Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006537.1 Hibiscus syriacus cultivar Beakdansim tig00015959_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: 372459
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 2
Found at i:1208 original size:22 final size:20
Alignment explanation
Indices: 1183--1222 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1173 GGTCAACGCC
1183 GGTCAAAGTTCTGGTCAACAGT
1 GGTCAAAG-TC-GGTCAACAGT
*
1205 GGTCAACGTCGGTCAACA
1 GGTCAAAGTCGGTCAACA
1223 ATCAACGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.23
Consensus pattern (20 bp):
GGTCAAAGTCGGTCAACAGT
Found at i:1301 original size:29 final size:27
Alignment explanation
Indices: 1257--1382 Score: 79
Period size: 29 Copynumber: 4.6 Consensus size: 27
1247 GTCGACCATT
1257 TTACACAAA-TATCACCCTAACAAATTAA
1 TTACA-AAATTATCACCCT-ACAAATTAA
*
1285 TTACAAAATTAGTCACCTTCTACAAA-TAT
1 TTACAAAATTA-TCACC--CTACAAATTAA
* *
1314 TTACAAAACTAACA-CC--CAAATT--
1 TTACAAAATTATCACCCTACAAATTAA
1336 TTACACAAA-TATCACCCTAACAGTAATTAA
1 TTACA-AAATTATCACCCT-ACA--AATTAA
*
1366 TTACAAAATTAACACCC
1 TTACAAAATTATCACCC
1383 CCTACGTGCA
Statistics
Matches: 78, Mismatches: 5, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
22 9 0.12
23 9 0.12
24 1 0.01
25 1 0.01
26 2 0.03
27 4 0.05
28 13 0.17
29 20 0.26
30 17 0.22
31 2 0.03
ACGTcount: A:0.47, C:0.25, G:0.02, T:0.27
Consensus pattern (27 bp):
TTACAAAATTATCACCCTACAAATTAA
Found at i:17156 original size:287 final size:284
Alignment explanation
Indices: 16628--17169 Score: 913
Period size: 284 Copynumber: 1.9 Consensus size: 284
16618 GAAAAAAAAG
*
16628 ATATTTTAAATTTAGATAAATTTAGAATGGATTTATCTGAGTTTAATATTTAAATGATTTATATT
1 ATATTTTAAATTTAAATAAATTTAGAATGGATTTATCTGAGTTTAATATTTAAATGATTTATATT
* *
16693 TGAATACAAAAGGACACGCCAAATGACAAAAATTCTTATAACTAATTAATAAATATATAGCAAAA
66 TGAATACAAAAGGACACGCCAAATGACAAAAATCCTTATAACTAATTAATAAATATATAACAAAA
* *
16758 TAACAACAAAAGAGGAAGGAAAGTTATATTATACCTGTCAAGTTGTTATTCGAAAAATCAATCAT
131 TAACAAAAAAAGAGGAAGGAAAGTTATATTATACCTGTCAAGTTGTTATTCGAAAAATCAATAAT
* * * *
16823 TTCTAGAGAAATTATATTTTCGATAATTGATGGAATTGTACCTGAAATGTAAAATTAAATTTGAA
196 TTCTAGAGAAATTATATTTCCGATAACTGATGGAATTATACCTGAAATATAAAATTAAATTTGAA
16888 AAATAATTTGACAAAAACAATAAT
261 AAATAATTTGACAAAAACAATAAT
* * * *
16912 ATATTTTAAATTTAAATCATTTTAGAGTGGATTTATCTGAGTTTAATATTTAAATGATTTATGTT
1 ATATTTTAAATTTAAATAAATTTAGAATGGATTTATCTGAGTTTAATATTTAAATGATTTATATT
*
16977 TGAATACAAAAGGACACGTCAAATGACAAAAATCCTTATAACTAATTAATAAATATATAACAAAA
66 TGAATACAAAAGGACACGCCAAATGACAAAAATCCTTATAACTAATTAATAAATATATAACAAAA
*
17042 TAACAAAAAAAAAAGAGGAAGGAAAGTTATATTATACCTGTCAAGTTGTTATTCGAGAAATCAAT
131 TAAC---AAAAAAAGAGGAAGGAAAGTTATATTATACCTGTCAAGTTGTTATTCGAAAAATCAAT
*
17107 AATTTCTAGAGAAATTATATTTCCGATAACTGATGGGATTATACCTGAAATATAAAATTAAAT
193 AATTTCTAGAGAAATTATATTTCCGATAACTGATGGAATTATACCTGAAATATAAAATTAAAT
17170 AATCAGTCCA
Statistics
Matches: 239, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
284 126 0.53
287 113 0.47
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (284 bp):
ATATTTTAAATTTAAATAAATTTAGAATGGATTTATCTGAGTTTAATATTTAAATGATTTATATT
TGAATACAAAAGGACACGCCAAATGACAAAAATCCTTATAACTAATTAATAAATATATAACAAAA
TAACAAAAAAAGAGGAAGGAAAGTTATATTATACCTGTCAAGTTGTTATTCGAAAAATCAATAAT
TTCTAGAGAAATTATATTTCCGATAACTGATGGAATTATACCTGAAATATAAAATTAAATTTGAA
AAATAATTTGACAAAAACAATAAT
Found at i:17381 original size:21 final size:21
Alignment explanation
Indices: 17357--17396 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17347 ACGAAAATTG
*
17357 AATTTGAAT-ATTTTATTATAT
1 AATTTAAATAATTTT-TTATAT
17378 AATTTAAATAATTTTTTAT
1 AATTTAAATAATTTTTTAT
17397 TTTAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
AATTTAAATAATTTTTTATAT
Found at i:24289 original size:20 final size:20
Alignment explanation
Indices: 24246--24283 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
24236 AAATCTACCC
* *
24246 TTATATTATTATTATTATAT
1 TTATATTATAAATATTATAT
24266 TTATATTATAAATATTAT
1 TTATATTATAAATATTAT
24284 TATTATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATATTATAAATATTATAT
Found at i:24367 original size:23 final size:24
Alignment explanation
Indices: 24323--24381 Score: 102
Period size: 23 Copynumber: 2.5 Consensus size: 24
24313 TTATAAAGCC
*
24323 CAAAATAAAACCCTCAACCCTTTA
1 CAAAATACAACCCTCAACCCTTTA
24347 CAAAATACAACCC-CAACCCTTTA
1 CAAAATACAACCCTCAACCCTTTA
24370 CAAAATACAACC
1 CAAAATACAACC
24382 AGGCCTCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 22 0.65
24 12 0.35
ACGTcount: A:0.47, C:0.36, G:0.00, T:0.17
Consensus pattern (24 bp):
CAAAATACAACCCTCAACCCTTTA
Found at i:24412 original size:17 final size:18
Alignment explanation
Indices: 24390--24424 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
24380 CCAGGCCTCA
24390 AACCAG-ACCCAAAACCC
1 AACCAGAACCCAAAACCC
24407 AACCAGAACCCAAAACCC
1 AACCAGAACCCAAAACCC
24425 GAATATTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.49, C:0.46, G:0.06, T:0.00
Consensus pattern (18 bp):
AACCAGAACCCAAAACCC
Found at i:32314 original size:80 final size:81
Alignment explanation
Indices: 32178--32427 Score: 349
Period size: 80 Copynumber: 3.0 Consensus size: 81
32168 TAGGCCCATT
*
32178 GGCCCCAAGGCATATCCTTAGGTTGGTTACCTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTA
1 GGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTA
32243 AGGATATCCTTGGGTA
66 AGGATATCCTTGGGTA
* *
32259 GG-CCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTACGGATCTA
1 GGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTA
*
32323 AAGATATCCTTGGGTAGGCCCATA
66 AGGATATCCTT--G--GG----TA
* * * *
32347 GGCCCCAAGGTATATCCTTAGATTGGTTCCCTTTGCTATGTGCTTAGGGTAACCCTACGGATCTA
1 GGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTA
32412 AGGATATCCTTGGGTA
66 AGGATATCCTTGGGTA
32428 AGCTCATAGG
Statistics
Matches: 150, Mismatches: 10, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
80 69 0.46
81 4 0.03
82 1 0.01
84 2 0.01
85 2 0.01
87 1 0.01
88 4 0.03
89 67 0.45
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (81 bp):
GGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTA
AGGATATCCTTGGGTA
Found at i:32412 original size:89 final size:89
Alignment explanation
Indices: 32257--32500 Score: 346
Period size: 89 Copynumber: 2.7 Consensus size: 89
32247 TATCCTTGGG
* * *
32257 TAGG-CCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTACGGATC
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCTTAGGGTAACCCTACGGATC
*
32321 TAAAGATATCCTTGGGTAGGCCCA
66 TAAAGATATCCTTGGGTAAGCCCA
* *
32345 TAGGCCCCAAGGTATATCCTTAGATTGGTTCCCTTTGCTATGTGCTTAGGGTAACCCTACGGATC
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCTTAGGGTAACCCTACGGATC
* *
32410 TAAGGATATCCTTGGGTAAGCTCA
66 TAAAGATATCCTTGGGTAAGCCCA
* * * *
32434 TAGGCCCCAAGGTATATCCTTAGGTTGGCTCCCCTTTTGCTGTCTGATGAGGGTAAGCCCTACGG
1 TAGGCCCCAAGGTATATCCTTAGGTTGG-TTCCC-TTTGCTGTGTGCTTAGGGTAA-CCCTACGG
32499 AT
63 AT
32501 GTCGTTCTGG
Statistics
Matches: 138, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
88 4 0.03
89 103 0.75
90 4 0.03
91 17 0.12
92 10 0.07
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32
Consensus pattern (89 bp):
TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCTTAGGGTAACCCTACGGATC
TAAAGATATCCTTGGGTAAGCCCA
Found at i:36008 original size:12 final size:12
Alignment explanation
Indices: 35934--36009 Score: 57
Period size: 12 Copynumber: 6.3 Consensus size: 12
35924 TGACCTAGAG
*
35934 TCTGTTCTGATT
1 TCTGTTTTGATT
*
35946 TCTGATTTGGA-T
1 TCTG-TTTTGATT
*
35958 TCTGTTCTGGA-T
1 TCTGTT-TTGATT
* *
35970 TCTGTTATGATA
1 TCTGTTTTGATT
* *
35982 TCTGATTTGAAT
1 TCTGTTTTGATT
35994 TCTGTTTTGATT
1 TCTGTTTTGATT
36006 TCTG
1 TCTG
36010 ATATCTTTGT
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
11 4 0.08
12 42 0.84
13 4 0.08
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.54
Consensus pattern (12 bp):
TCTGTTTTGATT
Found at i:36179 original size:2 final size:2
Alignment explanation
Indices: 36172--36202 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
36162 CGGATGTGAG
*
36172 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36203 GTTTTCAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:39618 original size:12 final size:12
Alignment explanation
Indices: 39597--39675 Score: 52
Period size: 12 Copynumber: 6.6 Consensus size: 12
39587 ATGACCTGGA
*
39597 TTCTGTTCTGAT
1 TTCTGATCTGAT
39609 TTCTGATCTGGA-
1 TTCTGATCT-GAT
* * *
39621 TACAGTTCTGAT
1 TTCTGATCTGAT
* * *
39633 ATCTGATTTGAA
1 TTCTGATCTGAT
* *
39645 TTCTGATTTGAA
1 TTCTGATCTGAT
*
39657 TTCTGATTTGAT
1 TTCTGATCTGAT
39669 TTCTGAT
1 TTCTGAT
39676 ATATCCGTTT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
11 2 0.04
12 49 0.92
13 2 0.04
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (12 bp):
TTCTGATCTGAT
Found at i:39619 original size:24 final size:24
Alignment explanation
Indices: 39592--39663 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
39582 GATACATGAC
39592 CTGGATTCTGTTCTGATTTCTGAT
1 CTGGATTCTGTTCTGATTTCTGAT
* * *
39616 CTGGATACAGTTCTGATATCTGAT
1 CTGGATTCTGTTCTGATTTCTGAT
* * *
39640 TTGAATTCTGATT-TGAATTCTGAT
1 CTGGATTCTG-TTCTGATTTCTGAT
39664 TTGATTTCTG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 36 0.95
25 2 0.05
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (24 bp):
CTGGATTCTGTTCTGATTTCTGAT
Found at i:42402 original size:17 final size:17
Alignment explanation
Indices: 42373--42414 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
42363 TGTAAACCCT
42373 GTTGACTCGTTGACCAGC-
1 GTTGAC-CGTTGACCA-CA
42391 GTTGACCGTTGACCACA
1 GTTGACCGTTGACCACA
42408 GTTGACC
1 GTTGACC
42415 AGAACTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 16 0.70
18 6 0.26
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (17 bp):
GTTGACCGTTGACCACA
Found at i:45415 original size:80 final size:81
Alignment explanation
Indices: 45277--45529 Score: 319
Period size: 80 Copynumber: 3.0 Consensus size: 81
45267 GGTAGGCCCA
* * * *
45277 TAGGCCCCAAGGCATATCCTTAGGTTGATTACCTTTGCTGTGTGCTTAAGGTAACCCTACGGATA
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGATGTGTGCTTAAGGTAACCCTACGGATC
*
45342 TAAGAATATCCTTGGG
66 TAAGGATATCCTTGGG
*
45358 TAGG-CCCAAGGTATATCCTTAGGTTGGTTTCCTTTGATGTGTGCTTAAGGTAACCCTACGGATC
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGATGTGTGCTTAAGGTAACCCTACGGATC
45422 TAAGGATATCCTTGGGTAGG
66 TAAGGATATCCTT--G--GG
* * * * *
45442 CCCATAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTATGTGCTTAGGGTAACCCTACA
1 ----TAGGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGATGTGTGCTTAAGGTAACCCTACG
*
45507 GATCTAAGGATATTCTTGGG
62 GATCTAAGGATATCCTTGGG
45527 TAG
1 TAG
45530 TCTCATAGGC
Statistics
Matches: 151, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
80 67 0.44
81 7 0.05
82 1 0.01
84 2 0.01
85 2 0.01
87 1 0.01
88 4 0.03
89 67 0.44
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (81 bp):
TAGGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGATGTGTGCTTAAGGTAACCCTACGGATC
TAAGGATATCCTTGGG
Found at i:45463 original size:89 final size:89
Alignment explanation
Indices: 45358--45567 Score: 332
Period size: 89 Copynumber: 2.4 Consensus size: 89
45348 TATCCTTGGG
* * *
45358 TAGG-CCCAAGGTATATCCTTAGGTTGGTTTCCTTTGATGTGTGCTTAAGGTAACCCTACGGATC
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGATATGTGCTTAAGGTAACCCTACAGATC
45422 TAAGGATATCCTTGGGTAGGCCCA
66 TAAGGATATCCTTGGGTAGGCCCA
* *
45446 TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTATGTGCTTAGGGTAACCCTACAGATC
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGATATGTGCTTAAGGTAACCCTACAGATC
* * *
45511 TAAGGATATTCTTGGGTAGTCTCA
66 TAAGGATATCCTTGGGTAGGCCCA
*
45535 TAGGCCCCAAGGTATATCCTTAGGTTGGCTCCC
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCC
45568 CTTTTGCTGT
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 4 0.04
89 108 0.96
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (89 bp):
TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGATATGTGCTTAAGGTAACCCTACAGATC
TAAGGATATCCTTGGGTAGGCCCA
Found at i:61796 original size:14 final size:16
Alignment explanation
Indices: 61779--61810 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
61769 AAGAAAAAAG
61779 TATAT-TAAAAA-TGT
1 TATATATAAAAATTGT
61793 TATATATAAAAATTGT
1 TATATATAAAAATTGT
61809 TA
1 TA
61811 AAAGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 6 0.38
16 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TATATATAAAAATTGT
Found at i:72437 original size:2 final size:2
Alignment explanation
Indices: 72430--72458 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
72420 AGGGTGGAAG
72430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
72459 TTCAGGTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72912 original size:15 final size:16
Alignment explanation
Indices: 72879--72913 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
72869 TTATTGAATT
72879 AATTATATTACTATAA
1 AATTATATTACTATAA
*
72895 AATTATATTA-TGTAA
1 AATTATATTACTATAA
72910 AATT
1 AATT
72914 TTAAATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
AATTATATTACTATAA
Found at i:76612 original size:3 final size:3
Alignment explanation
Indices: 76604--76657 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
76594 TGTAATATAT
* **
76604 TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
76650 TAA -AA TAA
1 TAA TAA TAA
76658 CGATAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.12
3 37 0.88
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:76658 original size:32 final size:31
Alignment explanation
Indices: 76604--76663 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
76594 TGTAATATAT
*
76604 TAATAATAAAATAATAAGATAACGATAATAA
1 TAATAATAAAATAATAAAATAACGATAATAA
76635 TAATAATAATAATAATAAAATAACGATAA
1 TAATAATAA-AATAATAAAATAACGATAA
76664 AAAAAAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (31 bp):
TAATAATAAAATAATAAAATAACGATAATAA
Found at i:89413 original size:45 final size:46
Alignment explanation
Indices: 89356--89465 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 46
89346 TTTAATTTTA
*
89356 TTTTTATATTTATAATTGATGT-TC-TTAAT-TTTTGTAATCACACTT
1 TTTTTATATTTATAATTGATGTATCATTAATCTTTT-CAATCACA-TT
* *
89401 TTTTTATTTTTATAATTG--GTATCATTAATCTTTTCAATCTCATT
1 TTTTTATATTTATAATTGATGTATCATTAATCTTTTCAATCACATT
*
89445 TTTATATATTTATAATTGATG
1 TTTTTATATTTATAATTGATG
