Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008701.1 Hibiscus syriacus cultivar Beakdansim tig00111736_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: 113026
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2338 original size:39 final size:39
Alignment explanation
Indices: 2264--2338 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
2254 TTTTAGGGAC
* *
2264 CAAAGATGAAATTCTCATATGCACAATTTGGCCACCTAT
1 CAAAGATGAAATTCTCATATGCACAAGTTGACCACCTAT
* * *
2303 CAAAGATG-AATTTTCAATGTGTACAAGTTGACCACC
1 CAAAGATGAAATTCTC-ATATGCACAAGTTGACCACC
2339 AACCAACTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 6 0.20
39 24 0.80
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (39 bp):
CAAAGATGAAATTCTCATATGCACAAGTTGACCACCTAT
Found at i:2363 original size:17 final size:17
Alignment explanation
Indices: 2341--2374 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2331 TGACCACCAA
*
2341 CCAACTTGTCAACTTTG
1 CCAACTTGTCAAATTTG
2358 CCAACTTGTCAAATTTG
1 CCAACTTGTCAAATTTG
2375 ACAATTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35
Consensus pattern (17 bp):
CCAACTTGTCAAATTTG
Found at i:5702 original size:19 final size:19
Alignment explanation
Indices: 5678--5715 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5668 TTATATGTGT
5678 GACACGTGTCAGGTAACAA
1 GACACGTGTCAGGTAACAA
*
5697 GACACGTGTTAGGTAACAA
1 GACACGTGTCAGGTAACAA
5716 CCAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (19 bp):
GACACGTGTCAGGTAACAA
Found at i:6669 original size:57 final size:58
Alignment explanation
Indices: 6595--6709 Score: 178
Period size: 57 Copynumber: 2.0 Consensus size: 58
6585 ATATAAAGAA
* *
6595 ATTCGGATTTTAAAGGAGCACATTTTCATC-TTAGACAAGCCTTGCATCCGTCAGTGT
1 ATTCGGATTTCAAAGGAGCACATGTTCATCTTTAGACAAGCCTTGCATCCGTCAGTGT
* *
6652 ATTCGGATTTCAGAGGAGCACGTGTTCATCTTTTAGACAAGCCTTGCATCCGTCAGTG
1 ATTCGGATTTCAAAGGAGCACATGTTCATC-TTTAGACAAGCCTTGCATCCGTCAGTG
6710 CATGGAGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 26 0.50
59 26 0.50
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (58 bp):
ATTCGGATTTCAAAGGAGCACATGTTCATCTTTAGACAAGCCTTGCATCCGTCAGTGT
Found at i:10561 original size:17 final size:19
Alignment explanation
Indices: 10528--10563 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
10518 GGTATCGCAG
10528 AACGAATTTTGTCTTAAAA
1 AACGAATTTTGTCTTAAAA
10547 AACG-ATTTT-TCTTAAAA
1 AACGAATTTTGTCTTAAAA
10564 TTGTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (19 bp):
AACGAATTTTGTCTTAAAA
Found at i:26187 original size:751 final size:751
Alignment explanation
Indices: 24746--26246 Score: 2858
Period size: 751 Copynumber: 2.0 Consensus size: 751
24736 AATTCTCTTA
*
24746 ATTCTTCAAGAATTATGGATTTTTGACATATGTCAAGATTAAACCTTTCTTATACAATCTAAAAT
1 ATTCTTCAAGAATTATGGATTTTTGACATATGTCAAGATTAAACCTTTCTTATACAATCTAAAAC
* *
24811 CCCAAAATAAAATCTCTCGTTTCTTTACCCGAAATAATTCCTGATCACTACCAAATGACCAAATT
66 CCCAAAATAAAATCTCTCATTTCTTTACCCGAAATAATTCATGATCACTACCAAATGACCAAATT
24876 TTTACATTACCTCTCTTTGAGATTTTTAAACATTGTTTTTATCTTTTTCATGACTAAAAAAAGTC
131 TTTACATTACCTCTCTTTGAGATTTTTAAACATTGTTTTTATCTTTTTCATGACTAAAAAAAGTC
24941 ATACACTTACCTTTCATTAAGCCAATAAAGTCACACCATCGTCTTCTTAGACGCAAAACTGTTAT
196 ATACACTTACCTTTCATTAAGCCAATAAAGTCACACCATCGTCTTCTTAGACGCAAAACTGTTAT
25006 TTTTATACCAATAAAACCTGAAGGCATTGAGTACAAGATATTCACTTGGACATGAACCATCTTCT
261 TTTTATACCAATAAAACCTGAAGGCATTGAGTACAAGATATTCACTTGGACATGAACCATCTTCT
*
25071 AAGAAGACAAAAGATGGAGCATCTCGAATCAATTTTCTGAAGATGAGCCTGAATAATTGAGACAT
326 AAGAAGACAAAAGATGGAGCATCTCGAATAAATTTTCTGAAGATGAGCCTGAATAATTGAGACAT
* *
25136 ACTAGGAGAAAGAAGCAGAAAAAACAAAATTAATTTAAAATAATTCTGTCATGCATTAGTTACAT
391 ACTAGGAGAAAGAAGCAGAAAAAACAAAATTAATTTAAAATAATTCTATCATGCATTAATTACAT
25201 TGTTTTCAAGTGAATAAAAATTATTCCTGAAAATCTATCCCTCTGGGGATACATCTTCTGCAAAG
456 TGTTTTCAAGTGAATAAAAATTATTCCTGAAAATCTATCCCTCTGGGGATACATCTTCTGCAAAG
25266 TCTTCCATGTATGGAATGATGAACGCCTTTCTTTCATTATCCATTCATAAAAGGAGAAAATATAT
521 TCTTCCATGTATGGAATGATGAACGCCTTTCTTTCATTATCCATTCATAAAAGGAGAAAATATAT
25331 ATCCATTGTGTTCCCATTTGAGCCTAAATTATATTTTCTTTTGATTCAACCCTAACCAAAGATCA
586 ATCCATTGTGTTCCCATTTGAGCCTAAATTATATTTTCTTTTGATTCAACCCTAACCAAAGATCA
*
25396 CCCTCCACACTGGGGGGAAAGGTGAAGGAAATCAGCTCGCATGAGTGAAGATCATCAAATCAGAT
651 CCCTCCACACTAGGGGGAAAGGTGAAGGAAATCAGCTCGCATGAGTGAAGATCATCAAATCAGAT
25461 GAGATACCGAAAGGTGAACCAAATGCAAAGTGCGAT
716 GAGATACCGAAAGGTGAACCAAATGCAAAGTGCGAT
25497 ATTCTTCAAGAATTATGGATTTTTGACATATGTCAAGATTAAACCTTTCTTATACAATCTAAAAC
1 ATTCTTCAAGAATTATGGATTTTTGACATATGTCAAGATTAAACCTTTCTTATACAATCTAAAAC
25562 CCCAAAATAAAATCTCTCATTTCTTTACCCGAAATAATTCATGATCACTACCAAATGACCAAATT
66 CCCAAAATAAAATCTCTCATTTCTTTACCCGAAATAATTCATGATCACTACCAAATGACCAAATT
25627 TTTACATTACCTCTCTTTGAGATTTTTAAACATTGTTTTTATCTTTTTCATGACTAAAAAAAGTC
131 TTTACATTACCTCTCTTTGAGATTTTTAAACATTGTTTTTATCTTTTTCATGACTAAAAAAAGTC
*
25692 ATACACTTACCTTTCATTGAGCCAATAAAGTCACACCATCGTCTTCTTAGACGCAAAACTGTTAT
196 ATACACTTACCTTTCATTAAGCCAATAAAGTCACACCATCGTCTTCTTAGACGCAAAACTGTTAT
* *
25757 TTTTATACCAATAAAACCTGAAGGCATTGAGTACAAGATGTTCACTTGGACATGAACCTTCTTCT
261 TTTTATACCAATAAAACCTGAAGGCATTGAGTACAAGATATTCACTTGGACATGAACCATCTTCT
*
25822 AAGAAGACACAAGATGGAGCATCTCGAATAAATTTTCTGAAGATGAGCCTGAATAATTGAGACAT
326 AAGAAGACAAAAGATGGAGCATCTCGAATAAATTTTCTGAAGATGAGCCTGAATAATTGAGACAT
* *
25887 GCTGGGAGAAAGAAGCAGAAAAAACAAAATTAATTTAAAATAATTCTATCATGCATTAATTACAT
391 ACTAGGAGAAAGAAGCAGAAAAAACAAAATTAATTTAAAATAATTCTATCATGCATTAATTACAT
25952 TGTTTTCAAGTGAATAAAAATTATTCCTGAAAATCTATCCCTCTGGGGATACATCTTCTGCAAAG
456 TGTTTTCAAGTGAATAAAAATTATTCCTGAAAATCTATCCCTCTGGGGATACATCTTCTGCAAAG
26017 TCTTCCATGTATGGAATGATGAACGCCTTTCTTTCATTATCCATTCATAAAAGGAGAAAATATAT
521 TCTTCCATGTATGGAATGATGAACGCCTTTCTTTCATTATCCATTCATAAAAGGAGAAAATATAT
* *
26082 ATCCCTTGTGTTCCCATTTGAGCCTAAATTATATTTTCTTTTGATTCAACCCTAACCAAGGATCA
586 ATCCATTGTGTTCCCATTTGAGCCTAAATTATATTTTCTTTTGATTCAACCCTAACCAAAGATCA
*
26147 CCCTCCACACTAGGGGGAAAGGTGAAGGAAATCTGCTCGCATGAGTGAAGATCATCAAATCAGAT
651 CCCTCCACACTAGGGGGAAAGGTGAAGGAAATCAGCTCGCATGAGTGAAGATCATCAAATCAGAT
26212 GAGATACCGAAAGGTGAACCAAATGCAAAGTGCGA
716 GAGATACCGAAAGGTGAACCAAATGCAAAGTGCGA
26247 ATATCAAATC
Statistics
Matches: 734, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
751 734 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (751 bp):
ATTCTTCAAGAATTATGGATTTTTGACATATGTCAAGATTAAACCTTTCTTATACAATCTAAAAC
CCCAAAATAAAATCTCTCATTTCTTTACCCGAAATAATTCATGATCACTACCAAATGACCAAATT
TTTACATTACCTCTCTTTGAGATTTTTAAACATTGTTTTTATCTTTTTCATGACTAAAAAAAGTC
ATACACTTACCTTTCATTAAGCCAATAAAGTCACACCATCGTCTTCTTAGACGCAAAACTGTTAT
TTTTATACCAATAAAACCTGAAGGCATTGAGTACAAGATATTCACTTGGACATGAACCATCTTCT
AAGAAGACAAAAGATGGAGCATCTCGAATAAATTTTCTGAAGATGAGCCTGAATAATTGAGACAT
ACTAGGAGAAAGAAGCAGAAAAAACAAAATTAATTTAAAATAATTCTATCATGCATTAATTACAT
TGTTTTCAAGTGAATAAAAATTATTCCTGAAAATCTATCCCTCTGGGGATACATCTTCTGCAAAG
TCTTCCATGTATGGAATGATGAACGCCTTTCTTTCATTATCCATTCATAAAAGGAGAAAATATAT
ATCCATTGTGTTCCCATTTGAGCCTAAATTATATTTTCTTTTGATTCAACCCTAACCAAAGATCA
CCCTCCACACTAGGGGGAAAGGTGAAGGAAATCAGCTCGCATGAGTGAAGATCATCAAATCAGAT
GAGATACCGAAAGGTGAACCAAATGCAAAGTGCGAT
Found at i:26281 original size:15 final size:15
Alignment explanation
