
Matches: 196, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
134 13 0.07
135 1 0.01
138 3 0.02
140 90 0.46
141 89 0.45
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.44
Consensus pattern (136 bp):
CATCCGTTCATGCAGTTTTAGTTATGGCATCCTTTAATGCCTTAATGCATCCGTTCATGCATTTA
TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGAATCCTTTCATGCC
TTAATG
Found at i:18144 original size:45 final size:44
Alignment explanation
Indices: 17947--18340 Score: 322
Period size: 45 Copynumber: 9.0 Consensus size: 44
17937 CATGCCTTAA
* ** *
17947 TGCATCCTTTCATGCAT-TAATGCATCCTTTCATGCATTTTTAGTTAT
1 TGCATCCTTTCATGCCTATAATGCA-CCCAT-ATGCATTATTA-TT-T
* * * * *
17994 GGCATCCTTTCATGCCT-TAATGCATCTATTCATGCATTTTTAGTTA
1 TGCATCCTTTCATGCCTATAATGCACCCA-T-ATGCATTATTA-TTT
* * ** *
18040 CGACATCCTTTAATGCCT-TAATGCATCCTTTCATGCATTTTTAGTTAT
1 TG-CATCCTTTCATGCCTATAATGCA-CCCAT-ATGCATTATTA-TT-T
* * *
18088 GGCATCCTTTCATGCCTATAATACACCAATATGCATTATTATTT
1 TGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
* *
18132 TAGCATCCTTTCATACCTATAATGCACCCATATGCATTAATATTT
1 T-GCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
*
18177 TGGCATTCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
1 T-GCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
*
18222 TG-------GCAT-CCTATAATGCACCCATATGCATTATTATTT
1 TGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
*
18258 TG-------GCAT-CCTATAATGCACCCATATGCATTATTATTT
1 TGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
18294 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
1 T-GCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
18339 TG
1 TG
18341 TTCATTCGTT
Statistics
Matches: 305, Mismatches: 27, Indels: 33
0.84 0.07 0.09
Matches are distributed among these distances:
36 67 0.22
37 4 0.01
44 6 0.02
45 114 0.37
46 13 0.04
47 92 0.30
48 9 0.03
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (44 bp):
TGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
Found at i:18232 original size:36 final size:36
Alignment explanation
Indices: 18192--18302 Score: 222
Period size: 36 Copynumber: 3.1 Consensus size: 36
18182 TTCTTTCATG
18192 CCTATAATGCACCCATATGCATTATTATTTTGGCAT
1 CCTATAATGCACCCATATGCATTATTATTTTGGCAT
18228 CCTATAATGCACCCATATGCATTATTATTTTGGCAT
1 CCTATAATGCACCCATATGCATTATTATTTTGGCAT
18264 CCTATAATGCACCCATATGCATTATTATTTTGGCAT
1 CCTATAATGCACCCATATGCATTATTATTTTGGCAT
18300 CCT
1 CCT
18303 TTCATGCCTA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 75 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (36 bp):
CCTATAATGCACCCATATGCATTATTATTTTGGCAT
Found at i:18887 original size:20 final size:21
Alignment explanation
Indices: 18841--18893 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
18831 TCTGTTAATA
18841 ATGGTATCGATA-CCATCCTC
1 ATGGTATCGATACCCATCCTC
* *
18861 ATAGTATCGATACCCCT-CTC
1 ATGGTATCGATACCCATCCTC
*
18881 TTGGTATCGATAC
1 ATGGTATCGATAC
18894 TGCTTGCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (21 bp):
ATGGTATCGATACCCATCCTC
Found at i:19830 original size:14 final size:13
Alignment explanation
Indices: 19810--19858 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
19800 TTAAATTAAA
19810 TAAATAAATTATT
1 TAAATAAATTATT
*
19823 TAAAATAAATTA-A
1 T-AAATAAATTATT
*