89466 ACCCTAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
43 2 0.04
44 20 0.36
45 28 0.51
46 5 0.09
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.58
Consensus pattern (46 bp):
TTTTTATATTTATAATTGATGTATCATTAATCTTTTCAATCACATT
Found at i:89523 original size:46 final size:46
Alignment explanation
Indices: 89431--89566 Score: 151
Period size: 42 Copynumber: 3.0 Consensus size: 46
89421 ATCATTAATC
89431 TTTTCAATCTCATTTTTATATATTTATAATTGATGACCCTAATTTTT
1 TTTTCAATCTCATTTTTATATATTTATAATTGA-GACCCTAATTTTT
89478 TTTTCAATCTCATTTTT-TA-ACTTTATAATTGA-ACTCCTAA--TTT
1 TTTTCAATCTCATTTTTATATA-TTTATAATTGAGAC-CCTAATTTTT
* * * *
89521 TTTT-AATCTTACTTTT-TACATTTATAATTGAGACCCCTAATCTTT
1 TTTTCAATCTCATTTTTATATATTTATAATTGAGA-CCCTAATTTTT
89566 T
1 T
89567 ACTCACTTTT
Statistics
Matches: 80, Mismatches: 2, Indels: 16
0.82 0.02 0.16
Matches are distributed among these distances:
42 23 0.29
43 14 0.17
44 3 0.04
45 10 0.12
46 13 0.16
47 17 0.21
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.54
Consensus pattern (46 bp):
TTTTCAATCTCATTTTTATATATTTATAATTGAGACCCTAATTTTT
Found at i:89567 original size:42 final size:44
Alignment explanation
Indices: 89429--89584 Score: 139
Period size: 42 Copynumber: 3.6 Consensus size: 44
89419 GTATCATTAA
* *
89429 TCTTTTCAATCTCATTTTTATATATTTATAATTGATGA-CCCTAATTT
1 TCTTTTCAATCTCACTTTT-TACATTTATAATTGA-GACCCCTAA--T
* * *
89476 TTTTTTCAATCTCATTTTTTA-ACTTTATAATTGA-ACTCCTAAT
1 TCTTTTCAATCTCACTTTTTACA-TTTATAATTGAGACCCCTAAT
* *
89519 T-TTTTTAATCTTACTTTTTACATTTATAATTGAGACCCCTAA-
1 TCTTTTCAATCTCACTTTTTACATTTATAATTGAGACCCCTAAT
*
89561 TCTTTT--A-CTCACTTTTTACCTTTA
1 TCTTTTCAATCTCACTTTTTACATTTA
89585 AAATCGAGGC
Statistics
Matches: 96, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
40 15 0.16
41 1 0.01
42 28 0.29
43 14 0.15
44 1 0.01
45 6 0.06
46 13 0.14
47 18 0.19
ACGTcount: A:0.26, C:0.17, G:0.03, T:0.53
Consensus pattern (44 bp):
TCTTTTCAATCTCACTTTTTACATTTATAATTGAGACCCCTAAT
Found at i:89911 original size:43 final size:44
Alignment explanation
Indices: 89864--90187 Score: 229
Period size: 43 Copynumber: 7.4 Consensus size: 44
89854 TTTATTTTTA
* * * *
89864 TTTTTATATTTATAATTGATGTCCCCAATTTTTGT-AATCACAC
1 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCAC
* * *
89907 TTTTTATTTTTATAATTG-GGACCATTAA-TTTTTTCAATCTCAC
1 TTTTTATATTTATAATTGATGACC-CTAATTTTTTTCAATCTCAC
89950 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCAC
1 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCAC
* * *
89994 TTTTTACATTTATAATTGA--ACTTCTAATTTTTTT-AATCTTAC
1 TTTTTATATTTATAATTGATGAC-CCTAATTTTTTTCAATCTCAC
* * * *
90036 TTTTTACATTTATAATTGAGGCCCCTAGGCCCTAGTTTTTTT-AATATCAC
1 TTTTTATATTTATAATTGA------T-GACCCTAATTTTTTTCAATCTCAC
* ** * ** *
90086 TTTTGACCTTTAAAATTGA-GGTCTTAATTTTTTT-AATCTCAC
1 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCAC
** * * * *
90128 TTTTTACCTTTAAAATTGAGGTCCTTAATTTTTTTCAATCAT-AC
1 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATC-TCAC
*
90172 TTTTTA-CTTTATAATT
1 TTTTTATATTTATAATT
90188 TAAACCCCTA
Statistics
Matches: 235, Mismatches: 29, Indels: 34
0.79 0.10 0.11
Matches are distributed among these distances:
42 73 0.31
43 79 0.34
44 49 0.21
45 1 0.00
50 32 0.14
51 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.52
Consensus pattern (44 bp):
TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCAC
Found at i:90016 original size:21 final size:21
Alignment explanation
Indices: 89992--90054 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
89982 TTTCAATCTC
89992 ACTTTTTACATTTATAATTGA
1 ACTTTTTACATTTATAATTGA
* * ** * *
90013 ACTTCTAATTTTTTTAATCT-T
1 ACTTTTTACATTTATAAT-TGA
90034 ACTTTTTACATTTATAATTGA
1 ACTTTTTACATTTATAATTGA
90055 GGCCCCTAGG
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.56
Consensus pattern (21 bp):
ACTTTTTACATTTATAATTGA
Found at i:90062 original size:86 final size:84
Alignment explanation
Indices: 89864--90187 Score: 278
Period size: 86 Copynumber: 3.7 Consensus size: 84
89854 TTTATTTTTA
* * * * *
89864 TTTTTATATTTATAATTGATGTCCCC-AATTTTTGTAATCACACTTTTTATTTTTATAATTGGGA
1 TTTTTACATTTATAATTGA-GGCCCCTAATTTTTTTAATCTCACTTTTTA-CTTTATAATT--GA
* *
89928 CCAT-TAATTTTTTCAATCTCAC
62 ACATCTAATTTTTTTAATCTCAC
* * *
89950 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCACTTTTTACATTTATAATTGAAC
1 TTTTTACATTTATAATTGAGGCCCCTAATTTTTTT-AATCTCACTTTTTAC-TTTATAATTGAAC
* *
90015 TTCTAATTTTTTTAATCTTAC
64 ATCTAATTTTTTTAATCTCAC
* * *
90036 TTTTTACATTTATAATTGAGGCCCCTAGGCCCTAGTTTTTTTAATATCACTTTTGACCTTTAAAA
1 TTTTTACATTTATAATTGAGGCCCCTA------A-TTTTTTTAATCTCACTTTTTA-CTTTATAA
**
90101 TTG-AGGTCTTAATTTTTTTAATCTCAC
58 TTGAACATC-TAATTTTTTTAATCTCAC
* * * *
90128 TTTTTACCTTTAAAATTGAGGTCCTTAATTTTTTTCAATCAT-ACTTTTTACTTTATAATT
1 TTTTTACATTTATAATTGAGGCCCCTAATTTTTTT-AATC-TCACTTTTTACTTTATAATT
90188 TAAACCCCTA
Statistics
Matches: 197, Mismatches: 26, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
85 23 0.12
86 78 0.40
87 23 0.12
91 3 0.02
92 62 0.31
93 8 0.04
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.52
Consensus pattern (84 bp):
TTTTTACATTTATAATTGAGGCCCCTAATTTTTTTAATCTCACTTTTTACTTTATAATTGAACAT
CTAATTTTTTTAATCTCAC
Found at i:90114 original size:92 final size:93
Alignment explanation
Indices: 89972--90148 Score: 241
Period size: 92 Copynumber: 1.9 Consensus size: 93
89962 TAATTGATGA
* * * *
89972 CCCTAATTTTTTTCAATCTCACTTTTTACATTTATAATTGAACTTCTAATTTTTTTAATCTTACT
1 CCCTAATTTTTTTCAATATCACTTTTGACATTTAAAATTGAACTTCTAATTTTTTTAATCTCACT
*
90037 TTTTACATTTATAATTGAGGCCCCTAGG
66 TTTTACATTTAAAATTGAGGCCCCTAGG
* * **
90065 CCCTAGTTTTTTT-AATATCACTTTTGACCTTTAAAATTG-AGGTCTTAATTTTTTTAATCTCAC
1 CCCTAATTTTTTTCAATATCACTTTTGACATTTAAAATTGAACTTC-TAATTTTTTTAATCTCAC
*
90128 TTTTTACCTTTAAAATTGAGG
65 TTTTTACATTTAAAATTGAGG
90149 TCCTTAATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
91 3 0.04
92 58 0.79
93 12 0.16
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (93 bp):
CCCTAATTTTTTTCAATATCACTTTTGACATTTAAAATTGAACTTCTAATTTTTTTAATCTCACT
TTTTACATTTAAAATTGAGGCCCCTAGG
Found at i:90200 original size:43 final size:43
Alignment explanation
Indices: 90065--90201 Score: 118
Period size: 42 Copynumber: 3.2 Consensus size: 43
90055 GGCCCCTAGG
* * * **
90065 CCCTAGTTTTTTTAATATCACTTTTGACCTTTAAAATTG-AGG
1 CCCTAATTTTTTTAATCTCACTTTTTACCTTTAAAATTGAAAC
* * ***
90107 TCTTAATTTTTTTAATCTCACTTTTTACCTTTAAAATTGAGGT
1 CCCTAATTTTTTTAATCTCACTTTTTACCTTTAAAATTGAAAC
* * *
90150 CCTTAATTTTTTTCAATCAT-ACTTTTTA-CTTTATAATTTAAAC
1 CCCTAATTTTTTT-AATC-TCACTTTTTACCTTTAAAATTGAAAC
90193 CCCTAATTT
1 CCCTAATTT
90202 AATCATTTTC
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
42 34 0.44
43 31 0.40
44 12 0.15
45 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (43 bp):
CCCTAATTTTTTTAATCTCACTTTTTACCTTTAAAATTGAAAC
Found at i:90328 original size:21 final size:21
Alignment explanation
Indices: 90304--90346 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
90294 TCAAGACCCA
*
90304 GAAAATATCTGAGACGACTCT
1 GAAAATATCTCAGACGACTCT
* *
90325 GAAAATGTCTCAGACGGCTCT
1 GAAAATATCTCAGACGACTCT
90346 G
1 G
90347 GGTGTAACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (21 bp):
GAAAATATCTCAGACGACTCT