Indices: 26261--26304 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
26251 CAAATCAAAA
26261 CAAAGAAAAAAGAAG
1 CAAAGAAAAAAGAAG
*
26276 CAAAGAAAAAAACAAAG
1 CAAAG-AAAAAA-GAAG
26293 -AAAGAAAAAAGA
1 CAAAGAAAAAAGA
26305 CAAGAAGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.04
15 11 0.44
16 10 0.40
17 3 0.12
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (15 bp):
CAAAGAAAAAAGAAG
Found at i:26287 original size:16 final size:17
Alignment explanation
Indices: 26256--26307 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
26246 AATATCAAAT
*
26256 CAAAACAAAG-AAAAAA
1 CAAAGCAAAGAAAAAAA
*
26272 -GAAGCAAAGAAAAAAA
1 CAAAGCAAAGAAAAAAA
26288 CAAAG-AAAGAAAAAAGA
1 CAAAGCAAAGAAAAAA-A
26305 CAA
1 CAA
26308 GAAGCACATG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 7 0.23
16 16 0.53
17 7 0.23
ACGTcount: A:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (17 bp):
CAAAGCAAAGAAAAAAA
Found at i:26309 original size:16 final size:16
Alignment explanation
Indices: 26262--26310 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
26252 AAATCAAAAC
26262 AAAGAAAAAAG--AAG
1 AAAGAAAAAAGACAAG
26276 CAAAGAAAAAA-ACAAAG
1 -AAAGAAAAAAGAC-AAG
26293 AAAGAAAAAAGACAAG
1 AAAGAAAAAAGACAAG
26309 AA
1 AA
26311 GCACATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 10 0.33
16 15 0.50
17 5 0.17
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAGACAAG
Found at i:27563 original size:35 final size:38
Alignment explanation
Indices: 27480--27573 Score: 106
Period size: 35 Copynumber: 2.6 Consensus size: 38
27470 ACGAAGCGTC
* *
27480 GTCTCGCTAGAGATAGTTTTTCTAAAAAATAAAATTTT
1 GTCTCGCTTGAGACAGTTTTTCTAAAAAATAAAATTTT
* *
27518 GTCTCGCTTGAGACAGTTTTT-T-AAAAA-CAATTTTT
1 GTCTCGCTTGAGACAGTTTTTCTAAAAAATAAAATTTT
* *
27553 TTCTCGCTTGAGATA-TTTTTC
1 GTCTCGCTTGAGACAGTTTTTC
27574 CTCTGAGATA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 5 0.10
35 19 0.39
36 5 0.10
37 1 0.02
38 19 0.39
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (38 bp):
GTCTCGCTTGAGACAGTTTTTCTAAAAAATAAAATTTT
Found at i:27749 original size:65 final size:65
Alignment explanation
Indices: 27680--27840 Score: 232
Period size: 65 Copynumber: 2.5 Consensus size: 65
27670 CTTCCTTAAG
* * *
27680 ACATCATCTTTGAGATCGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAA
1 ACATCATCTTTGAGATCGTTTCTCTTGAAACAAATTTCGTCTCCCTCGAGACAGTTTATCTTGAA
* * * *
27745 ACATCATCTTTGAGATCGTTTCCCTTGAAAGAAGTTTTGTCTCCCTCGAGACAGTTTATCTTGAA
1 ACATCATCTTTGAGATCGTTTCTCTTGAAACAAATTTCGTCTCCCTCGAGACAGTTTATCTTGAA
* *
27810 ACACCCATCTTTGAGATTGTTTCTCTTGAAA
1 ACA-TCATCTTTGAGATCGTTTCTCTTGAAA
27841 TGAATTTTAT
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
65 61 0.72
66 24 0.28
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (65 bp):
ACATCATCTTTGAGATCGTTTCTCTTGAAACAAATTTCGTCTCCCTCGAGACAGTTTATCTTGAA
Found at i:28131 original size:131 final size:132
Alignment explanation
Indices: 27893--28247 Score: 371
Period size: 131 Copynumber: 2.7 Consensus size: 132
27883 CTTGAAAAAA
* * * * * *
27893 ATCCCTAAAGATGGTATGTCGTCCTCATCGCATAGGAACCATATCATCCACCGACCAGACCTCCT
1 ATCCCTAAAGATGGCATATCGTCCTCATCACGTAGGAACCATGTCATCCACCGACTAGACCTCCT
** ** *
27958 CATCACA-TACAAGCCGTGTCACCCCTAGATAAACAGCCGTCCTCA-TCACGTAGGAACCGTGTT
66 CATCA-AGTAGGAGCCGTGTCACCCCTAGATAAACAAACGTCCTCATTCA-GGAGGAACCGTGTT
28021 AT-C
129 ATCC
* * * *
28024 ATCCCTAAAGATGGCATATCATCCTCATCATGTAGGAACCGTGTCATCCACCGACTAGACCTCTT
1 ATCCCTAAAGATGGCATATCGTCCTCATCACGTAGGAACCATGTCATCCACCGACTAGACCTCCT
* * *
28089 CATCAAGTAGGAGCCGTGTCACCCCTAGAT-AACTAAATGTCCTCATTGAGGAGGAACTGTGTTA
66 CATCAAGTAGGAGCCGTGTCACCCCTAGATAAAC-AAACGTCCTCATTCAGGAGGAACCGTGTTA
28153 TCACC
130 T--CC
* * * * *
28158 ATCCCTAAAGGTGGCCA-AGACGTCCTCATCACGTAGGAACAATGTCATCTACCGA-TCAGATCT
1 ATCCCTAAAGATGG-CATA-TCGTCCTCATCACGTAGGAACCATGTCATCCACCGACT-AGACCT
* *
28221 CCTCATCACGTAGGAGTCGTGTCACCC
63 CCTCATCAAGTAGGAGCCGTGTCACCC
28248 TTAAATGACC
Statistics
Matches: 186, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
130 4 0.02
131 103 0.55
132 2 0.01
134 16 0.09
135 61 0.33
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (132 bp):
ATCCCTAAAGATGGCATATCGTCCTCATCACGTAGGAACCATGTCATCCACCGACTAGACCTCCT
CATCAAGTAGGAGCCGTGTCACCCCTAGATAAACAAACGTCCTCATTCAGGAGGAACCGTGTTAT
CC
Found at i:28454 original size:3 final size:3
Alignment explanation
Indices: 28446--28537 Score: 130
Period size: 3 Copynumber: 30.7 Consensus size: 3
28436 AAAACAATTG
* * * * *
28446 TTA TTA TTA TTG TTG TTG TTG TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
28494 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28538 TAACATATTT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:29125 original size:20 final size:21
Alignment explanation
Indices: 29082--29142 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
29072 AAAAATACAG
*
29082 AGAGAAACTAAAAGAAAAC--C
1 AGAGAAA-TAAAAGAAAACAAA
29102 AGAGAAA-AAAAGAAAACAAA
1 AGAGAAATAAAAGAAAACAAA
*
29122 AGAGAAATAAAAGGAAACAAA
1 AGAGAAATAAAAGAAAACAAA
29143 TTCGAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
18 10 0.28
20 14 0.39
21 12 0.33
ACGTcount: A:0.72, C:0.08, G:0.16, T:0.03
Consensus pattern (21 bp):
AGAGAAATAAAAGAAAACAAA
Found at i:29139 original size:21 final size:20
Alignment explanation
Indices: 29102--29142 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
29092 AAAGAAAACC
29102 AGAGAAAAAAAGAAAACAAA
1 AGAGAAAAAAAGAAAACAAA
*
29122 AGAGAAATAAAAGGAAACAAA
1 AGAGAAA-AAAAGAAAACAAA
29143 TTCGAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (20 bp):
AGAGAAAAAAAGAAAACAAA
Found at i:31240 original size:15 final size:15
Alignment explanation
Indices: 31222--31254 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
31212 CTGATTTTTT
*
31222 TAAAAAAACCGGTTA
1 TAAAAAAACCGATTA
31237 TAAAAAAACCGATTA
1 TAAAAAAACCGATTA
31252 TAA
1 TAA
31255 TATTATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.21
Consensus pattern (15 bp):
TAAAAAAACCGATTA
Found at i:31343 original size:33 final size:33
Alignment explanation
Indices: 31296--31399 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
31286 ACAAAGTTTA
* *
31296 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
31328 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
31361 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
31394 CGATAA
1 CGATAA
31400 TTGAAACAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 4 0.06
33 63 0.94
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:31419 original size:21 final size:21
Alignment explanation
Indices: 31394--31435 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
31384 CTTCCAAGTT
31394 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
31415 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
31436 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:36452 original size:26 final size:28
Alignment explanation
Indices: 36373--36551 Score: 110
Period size: 29 Copynumber: 6.4 Consensus size: 28
36363 CGAAACCTCC
* * *
36373 AATATAGTTTTTGGAAATATTTATTATGT
1 AATATAGTTTTT-GAAACATTAATTATAT
*
36402 AAAATAG-TTTTGAAAAACATT-ATTATAT
1 AATATAGTTTTTG--AAACATTAATTATAT
36430 AATATAGTTTTTGAAA-A-TAA-T-TAT
1 AATATAGTTTTTGAAACATTAATTATAT