19836 TAAGTAAATTATT
1 TAAATAAATTATT
19849 TGAAATAAAT
1 T-AAATAAAT
19859 AAATAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 9 0.31
13 3 0.10
14 17 0.59
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (13 bp):
TAAATAAATTATT
Found at i:19831 original size:22 final size:22
Alignment explanation
Indices: 19800--19888 Score: 99
Period size: 22 Copynumber: 3.9 Consensus size: 22
19790 TTCATACCCC
*
19800 TTAAATTAAATAAATAAATTAT
1 TTAAAATAAATAAATAAATTAT
19822 TTAAAATAAATTAATAAGTAAATTAT
1 TTAAAATAAA-T-A-AA-TAAATTAT
*
19848 TTGAAATAAATAAATAAATTAT
1 TTAAAATAAATAAATAAATTAT
*
19870 TCT-AAATGAATAAATAAAT
1 T-TAAAATAAATAAATAAAT
19889 GAAAATTATC
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
22 33 0.56
23 4 0.07
24 2 0.03
25 3 0.05
26 17 0.29
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (22 bp):
TTAAAATAAATAAATAAATTAT
Found at i:19843 original size:26 final size:26
Alignment explanation
Indices: 19801--19866 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
19791 TCATACCCCT
19801 TAAATTAAATAAATAAATTATTTAAAA
1 TAAATT-AATAAATAAATTATTTAAAA
* *
19828 TAAATTAATAAGTAAATTATTTGAAA
1 TAAATTAATAAATAAATTATTTAAAA
*
19854 TAAATAAATAAAT
1 TAAATTAATAAAT
19867 TATTCTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
26 29 0.83
27 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (26 bp):
TAAATTAATAAATAAATTATTTAAAA
Found at i:19881 original size:26 final size:24
Alignment explanation
Indices: 19806--19897 Score: 89
Period size: 26 Copynumber: 3.7 Consensus size: 24
19796 CCCCTTAAAT
19806 TAAATAAATAAATTATTTAAAATAAA
1 TAAATAAATAAATTATTT-AAAT-AA
* * *
19832 TTAATAAGTAAATTATTT-GA-AA
1 TAAATAAATAAATTATTTAAATAA
19854 TAAATAAATAAATTATTCTAAATGAA
1 TAAATAAATAAATTATT-TAAAT-AA
19880 TAAATAAATGAAAATTAT
1 TAAATAAAT--AAATTAT
19898 CCTCGGATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
22 17 0.31
23 1 0.02
24 2 0.04
26 27 0.50
28 7 0.13
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (24 bp):
TAAATAAATAAATTATTTAAATAA
Found at i:23118 original size:18 final size:19
Alignment explanation
Indices: 23079--23120 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
23069 TTTATTTTAC
*
23079 TTTA-TATTTTTTACTATC
1 TTTATTATTTTTTACTATA
*
23097 TTTATTATTTTTTTCT-TA
1 TTTATTATTTTTTACTATA
23115 TTTATT
1 TTTATT
23121 TTAATTAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATTATTTTTTACTATA
Found at i:26978 original size:7 final size:7
Alignment explanation
Indices: 26966--27016 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
26956 AAAAAATGAG
26966 AAAGAAA
1 AAAGAAA
26973 AAAGAAA
1 AAAGAAA
26980 GAAA-AAA
1 -AAAGAAA
*
26987 ATAGAAAA
1 AAAG-AAA
26995 AAAGAAA
1 AAAGAAA
27002 AAAGAAAA
1 AAAG-AAA
27010 AAAGAAA
1 AAAGAAA
27017 GAAAACCGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 2 0.05
7 20 0.53
8 16 0.42
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:26982 original size:15 final size:15
Alignment explanation
Indices: 26966--27016 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
26956 AAAAAATGAG
*
26966 AAAGAAAAAAGAAAG
1 AAAGAAAAAAGAAAA
*
26981 AAA-AAAATAGAAAA
1 AAAGAAAAAAGAAAA
26995 AAAGAAAAAAGAAAA
1 AAAGAAAAAAGAAAA
27010 AAAGAAA
1 AAAGAAA
27017 GAAAACCGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAGAAAAAAGAAAA
Found at i:26982 original size:25 final size:25
Alignment explanation
Indices: 26954--27021 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 25
26944 AAAAAATATG
*
26954 AGAAAAAATGAGAAAGAAAA-AAGAA
1 AGAAAAAAT-AGAAAGAAAAGAAAAA
26979 AGAAAAAAATAGAAA-AAAAGAAAAA
1 AG-AAAAAATAGAAAGAAAAGAAAAA
27004 AGAAAAAA-AGAAAGAAAA
1 AGAAAAAATAGAAAGAAAA
27022 CCGATCAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 5 0.13
24 14 0.36
25 13 0.33
26 7 0.18
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (25 bp):
AGAAAAAATAGAAAGAAAAGAAAAA
Found at i:27000 original size:18 final size:17
Alignment explanation
Indices: 26954--27021 Score: 61
Period size: 18 Copynumber: 4.0 Consensus size: 17
26944 AAAAAATATG
* *
26954 AGAAAAAATGAGAAAGAA
1 AGAAAAAAAGA-AAAAAA
*
26972 A-AAAGAAAGAAAAAAA
1 AGAAAAAAAGAAAAAAA
26988 TAGAAAAAAAG--AAAAA
1 -AGAAAAAAAGAAAAAAA
27004 AGAAAAAAAGAAAGAAAA
1 AGAAAAAAAGAAA-AAAA
27022 CCGATCAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 10 0.24
16 10 0.24
17 9 0.22
18 12 0.29
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (17 bp):
AGAAAAAAAGAAAAAAA
Found at i:27003 original size:29 final size:27
Alignment explanation
Indices: 26966--27021 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 27
26956 AAAAAATGAG
26966 AAAGAAAAAAGAAAGAAAAAAATAGAAAA
1 AAAGAAAAAAGAAA-AAAAAAA-AGAAAA
*
26995 AAAGAAAAAAGAAAAAAAGAAAGAAAA
1 AAAGAAAAAAGAAAAAAAAAAAGAAAA
27022 CCGATCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 6 0.23
28 6 0.23
29 14 0.54
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (27 bp):
AAAGAAAAAAGAAAAAAAAAAAGAAAA
Found at i:27695 original size:28 final size:28
Alignment explanation
Indices: 27635--27698 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
27625 CGCAATAAGC
27635 CAACCTAAAACACATTACCTCCCCAAAT
1 CAACCTAAAACACATTACCTCCCCAAAT
* * * *
27663 TAACCTGAAACACATTACCTTCCCAAGT
1 CAACCTAAAACACATTACCTCCCCAAAT
27691 CAACCTAA
1 CAACCTAA
27699 GCCTTATTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.41, C:0.36, G:0.03, T:0.20
Consensus pattern (28 bp):
CAACCTAAAACACATTACCTCCCCAAAT
Found at i:28928 original size:57 final size:55
Alignment explanation
Indices: 28857--29013 Score: 232
Period size: 52 Copynumber: 2.9 Consensus size: 55
28847 AAAAGATTTT
*
28857 TTTAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTC-AATGAAT
1 TTTAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTCAAATG-AG
* *
28912 TCTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATG-T--TTTCAAATGAG
1 T-TT-AAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTCAAATGAG
28966 TTTAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTC
1 TTTAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTC
29014 CAAAAACTGT
Statistics
Matches: 91, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
52 35 0.38
53 3 0.03
54 6 0.07
55 9 0.10
56 3 0.03
57 35 0.38
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.40
Consensus pattern (55 bp):
TTTAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTCAAATGAG
Found at i:29097 original size:97 final size:96
Alignment explanation
Indices: 28932--29114 Score: 278
Period size: 97 Copynumber: 1.9 Consensus size: 96
28922 AGCTAAGCCT
* *