Found at i:99580 original size:2 final size:2
Alignment explanation
Indices: 99567--99600 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
99557 AACCATCCCG
* *
99567 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
99601 ATTCTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:99621 original size:3 final size:3
Alignment explanation
Indices: 99613--99648 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
99603 TCTATTTTAT
99613 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
99649 GTAAATTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:100186 original size:29 final size:29
Alignment explanation
Indices: 100151--100232 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
100141 AAACTAAATT
*
100151 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
100180 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
100209 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
100233 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:101542 original size:15 final size:15
Alignment explanation
Indices: 101519--101548 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
101509 ACGAGGCTGG
101519 AATTACAACAATAAC
1 AATTACAACAATAAC
*
101534 AATTCCAACAATAAC
1 AATTACAACAATAAC
101549 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:104943 original size:29 final size:29
Alignment explanation
Indices: 104908--104989 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
104898 AAACTAAATT
*
104908 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
104937 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
104966 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
104990 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:109302 original size:37 final size:36
Alignment explanation
Indices: 109243--109362 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
109233 ATCCCATTAT
* *
109243 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
109279 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
109315 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
109350 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
109363 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:109318 original size:21 final size:21
Alignment explanation
Indices: 109294--109354 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
109284 TTCAAAGAAA
109294 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
109315 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
109329 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
109350 CATTT
1 CATTT
109355 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:109371 original size:35 final size:36
Alignment explanation
Indices: 109245--109389 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
109235 CCCATTATCA
*
109245 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
109280 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
109317 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
109353 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
109387 TTT
1 TTT
109390 AATACTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:113917 original size:37 final size:36
Alignment explanation
Indices: 113858--113977 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
113848 ATCCCATTAT
* *
113858 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
113894 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
113930 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
113965 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
113978 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:113933 original size:21 final size:21
Alignment explanation
Indices: 113909--113969 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
113899 TTCAAAGAAA
113909 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
113930 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
113944 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
113965 CATTT
1 CATTT
113970 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:113986 original size:35 final size:36
Alignment explanation
Indices: 113860--114004 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
113850 CCCATTATCA
*
113860 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
113895 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
113932 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
113968 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
114002 TTT
1 TTT
114005 AATACTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:115625 original size:34 final size:34
Alignment explanation
Indices: 115582--115652 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
115572 AATAACCCAT
115582 GAATTTAGTCCATATTGGCCAAACAACCGAACAG
1 GAATTTAGTCCATATTGGCCAAACAACCGAACAG
115616 GAATTTAGTCCATATTGGCCAAACAACCGAACAG
1 GAATTTAGTCCATATTGGCCAAACAACCGAACAG
115650 GAA
1 GAA
115653 AAAAATAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (34 bp):
GAATTTAGTCCATATTGGCCAAACAACCGAACAG
Found at i:117106 original size:31 final size:31
Alignment explanation
Indices: 117034--117109 Score: 143
Period size: 31 Copynumber: 2.5 Consensus size: 31
117024 CTGTCACTCT
*
117034 TGGTATAAAACATTTTCAATCTGTCACAATA
1 TGGTATAAAATATTTTCAATCTGTCACAATA
117065 TGGTATAAAATATTTTCAATCTGTCACAATA
1 TGGTATAAAATATTTTCAATCTGTCACAATA
117096 TGGTATAAAATATT
1 TGGTATAAAATATT
117110 CCTGGTGCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (31 bp):
TGGTATAAAATATTTTCAATCTGTCACAATA
Found at i:121752 original size:48 final size:48
Alignment explanation
Indices: 121682--121792 Score: 116
Period size: 48 Copynumber: 2.3 Consensus size: 48
121672 GTAAACGGAG
* * * *
121682 ATATTAGAAATCAAAACAGAATTTAGAACATATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACATATATCAAAACAGAATCC
* ** * *
121730 ATATCAGAAATCAGAACGGAATTCAGGTCATGTATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTCAGAACATATATCAAAACAGAATCC
*
121778 A-AGTCAAAAATCAGA
1 ATA-TCAGAAATCAGA
121793 TAAAATATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.02
48 51 0.98
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.22
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACATATATCAAAACAGAATCC
Found at i:137672 original size:25 final size:24
Alignment explanation
Indices: 137625--137677 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
137615 CCAGCCCACC
*
137625 CTAAAAGTTTATAAATTCATCCCT
1 CTAAAAGTTTAGAAATTCATCCCT
* **
137649 ACTAAAATTTTAGAAATTTGTCCCT
1 -CTAAAAGTTTAGAAATTCATCCCT
137674 CTAA
1 CTAA
137678 CATAAGATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAAAAGTTTAGAAATTCATCCCT
Found at i:139193 original size:21 final size:21
Alignment explanation
Indices: 139167--139221 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
139157 CCTGTTCATG
*
139167 TTAACATCACATCTCTT-AATA
1 TTAACATAACATCTCTTCAA-A
* **
139188 TTAACATTATGTCTCTTCAAA
1 TTAACATAACATCTCTTCAAA
139209 TTAACATAACATC
1 TTAACATAACATC
139222 ATAGTAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (21 bp):
TTAACATAACATCTCTTCAAA
Found at i:140048 original size:44 final size:44
Alignment explanation
Indices: 139986--140098 Score: 120
Period size: 48 Copynumber: 2.5 Consensus size: 44