* * ** *
36454 CATGTAGTTTTAAAAACCATTATTCTATAT
1 AATATAGTTTTTGAAA-CATTAAT-TATAT
36484 AATATAGTTTTT-AAA-A-TAATTATTAT
1 AATATAGTTTTTGAAACATTAATTA-TAT
36510 AATATAG-TTTTGAAAACTATT-ATTATAT
1 AATATAGTTTTTG-AAAC-ATTAATTATAT
36538 ATAGTATAGTTTTT
1 A-A-TATAGTTTTT
36552 TTAATATAAT
Statistics
Matches: 118, Mismatches: 13, Indels: 36
0.71 0.08 0.22
Matches are distributed among these distances:
24 15 0.13
25 8 0.07
26 16 0.14
27 10 0.08
28 20 0.17
29 27 0.23
30 18 0.15
31 4 0.03
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (28 bp):
AATATAGTTTTTGAAACATTAATTATAT
Found at i:36494 original size:30 final size:28
Alignment explanation
Indices: 36393--36550 Score: 104
Period size: 30 Copynumber: 5.8 Consensus size: 28
36383 TTGGAAATAT
*
36393 TTATTATGTA-AA-ATAGTTTTGAAAAACA
1 TTATTATATATAATATAGTTTT--AAAACA
*
36421 TTA-T-TATATAATATAGTTTTTGAAA-A
1 TTATTATATATAATATAG-TTTTAAAACA
* *
36447 -TA--AT-TATCATGTAGTTTTAAAAACCA
1 TTATTATATATAATATAGTTTT-AAAA-CA
* *
36473 TTATTCTATATAATATAGTTTTTAAA-A
1 TTATTATATATAATATAGTTTTAAAACA
*
36500 TAATTAT-TATAATATAGTTTTGAAAACTA
1 TTATTATATATAATATAGTTTT-AAAAC-A
*
36529 TTATTATATATAGTATAGTTTT
1 TTATTATATATAATATAGTTTT
36551 TTTAATATAA
Statistics
Matches: 101, Mismatches: 14, Indels: 28
0.71 0.10 0.20
Matches are distributed among these distances:
23 4 0.04
24 11 0.11
25 3 0.03
26 19 0.19
27 17 0.17
28 7 0.07
29 15 0.15
30 25 0.25
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (28 bp):
TTATTATATATAATATAGTTTTAAAACA
Found at i:36526 original size:56 final size:56
Alignment explanation
Indices: 36373--36573 Score: 214
Period size: 56 Copynumber: 3.6 Consensus size: 56
36363 CGAAACCTCC
* * * *
36373 AATATAGTTTTTGGAAATATTTATTATGTAAAATAGTTTTGAAAAACATTA-TTATAT
1 AATATAGTTTTTGAAAATAATTATTA--TAATATAGTTTTGAAAACCATTATTTATAT
* * *
36430 AATATAGTTTTTGAAAAT-A--ATTATCATGTAGTTTTAAAAACCATTATTCTATAT
1 AATATAGTTTTTGAAAATAATTATTATAATATAGTTTTGAAAACCATTATT-TATAT
*
36484 AATATAGTTTTT-AAAATAATTATTATAATATAGTTTTGAAAACTATTATTATATAT
1 AATATAGTTTTTGAAAATAATTATTATAATATAGTTTTGAAAACCATTATT-TATAT
* * * *
36540 AGTATAGTTTTTTTAATATAATTATTATTATATA
1 AATATAG-TTTTTGAAAATAATTATTATAATATA
36574 TAGCATAGTT
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
52 18 0.15
53 6 0.05
54 22 0.18
56 36 0.30
57 22 0.18
58 18 0.15
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (56 bp):
AATATAGTTTTTGAAAATAATTATTATAATATAGTTTTGAAAACCATTATTTATAT
Found at i:36571 original size:26 final size:27
Alignment explanation
Indices: 36491--36573 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 27
36481 TATAATATAG
*
36491 TTTTTAAAATAATTATTATAATATAGTT
1 TTTTTAATATAATTATTAT-ATATAGTT
*** *
36519 TTGAAAACTATTATTATATATAGTATAGTT
1 TTTTTAA-TATAATTAT-TATA-TATAGTT
36549 TTTTTAATATAATTATTATTATATA
1 TTTTTAATATAATTATTA-TATATA
36574 TAGCATAGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
28 10 0.24
29 18 0.43
30 14 0.33
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (27 bp):
TTTTTAATATAATTATTATATATAGTT
Found at i:36795 original size:27 final size:29
Alignment explanation
Indices: 36738--36795 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 29
36728 AGAGGTGCAC
* *
36738 AAAATATCCAAATATCCGATTTTGTGCAA
1 AAAATATCCAAATATCCGAATTTGGGCAA
* *
36767 AAAATATCCGAA-A-CCGAATTTGGGGAA
1 AAAATATCCAAATATCCGAATTTGGGCAA
36794 AA
1 AA
36796 CCGGTCTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 13 0.52
28 1 0.04
29 11 0.44
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.24
Consensus pattern (29 bp):
AAAATATCCAAATATCCGAATTTGGGCAA
Found at i:39038 original size:21 final size:21
Alignment explanation
Indices: 39014--39055 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
39004 AATTTATTTT
39014 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
39035 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
39056 AACTTGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:39092 original size:33 final size:33
Alignment explanation
Indices: 39050--39153 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
39040 TTTGTTTCAA
39050 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
* *
39083 TTATCGAACTTGAAAATTTTTAAATATTTGAAT
1 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
* *
39116 TTATCGAACTTGAAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
39148 TTATCG
1 TTATCG
39154 TAAACTTTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
32 6 0.09
33 59 0.91
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (33 bp):
TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
Found at i:39382 original size:21 final size:22
Alignment explanation
Indices: 39346--39387 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
39336 TGAAAAAAAA
39346 CCGGATCGAATAAAAA-CCGAT
1 CCGGATCGAATAAAAATCCGAT
* *
39367 CCGGATCGGATTAAAATCCGA
1 CCGGATCGAATAAAAATCCGA
39388 CTTCTGTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (22 bp):
CCGGATCGAATAAAAATCCGAT
Found at i:40697 original size:15 final size:15
Alignment explanation
Indices: 40677--40714 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
40667 AGAGCCTCTG
*
40677 AATCATTCAGCGCTT
1 AATCATTCAACGCTT
40692 AATCATTCAACGCTT
1 AATCATTCAACGCTT
40707 AATCATTC
1 AATCATTC
40715 TAAAGTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (15 bp):
AATCATTCAACGCTT
Found at i:42709 original size:14 final size:14
Alignment explanation
Indices: 42690--42716 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42680 ACCAGTTAAA
42690 GTTAATTAATTTTT
1 GTTAATTAATTTTT
42704 GTTAATTAATTTT
1 GTTAATTAATTTT
42717 CCTTTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
GTTAATTAATTTTT
Found at i:51415 original size:43 final size:42
Alignment explanation
Indices: 51355--51913 Score: 429
Period size: 44 Copynumber: 12.9 Consensus size: 42
51345 TACAAAAATG
* * * * *
51355 GTAAGGTCTTAACCTTGCATATAGCAAAAGAGCCTGGAAAACG
1 GTAAGG-CTTACCCTTGCACATAGCAAAGGAACCTGGAAAACT
* * * * *
51398 GTAAGGTCTTATCCTTGCACATAGTAGAGGAGCCTGGGAAACT
1 GTAAGG-CTTACCCTTGCACATAGCAAAGGAACCTGGAAAACT
*
51441 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAAACT
1 GTAAGGCTTACCCTTGCACATAGCAAAGGAACCT-GGAAAACT
* * *
51484 GTAAGGCTTACCCTTGCACACAGCAAATGAACCTGAGGAAACT
1 GTAAGGCTTACCCTTGCACATAGCAAAGGAACCTG-GAAAACT
* ** *
51527 GTAAGGCTTACCTTTGCACATAGCAAATAAACCTGGGGGAAACT
1 GTAAGGCTTACCCTTGCACATAGCAAAGGAACCT--GGAAAACT
* * *
51571 GTAAGGCTTACCCTTACACACAGCAAAGGAACCTGGGGGAAACT
1 GTAAGGCTTACCCTTGCACATAGCAAAGGAACCT--GGAAAACT
* * *
51615 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGGAAACT
1 GTAAGGCTTACCCTTGCACATAGCAAAGGAACCT--GGAAAACT
* * * **
51659 GTAAGGCATACCCTTGCACACAACAAATCAACCTAGGGAAAACT
1 GTAAGGCTTACCCTTGCACATAGCAAAGGAACCT--GGAAAACT
* * * * *
51703 GTAAGGCATACCCTTGCACACAACAAAGCAACCTAGGGGAAACT
1 GTAAGGCTTACCCTTGCACATAGCAAAGGAACCT--GGAAAACT
* * * * * *
51747 GTAAGGCTTACCCTTTCATACAACAAAGGAACCTGGGGGAAAGT
1 GTAAGGCTTACCCTTGCACATAGCAAAGGAACCT--GGAAAACT
* * * *
51791 GTAAGGCTTACCCGTT-CACACAACAAAGGAACTTGAGGGAAACT
1 GTAAGGCTTACCC-TTGCACATAGCAAAGGAACCT--GGAAAACT
* * ** * *
51835 TTAAGGCTTACCCATGCACGCAACAAAGGAACCTGGGGAAACT
1 GTAAGGCTTACCCTTGCACATAGCAAAGGAACCT-GGAAAACT