28932 AATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTAAAGAAACTAAGCCTGATTTTTAGGGGT
1 AATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTAAAGAAACTAAGCCTCATTTTCAGGGGT
*
28997 TTCTTGATGATGATTTCCAAAAACTGTTTTA
66 TTCTTGATGATAATTTCCAAAAACTGTTTTA
* **
29028 AATTTTGTA-GGGTTTTTTGATGTTTTCAAAATGAGTTTTTAGAAACTAAGCCTCATTTTCAGGG
1 AATTTT-TAGGGGTTTCTTGATGTTTTC-AAATGAGTTTAAAGAAACTAAGCCTCATTTTCAGGG
*
29092 GTTTCTTGATGATAATTTTCAAA
64 GTTTCTTGATGATAATTTCCAAA
29115 GAATTTTTAA
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
96 23 0.29
97 55 0.71
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (96 bp):
AATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTAAAGAAACTAAGCCTCATTTTCAGGGGT
TTCTTGATGATAATTTCCAAAAACTGTTTTA
Found at i:29144 original size:58 final size:57
Alignment explanation
Indices: 29068--29272 Score: 161
Period size: 58 Copynumber: 3.6 Consensus size: 57
29058 ATGAGTTTTT
*
29068 AGAAACTAAGCCTCATTTTCAGGGGTTTCTTGATGATAATTTTCAAAGAATTTTTAAA
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGAT-ATTTTCAAAGAATTTTTAAA
* * * *
29126 AGAAGCTAAGCCTAATTTTTAGGGGTTTATTGATG---TTTTCAAAATGAGTTTTT---
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATATTTTC-AAA-GAATTTTTAAA
* ** * * * * * * *
29179 AGAAACTAAGCATGGTTTTCATGGGTTTCTTGACGATTATCTCCAAATAAATTTCAAA
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGA-TATTTTCAAAGAATTTTTAAA
* * * *
29237 TGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGA
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGA
29273 CAACTGAAAA
Statistics
Matches: 110, Mismatches: 28, Indels: 18
0.71 0.18 0.12
Matches are distributed among these distances:
53 27 0.25
54 5 0.05
55 7 0.06
56 10 0.09
57 3 0.03
58 58 0.53
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (57 bp):
AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATATTTTCAAAGAATTTTTAAA
Found at i:29242 original size:111 final size:111
Alignment explanation
Indices: 29028--29263 Score: 339
Period size: 111 Copynumber: 2.1 Consensus size: 111
29018 AACTGTTTTA
* *
29028 AATTTTGTA-GGGTTTTTTGATGTTTTCAAAATGAGTTTTTAGAAACTAAGCCTCATTTTCAGGG
1 AATTTT-TAGGGGTTTATTGATGTTTTCAAAATGAGTTTTTAGAAACTAAGCATCATTTTCAGGG
* * * * *
29092 GTTTCTTGATGATAATTTTCAAAGAATTTTTAAAAGAAGCTAAGCCT
65 GTTTCTTGACGATAATCTCCAAAGAAATTTCAAAAGAAGCTAAGCCT
** *
29139 AATTTTTAGGGGTTTATTGATGTTTTCAAAATGAGTTTTTAGAAACTAAGCATGGTTTTCATGGG
1 AATTTTTAGGGGTTTATTGATGTTTTCAAAATGAGTTTTTAGAAACTAAGCATCATTTTCAGGGG
* * *
29204 TTTCTTGACGATTATCTCCAAATAAATTTCAAATGAAGCTAAGCCT
66 TTTCTTGACGATAATCTCCAAAGAAATTTCAAAAGAAGCTAAGCCT
29250 AATTTTTAGGGGTT
1 AATTTTTAGGGGTT
29264 CCTTGATGAC
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
110 2 0.02
111 109 0.98
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (111 bp):
AATTTTTAGGGGTTTATTGATGTTTTCAAAATGAGTTTTTAGAAACTAAGCATCATTTTCAGGGG
TTTCTTGACGATAATCTCCAAAGAAATTTCAAAAGAAGCTAAGCCT
Found at i:29657 original size:2 final size:2
Alignment explanation
Indices: 29650--29675 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29640 ACCATCATGC
29650 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
29676 CAGGCATTTG
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:30484 original size:91 final size:91
Alignment explanation