139976 TGTCTTTGAC
* * *
139986 CCAATGTTTCAAAGTACTTTTAAGGAAATGCTGGTCA-TTCTTTT
1 CCAATGTTTCAAATTACTTTTAAGGAAAAGCTGGCCATTTC-TTT
** *
140030 CCAATGTTTCAAATTACTTTGTTCTTTGGAAAAGGTGGCCATTTCTTT
1 CCAATGTTTCAAATTAC--T-TT-TAAGGAAAAGCTGGCCATTTCTTT
140078 CCAATGTTTCAAATTACTTTT
1 CCAATGTTTCAAATTACTTTT
140099 TGGAGAAGGT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
44 17 0.29
45 2 0.03
46 2 0.03
47 2 0.03
48 32 0.55
49 3 0.05
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (44 bp):
CCAATGTTTCAAATTACTTTTAAGGAAAAGCTGGCCATTTCTTT
Found at i:140488 original size:23 final size:23
Alignment explanation
Indices: 140458--140503 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
140448 TGTGGGTCCA
140458 AACACCATAGAGTCATTGCTCTG
1 AACACCATAGAGTCATTGCTCTG
140481 AACACCATAGAGTCATTGCTCTG
1 AACACCATAGAGTCATTGCTCTG
140504 GATTTGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (23 bp):
AACACCATAGAGTCATTGCTCTG
Found at i:144625 original size:2 final size:2
Alignment explanation
Indices: 144613--144681 Score: 86
Period size: 2 Copynumber: 34.0 Consensus size: 2
144603 TAATTAATTG
* * *
144613 AT AT AT GAT AT AT AT AG GT AT GT AT GA- AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
144656 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
144682 TGTTATCATA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.02
2 54 0.93
3 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (2 bp):
AT
Found at i:147587 original size:7 final size:7
Alignment explanation
Indices: 147575--147630 Score: 67
Period size: 7 Copynumber: 7.6 Consensus size: 7
147565 ATGGCATTAA
147575 GCAGTAG
1 GCAGTAG
147582 GCAGTAG
1 GCAGTAG
147589 GCAGTAG
1 GCAGTAG
*
147596 GCAGTAA
1 GCAGTAG
*
147603 ACAGTAG
1 GCAGTAG
147610 GCAGTAGTAG
1 GC---AGTAG
147620 GCAGTAG
1 GCAGTAG
147627 GCAG
1 GCAG
147631 GCCTTTGCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
7 35 0.83
10 7 0.17
ACGTcount: A:0.32, C:0.14, G:0.39, T:0.14
Consensus pattern (7 bp):
GCAGTAG
Found at i:156017 original size:143 final size:145
Alignment explanation
Indices: 155754--156029 Score: 484
Period size: 143 Copynumber: 1.9 Consensus size: 145
155744 ATATCAAATA
*
155754 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTTCAATCTTAAAAGAGTACACTTTTAA
1 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTACAATCTTAAAAGAGTACACTTTTAA
* *
155819 ACTAAGAAACTTGTATTCGTTGACACCTTACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
66 ACTAAGAAACATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
155884 CCTATACTTTGAATC
131 CCTATACTTTGAATC
*
155899 TACAATTAAAATCAAGGAAAATG-AA-ACTATGAAAATTACAATCTTAAAAGAGTACACTTTTAA
1 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTACAATCTTAAAAGAGTACACTTTTAA
* *
155962 ACTAAGAAGCATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCCTTGGACCGGTTGAA
66 ACTAAGAAACATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
156027 CCT
131 CCT
156030 GCACTTTGGT
Statistics
Matches: 125, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
143 100 0.80
144 2 0.02
145 23 0.18
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.29
Consensus pattern (145 bp):
TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTACAATCTTAAAAGAGTACACTTTTAA
ACTAAGAAACATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
CCTATACTTTGAATC
Found at i:160791 original size:2 final size:2
Alignment explanation
Indices: 160784--160851 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
160774 TGTCGTTACA
160784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
160826 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
160852 TTCATTTGTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:162190 original size:3 final size:3
Alignment explanation
Indices: 162177--162206 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
162167 ATGAGGTTCA
*
162177 TCC TTC TCC TCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
162207 GCCGCAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
TCC
Found at i:163503 original size:143 final size:145
Alignment explanation
Indices: 163240--163524 Score: 484
Period size: 143 Copynumber: 2.0 Consensus size: 145
163230 ATATCAAATA
163240 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTTCAATCTTAAAAGAGTACACTTTTAA
1 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTTCAATCTTAAAAGAGTACACTTTTAA
* *
163305 ACTAAGAAACTTGTATTCGTTGAAACCTTACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
66 ACTAAGAAACATGTATTCGTTGAAACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
*
163370 CCTATACTTTGAATC
131 CCTACACTTTGAATC
*
163385 TACAATTAAAATCAAGGAAAATG-AA-ACTATGAAAATTTCAATCTTAAAAGAGTACACTTTTAA
1 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTTCAATCTTAAAAGAGTACACTTTTAA
* * *
163448 ACTAAGAAGCATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCCTTGGACCGGTTGAA
66 ACTAAGAAACATGTATTCGTTGAAACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
*
163513 CCTGCACTTTGA
131 CCTACACTTTGA
163525 TACCCCTAAA
Statistics
Matches: 132, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
143 107 0.81
144 2 0.02
145 23 0.17
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (145 bp):
TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTTCAATCTTAAAAGAGTACACTTTTAA
ACTAAGAAACATGTATTCGTTGAAACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
CCTACACTTTGAATC
Found at i:180617 original size:52 final size:53
Alignment explanation
Indices: 180552--180658 Score: 162
Period size: 52 Copynumber: 2.0 Consensus size: 53
180542 CACAAGATGG
* *
180552 GGCACATAGAAATAGGAAACTAGTCTAGAGTTAGGGGATTACAACTAATTACAA
1 GGCACATA-AAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACAA
* *
180606 GGCACAT-AAATATGAGACTAGCCTAGAGTTAGGGGATTACAACTAATCACAA
1 GGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACAA
180658 G
1 G
180659 AATATTATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 42 0.86
54 7 0.14
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.21
Consensus pattern (53 bp):
GGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACAA
Found at i:190390 original size:44 final size:44
Alignment explanation
Indices: 190327--190415 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
190317 GAAATGAATG
190327 AAATAAAATTGAGTACCAAAATGATCAAAATACCCTTATGTCCT
1 AAATAAAATTGAGTACCAAAATGATCAAAATACCCTTATGTCCT
190371 AAATAAAATTGAGTACCAAAATGATCAAAATACCCTTATGTCCT
1 AAATAAAATTGAGTACCAAAATGATCAAAATACCCTTATGTCCT
190415 A
1 A
190416 GACTAAGTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.27
Consensus pattern (44 bp):
AAATAAAATTGAGTACCAAAATGATCAAAATACCCTTATGTCCT
Found at i:194717 original size:2 final size:2
Alignment explanation
Indices: 194710--194754 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
194700 CTAATTAATA
194710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
194752 AT A
1 AT A
194755 AACATAAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:196374 original size:28 final size:24
Alignment explanation
Indices: 196322--196376 Score: 65
Period size: 28 Copynumber: 2.1 Consensus size: 24
196312 TCATTTAATA
*
196322 AAATTAATAAAATTATTTAAATGT
1 AAATTAATAAAATTATTAAAATGT
196346 AAATTAGATAAAACATTATTAATAATGT