* ** * *
51878 GTAAGCCTTA-TTTTGCATACAGCAAAGGAACCTGGA
1 GTAAGGCTTACCCTTGCACATAGCAAAGGAACCTGGA
51914 GAAAACAGGG
Statistics
Matches: 454, Mismatches: 56, Indels: 14
0.87 0.11 0.03
Matches are distributed among these distances:
41 2 0.00
42 41 0.09
43 136 0.30
44 272 0.60
45 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (42 bp):
GTAAGGCTTACCCTTGCACATAGCAAAGGAACCTGGAAAACT
Found at i:51596 original size:44 final size:44
Alignment explanation
Indices: 51433--51912 Score: 619
Period size: 44 Copynumber: 11.0 Consensus size: 44
51423 AGAGGAGCCT
*
51433 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-G
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* * *
51476 GGAAAACTGTAAGGCTTACCCTTGCACACAGCAAATGAACCT-G
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* * * * **
51519 AGGAAACTGTAAGGCTTACCTTTGCACATAGCAAATAAACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* *
51563 GGGAAACTGTAAGGCTTACCCTTACACACAGCAAAGGAACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
51607 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* ** *
51651 GGGAAACTGTAAGGCATACCCTTGCACACAACAAATCAACCTAG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* * * *
51695 GGAAAACTGTAAGGCATACCCTTGCACACAACAAAGCAACCTAG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* *
51739 GGGAAACTGTAAGGCTTACCCTTTCATACAACAAAGGAACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* * *
51783 GGGAAAGTGTAAGGCTTACCCGTT-CACACAACAAAGGAACTTGA
1 GGGAAACTGTAAGGCTTACCC-TTGCACACAACAAAGGAACCTGG
* * *
51827 GGGAAACTTTAAGGCTTACCCATGCACGCAACAAAGGAACCT-G
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* ** * *
51870 GGGAAACTGTAAGCCTTA-TTTTGCATACAGCAAAGGAACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
51913 AGAAAACAGG
Statistics
Matches: 388, Mismatches: 45, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
42 17 0.04
43 96 0.25
44 273 0.70
45 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (44 bp):
GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
Found at i:52412 original size:10 final size:10
Alignment explanation
Indices: 52395--52531 Score: 61
Period size: 10 Copynumber: 13.2 Consensus size: 10
52385 AAAAATATTG
52395 AAAA-AAAAT
1 AAAACAAAAT
52404 AAAACAAAAT
1 AAAACAAAAT
52414 AAAACAAAAT
1 AAAACAAAAT
*
52424 AAATA-AAATGGT
1 AAA-ACAAA--AT
*
52436 AAAATAGAAAT
1 AAAACA-AAAT
*
52447 AAAACAAAAC
1 AAAACAAAAT
*
52457 AAAA-TAAAT
1 AAAACAAAAT
*
52466 AAAAATAAAAAT
1 -AAAA-CAAAAT
*
52478 AGAACAAAAAT
1 AAAAC-AAAAT
52489 AAGAACAAAGA-
1 AA-AACAAA-AT
*
52500 AAAA-ATAAT
1 AAAACAAAAT
*
52509 AAAA-AAAAG
1 AAAACAAAAT
52518 AAACACAAATAT
1 AAA-ACAAA-AT
52530 AA
1 AA
52532 CGAAAAGAGA
Statistics
Matches: 98, Mismatches: 14, Indels: 29
0.70 0.10 0.21
Matches are distributed among these distances:
8 1 0.01
9 19 0.19
10 35 0.36
11 25 0.26
12 16 0.16
13 2 0.02
ACGTcount: A:0.77, C:0.06, G:0.05, T:0.12
Consensus pattern (10 bp):
AAAACAAAAT
Found at i:52432 original size:5 final size:5
Alignment explanation
Indices: 52395--52475 Score: 60
Period size: 5 Copynumber: 15.8 Consensus size: 5
52385 AAAAATATTG
* *
52395 AAAA- AAAAT AAAAC AAAAT AAAAC AAAAT -AAAT AAAATGGT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA---T AAAAT
* *
52441 AGAAAT AAAAC AAAAC AAAAT -AAAT AAAAAT AAAA
1 A-AAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
52476 ATAGAACAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
4 12 0.19
5 37 0.59
6 9 0.14
8 5 0.08
ACGTcount: A:0.78, C:0.05, G:0.04, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:52464 original size:48 final size:50
Alignment explanation
Indices: 52357--52474 Score: 136
Period size: 48 Copynumber: 2.4 Consensus size: 50
52347 CATAAATATG
*
52357 AAAATAATAATCAAAA-AAATAACAAAGGAAAAATATTGAAAAAAAATAAAAC
1 AAAATAA-AA-CAAAATAAATAACAAAGGAAAAATA-TGAAAAAAAACAAAAC
* * *
52409 AAAATAAAACAAAATAAATAA-AATGGTAAAATA-GAAATAAAACAAAAC
1 AAAATAAAACAAAATAAATAACAAAGGAAAAATATGAAAAAAAACAAAAC
52457 AAAATAAATA-AAAATAAA
1 AAAATAAA-ACAAAATAAA
52475 AATAGAACAA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
48 29 0.48
49 1 0.02
50 15 0.25
51 8 0.13
52 7 0.12
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (50 bp):
AAAATAAAACAAAATAAATAACAAAGGAAAAATATGAAAAAAAACAAAAC
Found at i:52496 original size:38 final size:37
Alignment explanation
Indices: 52398--52513 Score: 116
Period size: 37 Copynumber: 3.1 Consensus size: 37
52388 AATATTGAAA
*
52398 AAAAATAAAAC-AAAATAAAACAAAATAAAT-AAAAT
1 AAAAATAGAACAAAAATAAAACAAAATAAATAAAAAT
* *
52433 GGTAAAATAGAA-ATAAAACAAAACAAAATAAATAAAAAT
1 --AAAAATAGAACA-AAAATAAAACAAAATAAATAAAAAT
*
52472 AAAAATAGAACAAAAATAAGAACAAAGA-AAA-AATAAT
1 AAAAATAGAACAAAAATAA-AACAAA-ATAAATAAAAAT
52509 AAAAA
1 AAAAA
52514 AAAGAAACAC
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
37 33 0.49
38 28 0.42
39 6 0.09
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (37 bp):
AAAAATAGAACAAAAATAAAACAAAATAAATAAAAAT
Found at i:52513 original size:37 final size:37
Alignment explanation
Indices: 52398--52481 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 37
52388 AATATTGAAA
* *
52398 AAAAATA-AAACAAAATAAAACAAAATAAAT-AAAAT
1 AAAAATAGAAATAAAACAAAACAAAATAAATAAAAAT
*
52433 GGTAAAATAGAAATAAAACAAAACAAAATAAATAAAAAT
1 --AAAAATAGAAATAAAACAAAACAAAATAAATAAAAAT
52472 AAAAATAGAA
1 AAAAATAGAA
52482 CAAAAATAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 15 0.37
38 21 0.51
39 5 0.12
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (37 bp):
AAAAATAGAAATAAAACAAAACAAAATAAATAAAAAT
Found at i:52582 original size:2 final size:2
Alignment explanation
Indices: 52577--52620 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
52567 AATAAAAATA
52577 AT AT AT AT AT AT AT AT AT AT A- AT GA- AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
52617 AT AT
1 AT AT
52621 TAATAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 3 0.08
2 34 0.89
3 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:52598 original size:21 final size:20
Alignment explanation
Indices: 52574--52625 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 20
52564 TTAAATAAAA
52574 ATAATATATATATATATATAT
1 ATAATATA-ATATATATATAT
*
52595 ATAAT-GAATATATATATAT
1 ATAATATAATATATATATAT
52614 ATAATATTAATA
1 ATAATA-TAATA
52626 ATAATAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 17 0.63
20 1 0.04
21 9 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATAATATAATATATATATAT
Found at i:52607 original size:15 final size:14
Alignment explanation
Indices: 52568--52631 Score: 64
Period size: 15 Copynumber: 4.6 Consensus size: 14
52558 AAAAAATTAA
*
52568 ATAAAAATA-ATAT
1 ATAATAATATATAT
52581 AT-ATATATATATAT
1 ATAATA-ATATATAT
52595 ATAATGAATATATAT
1 ATAAT-AATATATAT
52610 ATATATAATAT-TA-
1 ATA-ATAATATATAT
52623 ATAATAATA
1 ATAATAATA
52632 ATGACAACGG
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
12 8 0.18
13 8 0.18
14 8 0.18
15 18 0.40
16 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
ATAATAATATATAT
Found at i:52945 original size:3 final size:3
Alignment explanation
Indices: 52939--52973 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
52929 ATAAATGAGA