Indices: 29934--30474 Score: 687
Period size: 91 Copynumber: 5.9 Consensus size: 91
29924 AGATAAACCA
* * * *
29934 ATCAACATTTCCAATGGAGAGTTCAAAATGAGAAGAACTCATCCAACGAGTGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
*
29999 AATGAGAATAACTTGTTCAA-CTATGG
66 AATGAGAAGAACTTGTTCAACCT-TGG
* **
30025 ATCAA-AGTTTCTAGTGGGGAGTTCATAATGAGAAGAACTCATTAAACGAGGGAGAAGAAGTTCA
1 ATCAACA-TTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
* *
30089 TAATAAGAAGAACTTATTCAACCTTGG
65 TAATGAGAAGAACTTGTTCAACCTTGG
* * * * *
30116 ATCAACGTTTCCAGTGGGAAGTTAATAATGAGAAGAACTCATCCAACGAGGGGGAAGATGTTCAT
1 ATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
30181 AATGAGAAGAACTTGTTCAACCTT-G
66 AATGAGAAGAACTTGTTCAACCTTGG
* * * *
30206 ACTCAATATTTCCACTGGGGAGTTCATAATGAGAAGAACTCGT-CAGATGAGGGAGAAGAAGTTC
1 A-TCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCA-ACGAGGGAGAAGAAGTTC
*
30270 ATATTGAGAAGAACTTGTTCAACCTTGG
64 ATAATGAGAAGAACTTGTTCAACCTTGG
** * *
30298 ATCAACATTTTTAGTGGGGAGTTCATAATGGGAAGAACTCATCCAATGAGGG-GAAAGAAGTTCA
1 ATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAG-AAGAAGTTCA
*
30362 TAATAAGAAGAACTTGTTCAACCTTGG
65 TAATGAGAAGAACTTGTTCAACCTTGG
* * * * * * ***
30389 CTCAACATTTCTAGTGGAGAGTTCATAATTAGTAGAACTCGTCCGTTGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
*
30454 AATGAGAAGAACTTTTTCAAC
66 AATGAGAAGAACTTGTTCAAC
30475 TTTAGCTCAA
Statistics
Matches: 392, Mismatches: 49, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
90 6 0.02
91 379 0.97
92 7 0.02
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (91 bp):
ATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTGG
Found at i:30534 original size:76 final size:76
Alignment explanation
Indices: 30447--30620 Score: 210
Period size: 76 Copynumber: 2.3 Consensus size: 76
30437 AGGGAGAAGA
* * *
30447 AGTTCATAATGAGAAGAACTTTTTCAACTTTAGCTCAATTCCAT-CATA-GA-ATGAGGGATTAA
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATT-CATCCATAGGAGATGA--GATCAA
30509 CATTTCCAGTGGAG
63 CATTTCCAGTGGAG
* * *
30523 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTTAGATCAAC
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATC-CATA-GGAGATGAGATCAAC
*
30588 ATTTTCAGTGGAG
64 ATTTCCAGTGGAG
*
30601 AGTTCATAATGAGAAAAACT
1 AGTTCATAATGAGAAGAACT
30621 CATCCGATGA
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
75 3 0.04
76 37 0.44
77 4 0.05
78 37 0.44
79 2 0.02
80 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (76 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCCATAGGAGATGAGATCAACAT
TTCCAGTGGAG
Found at i:32171 original size:15 final size:14
Alignment explanation
Indices: 32151--32180 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
32141 TGCATAAAAT
32151 AAAAATATTGTTTTA
1 AAAAATATT-TTTTA
32166 AAAAATATTTTTTA
1 AAAAATATTTTTTA
32180 A
1 A
32181 CTCCTCCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
AAAAATATTTTTTA
Found at i:39682 original size:14 final size:14
Alignment explanation
Indices: 39663--39690 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39653 TATTCCACTG
39663 AGCCTTTCGAAATA
1 AGCCTTTCGAAATA
39677 AGCCTTTCGAAATA
1 AGCCTTTCGAAATA
39691 CTTTGTCGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
AGCCTTTCGAAATA
Found at i:49090 original size:45 final size:46