1 AAATTA-AT-AAA-ATTATTAA-AATGT
196374 AAA
1 AAA
196377 GGAAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.23
25 2 0.08
26 3 0.12
27 7 0.27
28 8 0.31
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (24 bp):
AAATTAATAAAATTATTAAAATGT
Found at i:196403 original size:14 final size:14
Alignment explanation
Indices: 196381--196427 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
196371 TGTAAAGGAA
*
196381 AATTAATATAGTTT
1 AATTTATATAGTTT
196395 AATTTATATA----
1 AATTTATATAGTTT
196405 AA-TTATATAGTTT
1 AATTTATATAGTTT
196418 AATTTATATA
1 AATTTATATA
196428 AAGAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:196414 original size:23 final size:24
Alignment explanation
Indices: 196380--196429 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
196370 ATGTAAAGGA
196380 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
196404 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
196427 AAA
1 AAA
196430 GAAAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:197153 original size:15 final size:15
Alignment explanation
Indices: 197105--197167 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 15
197095 ACTATATTAA
197105 TATAAAT-TATAATT
1 TATAAATATATAATT
197119 TATAAACTATAT-A-T
1 TATAAA-TATATAATT
*
197133 T-T---TATATAGTT
1 TATAAATATATAATT
*
197144 TATACATATATAATT
1 TATAAATATATAATT
197159 TATAAATAT
1 TATAAATAT
197168 TAACAAGTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 15
0.68 0.05 0.27
Matches are distributed among these distances:
9 5 0.13
11 2 0.05
12 1 0.03
13 1 0.03
14 8 0.21
15 18 0.47
16 3 0.08
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (15 bp):
TATAAATATATAATT
Found at i:197552 original size:21 final size:21
Alignment explanation
Indices: 197508--197552 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
197498 TTATAATTCT
* *
197508 TATTAATTTAATTAATATTGA
1 TATTAACTTAATTAATATTAA
197529 TATTAACTTATATTAATA-TAA
1 TATTAACTTA-ATTAATATTAA
197550 TAT
1 TAT
197553 AGTTTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTAACTTAATTAATATTAA
Found at i:197605 original size:31 final size:30
Alignment explanation
Indices: 197567--197751 Score: 144
Period size: 31 Copynumber: 5.8 Consensus size: 30
197557 TATAATTTGT
*
197567 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAAACTATAGT-TATAA
197598 AATTAATATTAATATAAACTATATGTTAT-A
1 AATTAATATTAATATAAACTATA-GTTATAA
* *
197628 AATTATATAATATAGTTTATAAACTATAGTTAATAT
1 AATTA-AT-AT-TA--ATATAAACTATAGTT-ATAA
*
197664 AATTAATATTAATAT--AGTATAGTTTATAA
1 AATTAATATTAATATAAACTATAG-TTATAA
*
197693 ACTATATACTATATTAATATAAATTATAGTTA-AGA
1 A--AT-TA--ATATTAATATAAACTATAGTTATA-A
*
197728 TAATTAACATTAATATAAACTATA
1 -AATTAATATTAATATAAACTATA
197752 TAGTACATTA
Statistics
Matches: 127, Mismatches: 9, Indels: 36
0.74 0.05 0.21
Matches are distributed among these distances:
29 10 0.08
30 8 0.06
31 48 0.38
32 6 0.05
33 6 0.05
34 18 0.14
35 19 0.15
36 12 0.09
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAACTATAGTTATAA
Found at i:197607 original size:65 final size:62
Alignment explanation
Indices: 197538--197745 Score: 190
Period size: 65 Copynumber: 3.2 Consensus size: 62
197528 ATATTAACTT
*
197538 ATATTAATATAATATAGTTTATAATTTGTAATTAATATTAATATAAAATATAGTCTATAAAATTA
1 ATATTAATATAATATAGTTTATAATTTATAA-T-ATATTAATATAAAATATAGT-TATAAAATTA
* *
197603 ATATTAATATAAACTATA-TGTTATAAATTATATAATATAGTT--TATAAACTATAGTTAATATA
1 ATATTAATAT-AA-TATAGT-TTAT-AATT-TATAATATA-TTAATATAAAATATAGTT-ATAAA
197665 ATTA
59 ATTA
* * * *
197669 ATATTAATATAGTATAGTTTATAAACTATATACTATATTAATATAAATTATAGTTA-AGATAATT
1 ATATTAATATAATATAGTTTAT-AA-TTTATAATATATTAATATAAAATATAGTTATA-A-AATT
197733 A
62 A
*
197734 ACATTAATATAA
1 ATATTAATATAA
197746 ACTATATAGT
Statistics
Matches: 120, Mismatches: 10, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
63 3 0.03
64 20 0.17
65 42 0.35
66 33 0.28
67 11 0.09
68 7 0.06
69 4 0.03
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (62 bp):
ATATTAATATAATATAGTTTATAATTTATAATATATTAATATAAAATATAGTTATAAAATTA
Found at i:197619 original size:24 final size:25
Alignment explanation
Indices: 197574--197620 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
197564 TGTAATTAAT
**
197574 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
197599 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
197621 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:197687 original size:29 final size:29
Alignment explanation
Indices: 197652--197744 Score: 78
Period size: 29 Copynumber: 3.0 Consensus size: 29
197642 GTTTATAAAC
197652 TATAGTTAATATAATTAATATTAATATAG
1 TATAGTTAATATAATTAATATTAATATAG
* * *
197681 TATAGTTTATAAACTATATACTATATTAATATAAAT
1 TATAGTTAATATA--AT-TA--ATATTAATAT--AG
* *
197717 TATAGTTAAGATAATTAACATTAATATA
1 TATAGTTAATATAATTAATATTAATATA
197745 AACTATATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
29 12 0.24
31 11 0.22
32 2 0.04
33 2 0.04
34 12 0.24
36 11 0.22
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
TATAGTTAATATAATTAATATTAATATAG
Found at i:197688 original size:131 final size:132
Alignment explanation
Indices: 197538--197787 Score: 323
Period size: 131 Copynumber: 1.9 Consensus size: 132
197528 ATATTAACTT
** * *
197538 ATATTAATATAATATAGTTTATAATTTGTA-ATTAATATTAATATAAAATATAGTCTATA-A-AA
1 ATATTAATATAATATAGTTTATAAACTATATACT-ATATTAATATAAAATATAGT-TA-AGATAA
* *
197600 TTAATATTAATATAAACTATAT-GT-TATAAATTATATAA-TATAGTTTATAAACTATAGTTAAT
63 TTAACATTAATATAAACTATATAGTACATAAA-TATA-AACTATAGTTTATAAACTATAGTTAAT
197662 ATAATTA
126 ATAATTA
* *
197669 ATATTAATATAGTATAGTTTATAAACTATATACTATATTAATATAAATTATAGTTAAGATAATTA
1 ATATTAATATAATATAGTTTATAAACTATATACTATATTAATATAAAATATAGTTAAGATAATTA
* *
197734 ACATTAATATAAACTATATAGTACATTAATATAAACTATAGTTTATAAATTATA
66 ACATTAATATAAACTATATAGTACATAAATATAAACTATAGTTTATAAACTATA
197788 TTTCTCATAC
Statistics
Matches: 103, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
129 1 0.01
130 3 0.03
131 70 0.68
132 25 0.24
133 4 0.04
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.43
Consensus pattern (132 bp):
ATATTAATATAATATAGTTTATAAACTATATACTATATTAATATAAAATATAGTTAAGATAATTA
ACATTAATATAAACTATATAGTACATAAATATAAACTATAGTTTATAAACTATAGTTAATATAAT
TA
Found at i:197693 original size:43 final size:40
Alignment explanation
Indices: 197632--197722 Score: 119
Period size: 43 Copynumber: 2.2 Consensus size: 40
197622 GTTATAAATT
* *
197632 ATATAATATAGTTTATAAACTATAGTTAATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATA--TAATAT-ATTAATATAA
*
197675 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
1 ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
197715 ATTATAGT
1 A-TATAGT
197723 TAAGATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 10 0.23
41 11 0.25
43 23 0.52
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (40 bp):
ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
Found at i:197721 original size:36 final size:34
Alignment explanation
Indices: 197537--197751 Score: 124
Period size: 31 Copynumber: 6.6 Consensus size: 34
197527 GATATTAACT
* *
197537 TATATTAATAT-AA-TATAGTTTAT-AATTTGTAA
1 TATATTAATATAAACTATAGTTTATAAATATAT-A
* *
197569 TTAATATTAATATAAAATATAGTCTATAAA-AT-TA