52939 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52974 ATGAGATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:61046 original size:14 final size:14
Alignment explanation
Indices: 61019--61052 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
61009 AATATTGAAA
61019 AAAATGAAAAAAAT
1 AAAATGAAAAAAAT
61033 AAAAT-AAAATAAAT
1 AAAATGAAAA-AAAT
61047 AAAATG
1 AAAATG
61053 GTAAAATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (14 bp):
AAAATGAAAAAAAT
Found at i:61104 original size:22 final size:21
Alignment explanation
Indices: 61016--61199 Score: 77
Period size: 22 Copynumber: 8.1 Consensus size: 21
61006 AAAAATATTG
*
61016 AAAAAAAT-GAAAAAAAT-AA
1 AAAAAAATAAAAAAAAATAAA
* **
61035 AATAAAATAAATAAAATGGTAAA
1 AAAAAAATAAA-AAAA-AATAAA
* * * *
61058 ATAGAAAT-AAACAAAACAAA
1 AAAAAAATAAAAAAAAATAAA
* *
61078 TAAAAAATAGAACAAAAATAAGA
1 AAAAAAATA-AAAAAAAATAA-A
61101 AAAAAAATAAAAAAAAATAAA
1 AAAAAAATAAAAAAAAATAAA
* *
61122 AAAAAACACAAATATAACGAAACGTGAA
1 AAAAAA-ATAAA-A-AA--AAA--TAAA
61150 AACAACAAATGAAATAAAAAATAAA
1 AA-AA-AAAT-AAA-AAAAAATAAA
*
61175 ATAAAAATAAAAATAAGAATAAA
1 AAAAAAATAAAAA-AA-AATAAA
61198 AA
1 AA
61200 TAATAGATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 34
0.67 0.14 0.19
Matches are distributed among these distances:
19 7 0.06
20 9 0.07
21 16 0.13
22 30 0.25
23 28 0.23
24 4 0.03
25 4 0.03
26 3 0.02
27 3 0.02
28 5 0.04
29 5 0.04
30 7 0.06
ACGTcount: A:0.76, C:0.05, G:0.06, T:0.13
Consensus pattern (21 bp):
AAAAAAATAAAAAAAAATAAA
Found at i:61112 original size:9 final size:9
Alignment explanation
Indices: 61016--61126 Score: 64
Period size: 9 Copynumber: 11.8 Consensus size: 9
61006 AAAAATATTG
*
61016 AAAAAAATG
1 AAAAAAATA
61025 AAAAAAATA
1 AAAAAAATA
61034 AAATAAAATA
1 AAA-AAAATA
*
61044 AATAAAAT-
1 AAAAAAATA
***
61052 GGTAAAATA
1 AAAAAAATA
* *
61061 GAAATAAACA
1 -AAAAAAATA
*
61071 AAACAAATA
1 AAAAAAATA
61080 AAAAATAGA-A
1 AAAAA-A-ATA
*
61090 CAAAAATAAGA
1 -AAAAA-AATA
61101 AAAAAAATAA
1 AAAAAAAT-A
61111 AAAAAAATA
1 AAAAAAATA
61120 AAAAAAA
1 AAAAAAA
61127 ACACAAATAT
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
8 6 0.07
9 37 0.46
10 29 0.36
11 9 0.11
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (9 bp):
AAAAAAATA
Found at i:61182 original size:18 final size:19
Alignment explanation
Indices: 61161--61202 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
61151 ACAACAAATG
61161 AAATAAAAAATAA-AATAA
1 AAATAAAAAATAAGAATAA
61179 AAAT-AAAAATAAGAATAA
1 AAATAAAAAATAAGAATAA
61197 AAATAA
1 AAATAA
61203 TAGATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 13 0.59
19 1 0.05
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (19 bp):
AAATAAAAAATAAGAATAA
Found at i:61187 original size:12 final size:12
Alignment explanation
Indices: 61161--61202 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
61151 ACAACAAATG
61161 AAATAAAAA-ATA
1 AAATAAAAATA-A
61173 AAATAAAAATAA
1 AAATAAAAATAA
*
61185 AAATAAGAATAA
1 AAATAAAAATAA
61197 AAATAA
1 AAATAA
61203 TAGATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 27 0.96
13 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (12 bp):
AAATAAAAATAA
Found at i:61225 original size:30 final size:29
Alignment explanation
Indices: 61187--61248 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
61177 AAAAATAAAA
61187 ATAAGAATAAAAATA-ATAGATATATATAT
1 ATAAGAATAAAAA-ACATAGATATATATAT
*
61216 ATAATGAATAAAAAACATATATATATATAT
1 ATAA-GAATAAAAAACATAGATATATATAT
61246 ATA
1 ATA
61249 TATATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (29 bp):
ATAAGAATAAAAAACATAGATATATATAT
Found at i:61237 original size:2 final size:2
Alignment explanation
Indices: 61232--61271 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
61222 AATAAAAAAC
61232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61272 TAATAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61280 original size:12 final size:12
Alignment explanation
Indices: 61206--61282 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 12
61196 AAAATAATAG
61206 ATATATATATATA
1 ATATATA-ATATA
*
61219 ATGA-ATAA-AAA
1 AT-ATATAATATA
*
61230 ACATAT-ATATA
1 ATATATAATATA
61241 TATATATATATATA
1 -ATATATA-ATATA
61255 TATATATAATATA
1 -ATATATAATATA
61268 ATAT-TAATAATA
1 ATATATAAT-ATA
61280 ATA
1 ATA
61283 ATGACAATGG
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
10 2 0.04
11 11 0.21
12 16 0.30
13 10 0.19
14 14 0.26
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (12 bp):
ATATATAATATA
Found at i:61652 original size:3 final size:3
Alignment explanation
Indices: 61644--61707 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
61634 ATAAACAAAA
* *
61644 AAT AAT AAT AAGT AAT CA- AAT AAA AAT AA- AAT AA- ACA- AAT AAAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT -AAT
61688 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
61708 AATGATTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 5 0.10
3 40 0.78
4 6 0.12
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:61760 original size:8 final size:8
Alignment explanation
Indices: 61747--61806 Score: 61
Period size: 8 Copynumber: 7.8 Consensus size: 8
61737 GTAACTATAT
61747 TATATAAA
1 TATATAAA
61755 TATAT--A
1 TATATAAA
*
61761 TATATATA
1 TATATAAA
*
61769 TATATATA
1 TATATAAA
*
61777 TATATATA
1 TATATAAA
61785 TATATAAA
1 TATATAAA
* *
61793 AATAAAAA
1 TATATAAA
61801 TATATA
1 TATATA
61807 CAAAAATGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
6 6 0.13
8 39 0.87
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TATATAAA
Found at i:61806 original size:2 final size:2
Alignment explanation
Indices: 61742--61790 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
61732 ATAATGTAAC
*
61742 TA TA T- TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61783 TA TA TA TA
1 TA TA TA TA
61791 AAAATAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:61848 original size:18 final size:18
Alignment explanation
Indices: 61827--61866 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
61817 AGGTAAAAAC
61827 AAATAAACAAATA-AAATA
1 AAATAAA-AAATATAAATA
*
61845 AAATAAAAAATATATATA
1 AAATAAAAAATATAAATA
61863 AAAT
1 AAAT
61867 GTCAGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAAAAATATAAATA
Found at i:61893 original size:52 final size:53
Alignment explanation
Indices: 61790--61901 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 53
61780 ATATATATAT
* *
61790 AAAAAT-AAAAATATATACAAAAATGTTAGGTAAAAACAAATAAACAAATAAA
1 AAAAATAAAAAATATATACAAAAATGTCAGATAAAAACAAATAAACAAATAAA
* * * * *
61842 ATAAAATAAAAAATATATA-TAAAATGTCAGAT-TAAATAAATAAATATATAAA
1 A-AAAATAAAAAATATATACAAAAATGTCAGATAAAAACAAATAAACAAATAAA
61894 AAAAATAA
1 AAAAATAA
61902 TTAAATCGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
51 7 0.14
52 18 0.35
53 15 0.29
54 11 0.22
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (53 bp):
AAAAATAAAAAATATATACAAAAATGTCAGATAAAAACAAATAAACAAATAAA
Found at i:61904 original size:29 final size:30
Alignment explanation
Indices: 61845--61907 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
61835 AAATAAAATA
* **
61845 AAATAAAAAATATATATAAAATGTCAGATT
1 AAATAAAAAATATATAAAAAAAATCAGATT