Alignment explanation
Indices: 48996--49305 Score: 188
Period size: 45 Copynumber: 6.6 Consensus size: 46
48986 TTTTTTGCTG
* * * * *
48996 ATAATGCACCCATAT-ACATT-CAATTATGGCATACTCTCATGGCGT
1 ATAATGCACCCATATGA-ATTACTATTTTGGCATCCTTTCATGGCCT
49041 -TAATGCACCCATATGAATTACTATTTTGGCATCCTTTCAT-GCCT
1 ATAATGCACCCATATGAATTACTATTTTGGCATCCTTTCATGGCCT
* * * **
49085 ATAATGCGCCCATATGCATTATTATTTTGGCATCCTTTCATTTATACACATT
1 ATAATGCACCCATATGAATTACTATTTTGGCATCCTTTCA--T-GGC-C--T
* ** * * * *
49137 ATTATTTGGCATCCTTTCAT-ACACATATTATTTTGGCATCCTTTCAT-ACTT
1 A-TA-AT-GCA-CCCAT-ATGA-A-TTACTATTTTGGCATCCTTTCATGGCCT
* * *
49188 ATAATGCACCTATAT-CATTATTATTTTGGCATCCTTTCAT-GCCT
1 ATAATGCACCCATATGAATTACTATTTTGGCATCCTTTCATGGCCT
* * * *
49232 ATAATGCAACCATATGCATTATTAATTTGGCATCCTTTCAT-GCCT
1 ATAATGCACCCATATGAATTACTATTTTGGCATCCTTTCATGGCCT
* * *
49277 ATAATGCACACATATGCATTATTATTTTG
1 ATAATGCACCCATATGAATTACTATTTTG
49306 TTCATTCATT
Statistics
Matches: 219, Mismatches: 28, Indels: 36
0.77 0.10 0.13
Matches are distributed among these distances:
44 57 0.26
45 108 0.49
46 2 0.01
47 5 0.02
48 3 0.01
49 2 0.01
50 3 0.01
51 2 0.01
52 2 0.01
53 2 0.01
54 3 0.01
55 2 0.01
56 4 0.02
57 3 0.01
58 21 0.10
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.40
Consensus pattern (46 bp):
ATAATGCACCCATATGAATTACTATTTTGGCATCCTTTCATGGCCT
Found at i:49148 original size:31 final size:30
Alignment explanation
Indices: 49101--49184 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 30
49091 CGCCCATATG
49101 CATTATTATTTTGGCATCCTTTCATTTATACA
1 CATTATTATTTTGGCATCCTTTCA--TATACA
49133 CATTATTA-TTTGGCATCCTTTC--ATACA
1 CATTATTATTTTGGCATCCTTTCATATACA
49160 CA-TATTATTTTGGCATCCTTTCATA
1 CATTATTATTTTGGCATCCTTTCATA
49185 CTTATAATGC
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
26 5 0.10
27 21 0.43
29 1 0.02
31 14 0.29
32 8 0.16
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (30 bp):
CATTATTATTTTGGCATCCTTTCATATACA
Found at i:49223 original size:44 final size:44
Alignment explanation
Indices: 49162--49305 Score: 227
Period size: 45 Copynumber: 3.2 Consensus size: 44
49152 TTCATACACA
* *
49162 TATTATTTTGGCATCCTTTCATACTTATAATGCACCTATAT-CAT
1 TATTATTTTGGCATCCTTTCATGCCTATAATGCACC-ATATGCAT
49206 TATTATTTTGGCATCCTTTCATGCCTATAATGCAACCATATGCAT
1 TATTATTTTGGCATCCTTTCATGCCTATAATGC-ACCATATGCAT
*
49251 TATTAATTTGGCATCCTTTCATGCCTATAATGCACACATATGCAT
1 TATTATTTTGGCATCCTTTCATGCCTATAATGCAC-CATATGCAT
49296 TATTATTTTG
1 TATTATTTTG
49306 TTCATTCATT
Statistics
Matches: 93, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
44 37 0.40
45 56 0.60
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (44 bp):
TATTATTTTGGCATCCTTTCATGCCTATAATGCACCATATGCAT
Found at i:49412 original size:17 final size:17
Alignment explanation
Indices: 49359--49414 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
49349 CTATCCTTTC
* *
49359 CATACATGAAATAAAAA
1 CATACATAAAATTAAAA
49376 CATAC-TAACTAATGTAAAA
1 CATACATAA--AAT-TAAAA
*
49395 CATACATTAAATTAAAA
1 CATACATAAAATTAAAA
49412 CAT
1 CAT
49415 TCTAACTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.06
17 13 0.41
18 6 0.19
19 9 0.28
20 2 0.06
ACGTcount: A:0.57, C:0.14, G:0.04, T:0.25
Consensus pattern (17 bp):
CATACATAAAATTAAAA
Done.