1 -T-ATATTAATATAAACTATAGTTTATAAATATATA
197603 -ATATTAATATAAACTATA-TGTTATAAATTATATAA
1 TATATTAATATAAACTATAGT-TTATAAA-TATAT-A
* *
197638 TATAGTT--TATAAACTATAGTTAATATA-AT-TA
1 TATA-TTAATATAAACTATAGTTTATAAATATATA
*
197669 -ATATTAATAT--AGTATAGTTTATAAACTATATA
1 TATATTAATATAAACTATAGTTTATAAA-TATATA
* *
197701 CTATATTAATATAAATTATAG-TTA-AGATA-AT-
1 -TATATTAATATAAACTATAGTTTATAAATATATA
*
197732 TAACATTAATATAAACTATA
1 T-ATATTAATATAAACTATA
197752 TAGTACATTA
Statistics
Matches: 147, Mismatches: 13, Indels: 46
0.71 0.06 0.22
Matches are distributed among these distances:
29 14 0.10
30 5 0.03
31 45 0.31
32 5 0.03
33 7 0.05
34 24 0.16
35 23 0.16
36 20 0.14
37 4 0.03
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (34 bp):
TATATTAATATAAACTATAGTTTATAAATATATA
Found at i:197775 original size:20 final size:21
Alignment explanation
Indices: 197734--197775 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
197724 AAGATAATTA
197734 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
197756 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
197776 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:198125 original size:2 final size:2
Alignment explanation
Indices: 198118--198182 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
198108 TTTAAGACAC
198118 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
198160 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
198183 CCCCCACCCC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:198368 original size:12 final size:12
Alignment explanation
Indices: 198343--198412 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
198333 ATGGGGATAT
* *
198343 CAGAAATCAAAA
1 CAGAATTCAGAA
198355 CAGAATTCAGAA
1 CAGAATTCAGAA
198367 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* **
198379 TAGAATTCAGCT
1 CAGAATTCAGAA
198391 CAGAATTCAGAA
1 CAGAATTCAGAA
*
198403 CAAAATTCAG
1 CAGAATTCAG
198413 GTCATGTATC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:203118 original size:24 final size:24
Alignment explanation
Indices: 203074--203178 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
203064 AAACGGAGAT
*
203074 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
203098 AAT-AGATATTAGAACAGAATTCAG
1 -ATCAGAAATCAGAACAGAATTCAG
203122 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
203146 -T--G-TATCAGAACAGAAATCAA
1 ATCAGAAATCAGAACAGAATTCAG
203166 ATCAGAAATCAGA
1 ATCAGAAATCAGA
203179 TAAAATATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
20 15 0.23
21 2 0.03
23 4 0.06
24 43 0.65
25 2 0.03
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:203127 original size:12 final size:12
Alignment explanation
Indices: 203076--203145 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
203066 ACGGAGATAT
* *
203076 CAGAAATCAAAA
1 CAGAATTCAGAA
203088 CAGAATTCAGAA
1 CAGAATTCAGAA
*
203100 TAGATATT-AGAA
1 CAGA-ATTCAGAA
*
203112 CAGAATTCAGAT
1 CAGAATTCAGAA
*
203124 CAGAAATCAGAA
1 CAGAATTCAGAA
203136 CAGAATTCAG
1 CAGAATTCAG
203146 TGTATCAGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 3 0.06
12 42 0.88
13 3 0.06
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:203164 original size:12 final size:12
Alignment explanation
Indices: 203076--203178 Score: 72
Period size: 12 Copynumber: 8.9 Consensus size: 12
203066 ACGGAGATAT
*
203076 CAGAAATCAAAA
1 CAGAAATCAGAA
*
203088 CAGAATTCAGAA
1 CAGAAATCAGAA
* * *
203100 TAGATATTAGAA
1 CAGAAATCAGAA
* *
203112 CAGAATTCAGAT
1 CAGAAATCAGAA
203124 CAGAAATCAGAA
1 CAGAAATCAGAA
*
203136 CAGAATTCAG--
1 CAGAAATCAGAA
* *
203146 -TG-TATCAGAA
1 CAGAAATCAGAA
203156 CAGAAATCA-AA
1 CAGAAATCAGAA
203167 TCAGAAATCAGA
1 -CAGAAATCAGA
203179 TAAAATATTT
Statistics
Matches: 66, Mismatches: 19, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
8 4 0.06
9 1 0.02
11 3 0.05
12 57 0.86
13 1 0.02
ACGTcount: A:0.51, C:0.15, G:0.16, T:0.18
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:207944 original size:12 final size:12
Alignment explanation
Indices: 207919--208011 Score: 75
Period size: 12 Copynumber: 7.8 Consensus size: 12
207909 ACGGAGATAT
* *
207919 CAGAAATCAAAA
1 CAGAATTCAGAA
207931 CAGAATTCAGAA
1 CAGAATTCAGAA
207943 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
207955 CAGAATTCAGATA
1 CAGAATTCAGA-A
* *
207968 -AAAAATCAGAA
1 CAGAATTCAGAA
**
207979 CAGAATTCAGGT
1 CAGAATTCAGAA
*
207991 CATGTA-TCAGAA
1 CA-GAATTCAGAA
208003 CAGAATTCA
1 CAGAATTCA
208012 AATCGGAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
11 5 0.08
12 53 0.84
13 5 0.08
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:207946 original size:24 final size:25
Alignment explanation
Indices: 207913--208025 Score: 110
Period size: 24 Copynumber: 4.6 Consensus size: 25
207903 CAGTAAACGG
*
207913 AGATATCAGAAATCAAAACAGAATTC
1 AGATA-CAGAAATCAGAACAGAATTC
*
207939 AGA-ACAGATATCAGAACAGAATTC
1 AGATACAGAAATCAGAACAGAATTC
*
207963 AGATA-AAAAATCAGAACAGAATTC
1 AGATACAGAAATCAGAACAGAATTC
* *
207987 AGGT-CATG-TATCAGAACAGAATTC
1 AGATACA-GAAATCAGAACAGAATTC
* *
208011 AAAT-CGGAAATCAGA
1 AGATACAGAAATCAGA
208026 TAAAATATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
23 1 0.01
24 66 0.92
25 2 0.03
26 3 0.04
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (25 bp):
AGATACAGAAATCAGAACAGAATTC
Found at i:208022 original size:48 final size:48
Alignment explanation
Indices: 207920--208025 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 48
207910 CGGAGATATC
* *
207920 AGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATTCAGATA
1 AGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATTCAAATA
* ** *
207968 AAAAATCAGAACAGAATTCAGGTCATG-TATCAGAACAGAATTCAAATC
1 AGAAATCAGAACAGAATTCAGAACA-GATATCAGAACAGAATTCAAATA
*
208016 GGAAATCAGA
1 AGAAATCAGA
208026 TAAAATATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 48 0.98
49 1 0.02
ACGTcount: A:0.51, C:0.15, G:0.16, T:0.18
Consensus pattern (48 bp):
AGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATTCAAATA
Found at i:212432 original size:22 final size:18
Alignment explanation
Indices: 212400--212494 Score: 91
Period size: 18 Copynumber: 4.8 Consensus size: 18
212390 TGATCATTAC
212400 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCAC----TAT
*
212422 GTCTCGAAGGACCACTAT
1 GTCCCGAAGGACCACTAT
* *
212440 GTCCTGAAGGACCACTAC
1 GTCCCGAAGGACCACTAT
212458 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCAC----TAT
212480 GTCCCGAAGGACCAC
1 GTCCCGAAGGACCAC
212495 CGTAACCCTC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
18 32 0.51
22 31 0.49
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:216034 original size:29 final size:28
Alignment explanation
Indices: 216002--216243 Score: 207
Period size: 29 Copynumber: 8.4 Consensus size: 28
215992 ACCCGACCCG
* * *
216002 GTGATATTTTGGGAATTAATTTGAAAAA
1 GTGATATTTTGGTAATTATTTTTAAAAA
* * *
216030 GGTGACATTTTGGGAATTTTTTTTAAATACA
1 -GTGATATTTTGGTAATTATTTTTAAA-A-A
* * *
216061 ATGATATTCTGGTAATTATTTTTAAAACG
1 GTGATATTTTGGTAATTATTTTTAAAA-A
* * *
216090 GTGACATTTTGGGAAATT-TTTGTAAAACA
1 GTGATATTTT-GGTAATTATTTTTAAAA-A
* *
216119 ATGACATTTTGGTAATTATTTTTAAAAA
1 GTGATATTTTGGTAATTATTTTTAAAAA
** *
216147 GTGATATTTTAATAATTATTTTTAAATCA