61875 AAATAAATAAATATATAAAAAAAAT-A-ATT
1 AAATAAA-AAATATATAAAAAAAATCAGATT
61904 AAAT
1 AAAT
61908 CGTAAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 7 0.24
30 8 0.28
31 14 0.48
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATAAAAAATATATAAAAAAAATCAGATT
Found at i:62940 original size:2 final size:2
Alignment explanation
Indices: 62927--62990 Score: 75
Period size: 2 Copynumber: 34.0 Consensus size: 2
62917 TGTAACCCAA
*
62927 AT AT AT AA AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62967 AT A- AT AT AT -T AT AT GAT AT A- AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT
62991 TGATGGACAA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
1 5 0.09
2 47 0.87
3 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:62954 original size:23 final size:25
Alignment explanation
Indices: 62928--62980 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 25
62918 GTAACCCAAA
62928 TATATAAATATAT-ATAT-ATATAT
1 TATATAAATATATAATATAATATAT
*
62951 TATATATATATATAATATAATATAT
1 TATATAAATATATAATATAATATAT
62976 TATAT
1 TATAT
62981 GATATAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 12 0.44
24 4 0.15
25 11 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TATATAAATATATAATATAATATAT
Found at i:62955 original size:25 final size:25
Alignment explanation
Indices: 62927--62990 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
62917 TGTAACCCAA
62927 ATATATAAATAT-ATATATATATATT
1 ATATATAAATATAATATA-ATATATT
*
62952 ATATATATATATAATATAATATATT
1 ATATATAAATATAATATAATATATT
62977 ATATGATATAATAT
1 ATAT-ATA-AATAT
62991 TGATGGACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 22 0.65
26 8 0.24
27 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
ATATATAAATATAATATAATATATT
Found at i:62957 original size:17 final size:18
Alignment explanation
Indices: 62929--62990 Score: 83
Period size: 18 Copynumber: 3.5 Consensus size: 18
62919 TAACCCAAAT
62929 ATATAA-ATATATATATA
1 ATATAATATATATATATA
*
62946 TATATTATATATATATATA
1 -ATATAATATATATATATA
*
62965 ATATAATATAT-TATATG
1 ATATAATATATATATATA
62982 ATATAATAT
1 ATATAATAT
62991 TGATGGACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
17 14 0.35
18 15 0.38
19 11 0.28
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAATATATATATATA
Found at i:67758 original size:129 final size:129
Alignment explanation
Indices: 67534--68088 Score: 555
Period size: 129 Copynumber: 4.3 Consensus size: 129
67524 AATTCCATTT
* *** * * *
67534 TCTATCTTGATCTGACCTACCCTGAAGAGCAATTGAGCAAATCATGTTTTCTTTGAATCTGACTT
1 TCTATCTTGATCTAACCTACCCTGAAGAGCAGCAGAGCAAATCCTCTTTTCTTTGAATCTGACCT
* * * * * * ** *
67599 ACCCT-AAAAAGTAACAAATCATATTCCATTAGATTTGACCTACCCTGAAGAGTAGTGGAGTAAA
66 ACCTTGAAGAA-CAACGAAGCAGATTCCATTAGATTTGACCTACCCTGAAGAGTAGTAAAGCAAA
* *
67663 TCTATCTTAATCAAACCTACCCTGAAGAGCAGCAGAGCAAATCCTCTTTTCTTTGAATCTGACCT
1 TCTATCTTGATCTAACCTACCCTGAAGAGCAGCAGAGCAAATCCTCTTTTCTTTGAATCTGACCT
* * *
67728 ACCTTGAAGAACAACGAAGCAGATTTCATTAGATTTGACCTACCCTGAAGAGTAATAGAGCAAA
66 ACCTTGAAGAACAACGAAGCAGATTCCATTAGATTTGACCTACCCTGAAGAGTAGTAAAGCAAA
* * * ** * *
67792 TTTATCTTGATTTGACCTACCCTGAAGAGCA--ATGCAGCATGTCC-CTTTTTCTTTAAATCTTA
1 TCTATCTTGATCTAACCTACCCTGAAGAGCAGCA-G-AGCAAATCCTC-TTTTCTTTGAATCTGA
** * ** * * *
67854 TATGCCTTGAAGAGTAGC-ATAGCACATTCCA-TAGATTTGACCTACCCTGAAGAGTAGTAAGGC
63 CCTACCTTGAAGAACAACGA-AGCAGATTCCATTAGATTTGACCTACCCTGAAGAGTAGTAAAGC
67917 AAA
127 AAA
* * * * * *
67920 TCTATCTTGATCTAACATACCCTGAAGAACAGCGGAGCATATCCCCTTTTCTTTGAATTTGACCT
1 TCTATCTTGATCTAACCTACCCTGAAGAGCAGCAGAGCAAATCCTCTTTTCTTTGAATCTGACCT
* * * * * *
67985 ACCTTGAAGAGCAGCGGAGCAGATTCCATTAGATTTGACATACCATGAAGAGTAGTAAAGTAAA
66 ACCTTGAAGAACAACGAAGCAGATTCCATTAGATTTGACCTACCCTGAAGAGTAGTAAAGCAAA
* * *
68049 TCTATCTTGAATCTAACCTACCCTAAAGAGAAGCGGAGCA
1 TCTATCTTG-ATCTAACCTACCCTGAAGAGCAGCAGAGCA
68089 GATTCCATTA
Statistics
Matches: 352, Mismatches: 63, Indels: 21
0.81 0.14 0.05
Matches are distributed among these distances:
127 1 0.00
128 106 0.30
129 215 0.61
130 30 0.09
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (129 bp):
TCTATCTTGATCTAACCTACCCTGAAGAGCAGCAGAGCAAATCCTCTTTTCTTTGAATCTGACCT
ACCTTGAAGAACAACGAAGCAGATTCCATTAGATTTGACCTACCCTGAAGAGTAGTAAAGCAAA
Found at i:67804 original size:41 final size:41
Alignment explanation
Indices: 67630--67824 Score: 133
Period size: 41 Copynumber: 4.6 Consensus size: 41
67620 TATTCCATTA
* * * * *
67630 GATTTGACCTACCCTGAAGAGTAGTGGAGTAAATCTATCTT
1 GATTTGACCTACCCTGAAGAGCAATAGAGCAAATTTATCTT
* *** ** *
67671 AATCAAACCTACCCTGAAGAGCAGCAGAGCAAATCCTCTTTTCTTT
1 GATTTGACCTACCCTGAAGAGCAATAGAGCAAA---T-TTATC-TT
* * * * * *
67717 GAATCTGACCTACCTTGAAGAACAA-CGAAGCAGATTTCAT-TA
1 G-ATTTGACCTACCCTGAAGAGCAATAG-AGCAAATTT-ATCTT
*
67759 GATTTGACCTACCCTGAAGAGTAATAGAGCAAATTTATCTT
1 GATTTGACCTACCCTGAAGAGCAATAGAGCAAATTTATCTT
67800 GATTTGACCTACCCTGAAGAGCAAT
1 GATTTGACCTACCCTGAAGAGCAAT
67825 GCAGCATGTC
Statistics
Matches: 116, Mismatches: 28, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
40 2 0.02
41 77 0.66
42 3 0.03
43 2 0.02
44 3 0.03
45 3 0.03
46 3 0.03
47 23 0.20
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (41 bp):
GATTTGACCTACCCTGAAGAGCAATAGAGCAAATTTATCTT
Found at i:68084 original size:83 final size:83
Alignment explanation
Indices: 67972--68170 Score: 274
Period size: 83 Copynumber: 2.4 Consensus size: 83
67962 CCCCTTTTCT
* * * *
67972 TTGAATTTGACCTACCTTGAAGAGCAGCGGAGCAGATTCCATTAGATTTGACATACCATGAAGAG
1 TTGAATATAACCTACCTTGAAGAGAAGCGGAGCAGATTCCATTAAATTTGACATACCATGAAGAG
*
68037 TAGTAAAGTAAATCTATC
66 TAGTAAAGCAAATCTATC
* * * * *
68055 TTGAATCTAACCTACCCTAAAGAGAAGCGGAGCAGATTCCATTAAATTTGACCTACCCTGAAGAG
1 TTGAATATAACCTACCTTGAAGAGAAGCGGAGCAGATTCCATTAAATTTGACATACCATGAAGAG
*
68120 TAGTAGAGCAAATCTATC
66 TAGTAAAGCAAATCTATC
* *
68138 TTG-ATATAACCTACCTTGAAGAGTAGCGAAGCA
1 TTGAATATAACCTACCTTGAAGAGAAGCGGAGCA
68171 TATCCCCTTT
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
82 25 0.25
83 76 0.75
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (83 bp):
TTGAATATAACCTACCTTGAAGAGAAGCGGAGCAGATTCCATTAAATTTGACATACCATGAAGAG
TAGTAAAGCAAATCTATC
Found at i:68129 original size:41 final size:41
Alignment explanation
Indices: 67975--68129 Score: 123
Period size: 41 Copynumber: 3.8 Consensus size: 41
67965 CTTTTCTTTG
* * *
67975 AATTTGACCTACCTTGAAGAGCAGCGGAGCAGATTCCATTA
1 AATTTGACCTACCCTGAAGAGTAGCAGAGCAGATTCCATTA
* * * * * * * * *
68016 GATTTGACATACCATGAAGAGTAGTAAAGTA-AATCTATCTTG
1 AATTTGACCTACCCTGAAGAGTAGCAGAGCAGATTCCA--TTA
* * * * *
68058 AATCTAACCTACCCTAAAGAGAAGCGGAGCAGATTCCATTA
1 AATTTGACCTACCCTGAAGAGTAGCAGAGCAGATTCCATTA
*
68099 AATTTGACCTACCCTGAAGAGTAGTAGAGCA
1 AATTTGACCTACCCTGAAGAGTAGCAGAGCA
68130 AATCTATCTT
Statistics
Matches: 80, Mismatches: 31, Indels: 6
0.68 0.26 0.05
Matches are distributed among these distances:
40 4 0.05
41 50 0.62
42 22 0.28
43 4 0.05
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (41 bp):
AATTTGACCTACCCTGAAGAGTAGCAGAGCAGATTCCATTA
Found at i:68150 original size:41 final size:41
Alignment explanation
Indices: 68025--68163 Score: 118
Period size: 41 Copynumber: 3.4 Consensus size: 41
68015 AGATTTGACA
* * * *
68025 TACCATGAAGAGTAGTAAAGTAAATCTATCTTGAATCTAACC
1 TACCCTGAAGAGTAGTAGAGCAAATCTATCTTG-ATATAACC
* * ** * * ** * *
68067 TACCCTAAAGAGAAGCGGAGCAGATTCCAT-TAAATTTGACC
1 TACCCTGAAGAGTAGTAGAGCA-AATCTATCTTGATATAACC
68108 TACCCTGAAGAGTAGTAGAGCAAATCTATCTTGATATAACC
1 TACCCTGAAGAGTAGTAGAGCAAATCTATCTTGATATAACC
*
68149 TACCTTGAAGAGTAG
1 TACCCTGAAGAGTAG
68164 CGAAGCATAT
Statistics
Matches: 71, Mismatches: 24, Indels: 5
0.71 0.24 0.05
Matches are distributed among these distances:
40 5 0.07
41 45 0.63
42 16 0.23
43 5 0.07
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (41 bp):
TACCCTGAAGAGTAGTAGAGCAAATCTATCTTGATATAACC
Found at i:68298 original size:40 final size:41
Alignment explanation
Indices: 68191--68298 Score: 112
Period size: 41 Copynumber: 2.7 Consensus size: 41
68181 TCTTTGAATA
* * * * *
68191 TGACCTACCCTGAAGATCAATGGAGCATATTCCTTTAGATT
1 TGACCTACCCTAAAGAGCAATGGAGCAAATTCATCTAGATT
* * * *
68232 TGACCTACCCTAAAGAGTATTCGAGCAAATTTATCTAG-TT
1 TGACCTACCCTAAAGAGCAATGGAGCAAATTCATCTAGATT
68272 TGACCTACCC-ATAAGAGCAATGGAGCA
1 TGACCTACCCTA-AAGAGCAATGGAGCA
68299 TATCTTTCTT
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
39 1 0.02
40 24 0.44
41 29 0.54
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (41 bp):
TGACCTACCCTAAAGAGCAATGGAGCAAATTCATCTAGATT
Found at i:68524 original size:21 final size:21
Alignment explanation
Indices: 68494--68535 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
68484 GCTATATTAT
68494 ATATAATAAA-TATATGTATAG
1 ATATAATAAAGTATA-GTATAG
*
68515 ATATATTAAAGTATAGTATAG
1 ATATAATAAAGTATAGTATAG
68536 TTTTTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (21 bp):
ATATAATAAAGTATAGTATAG
Found at i:68589 original size:30 final size:31
Alignment explanation
Indices: 68526--68652 Score: 118
Period size: 30 Copynumber: 4.1 Consensus size: 31
68516 TATATTAAAG
* * *
68526 TATAGTATAGTTTTTGAAAATAATTA-T-TA
1 TATAATATAGTTTTTAAAAACAATTATTATA
* *
68555 TATAATATAG-TTTTGAAAACCATTATTATA
1 TATAATATAGTTTTTAAAAACAATTATTATA
*
68585 TATAATATAGTTTTTTTAAAATAATAATTATTATA
1 TATAATATAG--TTTTT-AAA-AACAATTATTATA
* *
68620 TATAATATAG-TTTCAAAAACAATTATTACA
1 TATAATATAGTTTTTAAAAACAATTATTATA
68650 TAT
1 TAT
68653 TAAGTATTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
28 13 0.16
29 10 0.12
30 26 0.32
31 3 0.04
32 3 0.04
33 4 0.05
34 2 0.02
35 21 0.26
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (31 bp):
TATAATATAGTTTTTAAAAACAATTATTATA
Found at i:68708 original size:11 final size:10
Alignment explanation
Indices: 68679--68717 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
68669 TAAATATTTT
*
68679 TTTTATTTTA
1 TTTTATTTCA
*
68689 CTTTATTTCA
1 TTTTATTTCA
68699 TTTCTATTTCA
1 TTT-TATTTCA
68710 TTTTATTT
1 TTTTATTT
68718 GTTTACTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATTTCA
Found at i:69620 original size:36 final size:38
Alignment explanation
Indices: 69556--69632 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
69546 TTTTTATATT
69556 TTTAATTTTGTAAAACAAATTATATAAATATTATG-AA
1 TTTAATTTTGTAAAACAAATTATATAAATATTATGCAA
* *
69593 TTTAATTTTTTAAAGA-AAA-TATATAAATATTTTGCAA
1 TTTAATTTTGTAAA-ACAAATTATATAAATATTATGCAA
69630 TTT
1 TTT
69633 GTAATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 14 0.39
37 21 0.58
38 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (38 bp):
TTTAATTTTGTAAAACAAATTATATAAATATTATGCAA
Found at i:76620 original size:18 final size:17
Alignment explanation
Indices: 76565--76684 Score: 107
Period size: 17 Copynumber: 6.9 Consensus size: 17
76555 ATGTTTACAG
*
76565 TTTACAGTTAT-ATGACA
1 TTTACAGTTATCA-GATA
* * *
76582 TTTCACATTTATTATATA
1 TTT-ACAGTTATCAGATA
76600 TTTACAGTTATCAGATGA
1 TTTACAGTTATCAGAT-A
* * *
76618 TTTTCAATCATCAGATA
1 TTTACAGTTATCAGATA
*
76635 TTTACAGTTATCAGATGT
1 TTTACAGTTATCAGAT-A
* *
76653 TTTTCAGTTATAAGATA
1 TTTACAGTTATCAGATA
76670 TTTACAGTTATCAGA
1 TTTACAGTTATCAGA
76685 CGTAGATTAA
Statistics
Matches: 81, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
17 40 0.49
18 40 0.49
19 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (17 bp):
TTTACAGTTATCAGATA
Found at i:76636 original size:35 final size:35
Alignment explanation
Indices: 76597--76684 Score: 140
Period size: 35 Copynumber: 2.5 Consensus size: 35
76587 CATTTATTAT
*
76597 ATATTTACAGTTATCAGATGATTTTCAATCATCAG
1 ATATTTACAGTTATCAGATGATTTTCAATCATAAG
* * *
76632 ATATTTACAGTTATCAGATGTTTTTCAGTTATAAG
1 ATATTTACAGTTATCAGATGATTTTCAATCATAAG
76667 ATATTTACAGTTATCAGA
1 ATATTTACAGTTATCAGA
76685 CGTAGATTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (35 bp):
ATATTTACAGTTATCAGATGATTTTCAATCATAAG
Found at i:79089 original size:114 final size:114
Alignment explanation
Indices: 78378--79090 Score: 785
Period size: 114 Copynumber: 6.3 Consensus size: 114
78368 TAATATTTAA
* * ** * * *
78378 AAATGAAAAAGAATCTTAACTATTCACATCTTTTTATATTCAGTGAAATATCACCTTAAATTAGA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
* * * *
78443 ACTTCTTTCATATTGAATGAAAAATCTTATCTAGCATAATAATGATTTC
66 ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * * * * * *
78492 AAATGATAGAGAATCTTAAATATTAATGCCCCTTTGTATTCAGTGAAATAT-ATCTTAAATCAAA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
* * * * * *
78556 ACTTTTTTTTATATTAAATGAAAATTTTTATCTGGTATAATAATAATTTC
66 AC-TTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * * * * * *
78606 AAATTACAGAGAATCTTAACTTTTTATGT-CTTTT-T-TTC-GTAAAATTTCACCTCAAATAAGA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
* *
78667 ACTTATTTCATATTGAATGAAAAATCTTATCTGGTATAATAAT-ATTTC
66 ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * ** * * * * *
78715 AAATGAAAGAGAATCTTAACTAATCACATCCTTTTGTATTAATTAAAATAACACCTTAAATCAAA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
* ** *
78780 ACTTCTTTCATATTGAATGAACAATCTTATAAGGTACAATAACAATTTC
66 ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* *
78829 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTCAAATAAGA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
*
78894 ACTT-TTTCTATATTGAATGAAAAATCTTATTTGGTACAATAATAATTTC
66 ACTTCTTTC-ATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * ** * * * * * *
78943 AAATGATAGAGAATGTTAACTATTCACATCTTTTTCTTTTCAGTGATATATTACTTTAAATCAGA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
* **
79008 ACTTGTTTCATATTGAATGAAAAATCTTATC-GGTACAATAATAACCTC
66 ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
*
79056 AAATGACAGAGAATCTTAACTATTCATGTTCTTTT
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTT
79091 CTTTTTAGTG
Statistics
Matches: 495, Mismatches: 95, Indels: 19
0.81 0.16 0.03
Matches are distributed among these distances:
109 27 0.05
110 48 0.10
111 15 0.03
112 3 0.01
113 118 0.24
114 280 0.57
115 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (114 bp):
AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
Found at i:79796 original size:21 final size:20
Alignment explanation
Indices: 79772--79841 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
79762 TAGTATCTAG
*
79772 AATCACAAAGTGGCTCGATAT
1 AATCACAAAGAGGC-CGATAT
79793 AATCACAAAGAGGCCCGATAT
1 AATCACAAAGAGG-CCGATAT
*
79814 ATTCACAAAGAGGCCTGATAT
1 AATCACAAAGAGGCC-GATAT
79835 AATCACA
1 AATCACA
79842 CAATAACAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 2 0.05
21 41 0.93
22 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCACAAAGAGGCCGATAT
Found at i:80762 original size:19 final size:19
Alignment explanation
Indices: 80738--80788 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
80728 GAAAATATTC
80738 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
80757 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
80776 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
80789 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:80830 original size:65 final size:64
Alignment explanation
Indices: 80632--80839 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
80622 GCACCAAGTG
* *
80632 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
80696 -
64 A
*
80696 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
80758 GA
63 GA
* * * *
80760 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
80824 GA
63 GA
*
80826 TGCATCGGTGCATG
1 TGCATCGATGCATG
80840 CCTTTGAATA
Statistics
Matches: 125, Mismatches: 8, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
63 10 0.08
64 46 0.37
65 65 0.52
66 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:87286 original size:22 final size:21
Alignment explanation
Indices: 87244--87283 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
87234 GAGTTTGTTT
*
87244 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
87265 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
87284 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:89258 original size:64 final size:63
Alignment explanation
Indices: 89190--89370 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 63
89180 TTGGAACACT
* ***
89190 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
89254 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
89318 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
89371 CAATTAATTC
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
64 54 0.55
65 45 0.45
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:89342 original size:19 final size:19
Alignment explanation
Indices: 89318--89368 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
89308 GAAAATATTC
89318 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
89337 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
89356 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
89369 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:89344 original size:65 final size:65
Alignment explanation
Indices: 89211--89370 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 65
89201 TGCACCAAGT
* ***
89211 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
89275 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
89339 A
65 A
* *
89340 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
89371 CAATTAATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:91676 original size:2 final size:2
Alignment explanation
Indices: 91669--91701 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
91659 GATTAAAGTT
91669 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
91702 TGTGTTTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92442 original size:17 final size:17
Alignment explanation
Indices: 92420--92455 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
92410 GTTAAATGTT
* *
92420 TGTAATGTGTAATTTAA
1 TGTAATGCGTAATGTAA
92437 TGTAATGCGTAATGTAA
1 TGTAATGCGTAATGTAA
92454 TG
1 TG
92456 CAATATAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (17 bp):
TGTAATGCGTAATGTAA
Found at i:93948 original size:22 final size:25
Alignment explanation
Indices: 93907--93954 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
93897 TAAAAAAAAT
93907 AAAAATATATTACTAATTT-ATAAA
1 AAAAATATATTACTAATTTAATAAA
*
93931 AAAAAT-TATTA-TACTTTAATAAA
1 AAAAATATATTACTAATTTAATAAA
93954 A
1 A
93955 TTTGTCACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 11 0.50
24 6 0.27
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAAATATATTACTAATTTAATAAA
Found at i:96962 original size:36 final size:36
Alignment explanation
Indices: 96915--96985 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
96905 TTGAACTTAA
*
96915 GTTTATCAATGGAGGATGCTTCCCATGAGCCAATAG
1 GTTTATCAATGGAGGATGCTGCCCATGAGCCAATAG
96951 GTTTATCAATGGAGGATGCTGCCCATGAGCCAATA
1 GTTTATCAATGGAGGATGCTGCCCATGAGCCAATA
96986 ATAAGTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (36 bp):
GTTTATCAATGGAGGATGCTGCCCATGAGCCAATAG
Found at i:100675 original size:69 final size:71
Alignment explanation
Indices: 100588--100727 Score: 250
Period size: 69 Copynumber: 2.0 Consensus size: 71
100578 TTTGTCAGTT
100588 GCATTCTCTTCCTCTAACTCCCTGA-GTACTGGAGCACACATCATCTGACGTATCAAA-TCAACA
1 GCATTCTCTTCCTCTAACTCCCTGATGTACTGGAGCACAC-TCATCTGACGTATCAAACTCAACA
100651 CCTATAA
65 CCTATAA
100658 GCATTCT-TTCCTCTAACTCCCTGATGTACTGGAGCACACTCATCTGACGTATCAAACTCAACAC
1 GCATTCTCTTCCTCTAACTCCCTGATGTACTGGAGCACACTCATCTGACGTATCAAACTCAACAC
100722 CTATAA
66 CTATAA
100728 TTCTATTGGT
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
69 34 0.50
70 34 0.50
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.28
Consensus pattern (71 bp):
GCATTCTCTTCCTCTAACTCCCTGATGTACTGGAGCACACTCATCTGACGTATCAAACTCAACAC
CTATAA
Found at i:102421 original size:39 final size:39
Alignment explanation
Indices: 102367--102496 Score: 156
Period size: 39 Copynumber: 3.3 Consensus size: 39
102357 AAGGGCCTAG
* *
102367 GGTAAGGACTTACCCTATGCACAAAGCAGAGGA-TATTGC
1 GGTAAGGACTTACCCTATGCACAAAGTAGAGGAGT-CTGC
*
102406 GGTAA-GAGCTTACCCTATGCACAAAGTAGAGGAGTCTGT
1 GGTAAGGA-CTTACCCTATGCACAAAGTAGAGGAGTCTGC
* * **
102445 GGTAAGGACTTACCCTATGAACAAAGTAGAGGAGCCTAT
1 GGTAAGGACTTACCCTATGCACAAAGTAGAGGAGTCTGC
*
102484 GGTAAGGTCTTAC
1 GGTAAGGACTTAC
102497 AAGTCATAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
38 2 0.02
39 76 0.94
40 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.22
Consensus pattern (39 bp):
GGTAAGGACTTACCCTATGCACAAAGTAGAGGAGTCTGC
Found at i:103433 original size:27 final size:26
Alignment explanation
Indices: 103403--103477 Score: 62
Period size: 26 Copynumber: 2.8 Consensus size: 26
103393 CATTCTAGAA
103403 CTCGCAGGTATTTCAATCATTTTAAAG
1 CTCG-AGGTATTTCAATCATTTTAAAG
* ** *
103430 CTCGATGGTACTT-GGTCATTTTGAAG
1 CTCGA-GGTATTTCAATCATTTTAAAG
* *
103456 CTTGGGGGTATTTCAATCATTT
1 C-TCGAGGTATTTCAATCATTT
103478 AATCAATTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
26 18 0.50
27 18 0.50
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (26 bp):
CTCGAGGTATTTCAATCATTTTAAAG
Found at i:110070 original size:30 final size:29
Alignment explanation
Indices: 110025--110090 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 29
110015 TCAACAGTCA
110025 AAATCAATGTGGTCAACGGTGATTGACGG
1 AAATCAATGTGGTCAACGGTGATTGACGG
110054 AAATCAATGTTGGTCAACGGTGATTGACGG
1 AAATCAATG-TGGTCAACGGTGATTGACGG
*
110084 CAATCAA
1 AAATCAA
110091 CGGTCAATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 9 0.26
30 26 0.74
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24
Consensus pattern (29 bp):
AAATCAATGTGGTCAACGGTGATTGACGG
Done.