1 GTGATATTTTGGTAATTATTTTTAAA-AA
*
216176 GTGATATTTTAGTAATTATTTTTAAAACA
1 GTGATATTTTGGTAATTATTTTTAAAA-A
* * *
216205 GTGATATTCTGGAAATTATTTTAAAAAA
1 GTGATATTTTGGTAATTATTTTTAAAAA
216233 TGTGATATTTT
1 -GTGATATTTT
216244 TGTTATTTTC
Statistics
Matches: 175, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
28 30 0.17
29 116 0.66
30 28 0.16
31 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (28 bp):
GTGATATTTTGGTAATTATTTTTAAAAA
Found at i:216137 original size:58 final size:58
Alignment explanation
Indices: 216003--216243 Score: 242
Period size: 58 Copynumber: 4.2 Consensus size: 58
215993 CCCGACCCGG
* * * * *
216003 TGATATTTTGGGAATTAATTTGAAAA-AGGTGACATTTTGGGAATTTTTTTTAAATACAA
1 TGATATTTTGGTAATTATTTTTAAAACA-GTGACATTTTGGAAATTATTTTTAAA-ACAA
* * *
216062 TGATATTCTGGTAATTATTTTTAAAACGGTGACATTTTGGGAAATT-TTTGTAAAACAA
1 TGATATTTTGGTAATTATTTTTAAAACAGTGACATTTT-GGAAATTATTTTTAAAACAA
* * * * *
216120 TGACATTTTGGTAATTATTTTTAAAA-AGTGATATTTT-AATAATTATTTTTAAATCAG
1 TGATATTTTGGTAATTATTTTTAAAACAGTGACATTTTGGA-AATTATTTTTAAAACAA
* * *
216177 TGATATTTTAGTAATTATTTTTAAAACAGTGATATTCTGGAAATTA-TTTTAAAA-AA
1 TGATATTTTGGTAATTATTTTTAAAACAGTGACATTTTGGAAATTATTTTTAAAACAA
216233 TGTGATATTTT
1 --TGATATTTT
216244 TGTTATTTTC
Statistics
Matches: 153, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
55 1 0.01
56 5 0.03
57 49 0.32
58 52 0.34
59 40 0.26
60 6 0.04
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (58 bp):
TGATATTTTGGTAATTATTTTTAAAACAGTGACATTTTGGAAATTATTTTTAAAACAA
Found at i:216202 original size:86 final size:86
Alignment explanation
Indices: 216032--216243 Score: 228
Period size: 86 Copynumber: 2.4 Consensus size: 86
216022 TTGAAAAAGG
* * * * ** *
216032 TGACATTTTGGGAATTTTTTTTAAATACAATGATATTCTGGTAATTATTTTTAAAACGGTGACAT
1 TGACATTTTGGAAATTATTTTTAAA-A-AGTGATATTTTAATAATTATTTTTAAAACAGTGACAT
*
216097 TTTGGGAAATTTTTGTAAAACAA
64 TTTGAGAAATTTTTGTAAAACAA
* * *
216120 TGACATTTTGGTAATTATTTTTAAAAAGTGATATTTTAATAATTATTTTTAAATCAGTGATATTT
1 TGACATTTTGGAAATTATTTTTAAAAAGTGATATTTTAATAATTATTTTTAAAACAGTGACATTT
* * *
216185 T-AGTAATTATTTTTAAAACAG
66 TGAGAAATT-TTTGTAAAACAA
* * *
216206 TGATATTCTGGAAATTATTTTAAAAAATGTGATATTTT
1 TGACATTTTGGAAATTATTTTTAAAAA-GTGATATTTT
216244 TGTTATTTTC
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
85 5 0.05
86 66 0.63
87 11 0.10
88 23 0.22
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (86 bp):
TGACATTTTGGAAATTATTTTTAAAAAGTGATATTTTAATAATTATTTTTAAAACAGTGACATTT
TGAGAAATTTTTGTAAAACAA
Found at i:219478 original size:24 final size:24
Alignment explanation
Indices: 219436--219484 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
219426 TGCTAATGAT
*
219436 AATGTAAATAATGCTAATGATAAA
1 AATGTAAATAATGCAAATGATAAA
*
219460 AATGTAAATAAT-CAAAATGTTAAA
1 AATGTAAATAATGC-AAATGATAAA
219484 A
1 A
219485 TCACACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.57, C:0.04, G:0.10, T:0.29
Consensus pattern (24 bp):
AATGTAAATAATGCAAATGATAAA
Found at i:221450 original size:21 final size:22
Alignment explanation
Indices: 221368--221451 Score: 68
Period size: 21 Copynumber: 3.9 Consensus size: 22
221358 CAGAACCCCA
*
221368 GGGGGGTATCGATTCCC-C-TGT
1 GGGGGGAATCGATTCCCTCAT-T
* *
221389 GGGGGGAATCGGTTCCCCTTCA-A
1 GGGGGGAATCGATT-CCC-TCATT
* *
221412 AGGGGGAATCGGTTCCCTCATT
1 GGGGGGAATCGATTCCCTCATT
221434 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
221452 TGCACCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
21 26 0.51
22 11 0.22
23 13 0.25
24 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCTCATT
Found at i:228186 original size:20 final size:20
Alignment explanation
Indices: 228163--228218 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
228153 TTAATTTTAC
*
228163 AAATATAAAAAAATCAGAAA
1 AAATAAAAAAAAATCAGAAA
*
228183 AAATACAAAAAAAATCCGAAA
1 AAATA-AAAAAAAATCAGAAA
*
228204 AATTACAAAAAAAAT
1 AAATA-AAAAAAAAT
228219 TAGTATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.73, C:0.09, G:0.04, T:0.14
Consensus pattern (20 bp):
AAATAAAAAAAAATCAGAAA
Found at i:228195 original size:21 final size:21
Alignment explanation
Indices: 228169--228218 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
228159 TTACAAATAT
228169 AAAAAAATCAGAAAAAATACA
1 AAAAAAATCAGAAAAAATACA
* *
228190 AAAAAAATCCGAAAAATTACA
1 AAAAAAATCAGAAAAAATACA
228211 AAAAAAAT
1 AAAAAAAT
228219 TAGTATGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.74, C:0.10, G:0.04, T:0.12
Consensus pattern (21 bp):
AAAAAAATCAGAAAAAATACA
Found at i:230036 original size:20 final size:20
Alignment explanation
Indices: 230011--230062 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
230001 CAATTTAAAT
*
230011 ATGACTTGCTTTCCTCCGCA
1 ATGACTTGCTTTCCACCGCA
230031 ATGACTTGCTTTCCACCGCA
1 ATGACTTGCTTTCCACCGCA
230051 ATGACTTGCTTT
1 ATGACTTGCTTT
230063 TCTTCAGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.31, G:0.15, T:0.37
Consensus pattern (20 bp):
ATGACTTGCTTTCCACCGCA
Found at i:235603 original size:273 final size:274
Alignment explanation
Indices: 235116--235657 Score: 942
Period size: 273 Copynumber: 2.0 Consensus size: 274
235106 ATCATTTTGA
235116 CAAATTTAATTTTACAATTCAGGTACAATTCCATCGGTTATCGGAAATATAATTTCTCTAGAAAT
1 CAAATTTAATTTTACAATTCAGGTACAATTCCATCGGTTATCGGAAATATAATTTCTCTAGAAAT
* * * *
235181 TATTGATTTTTCGAATAACAACTTGGCATGTATAATATAACTTTCCTTCCTTTTTTTGTTGTTAT
66 TATTCATTTTTCGAATAACAACTTGACAGGTATAATATAACTTTCCTTCCTCTTTTTGTTGTTAT
* * *
235246 TTTGTTATACATTTATTAATTAGTTATAAGAATTTTTGTCATTTGATGTGTCCTTTTGTATTAAA
131 TTTGCTATACATTTATTAATTAGTTATAAGAATTTTTGTCATTTGACGTATCCTTTTGTATTAAA
* *
235311 ACATAAATCATTTAAATATTAAACACAGATAAATCCATTCTAAAATGATTTAAATTTTAATTATC
196 ACATAAATCATTTAAATATTAAACACAGATAAATCCATTCTAAAATGATTTAAATTTAAAATATC
235376 -TTATTTTTTTCGT
261 TTTATTTTTTTCGT
* *
235389 CAAATTTAATTTTACATTTCAGGTACAATTCCATCGGTTATCGGAAATATAATTTCTCTAGAGAT
1 CAAATTTAATTTTACAATTCAGGTACAATTCCATCGGTTATCGGAAATATAATTTCTCTAGAAAT
235454 TATTCATTTTTCGAATAACAACTTGACAGGTATAATATAACTTTCCTTCCTCTTTTTGTTGTTAT
66 TATTCATTTTTCGAATAACAACTTGACAGGTATAATATAACTTTCCTTCCTCTTTTTGTTGTTAT
* *
235519 TTTGCTATATATTTATTAATTAGTTATAAGAATTTTTGTCATTTGACGTATCCTTTTGTATTCAA
131 TTTGCTATACATTTATTAATTAGTTATAAGAATTTTTGTCATTTGACGTATCCTTTTGTATTAAA
* *
235584 ACATAAATCGTTTAAATATTAAACTCAGATAAATCCATTCTAAAATGATTTAAATTTAAAATATC
196 ACATAAATCATTTAAATATTAAACACAGATAAATCCATTCTAAAATGATTTAAATTTAAAATATC
235649 TTTATTTTT
261 TTTATTTTT
235658 AACTTGAAAT
Statistics
Matches: 253, Mismatches: 15, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
273 245 0.97
274 8 0.03
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (274 bp):
CAAATTTAATTTTACAATTCAGGTACAATTCCATCGGTTATCGGAAATATAATTTCTCTAGAAAT
TATTCATTTTTCGAATAACAACTTGACAGGTATAATATAACTTTCCTTCCTCTTTTTGTTGTTAT
TTTGCTATACATTTATTAATTAGTTATAAGAATTTTTGTCATTTGACGTATCCTTTTGTATTAAA
ACATAAATCATTTAAATATTAAACACAGATAAATCCATTCTAAAATGATTTAAATTTAAAATATC
TTTATTTTTTTCGT
Found at i:240195 original size:15 final size:15
Alignment explanation
Indices: 240173--240214 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
240163 TTAAATTAAA
240173 AAATATATATAATATT
1 AAATATATATAAT-TT
* *
240189 -TATATATTTAATTT
1 AAATATATATAATTT
240203 AAATATATATAA
1 AAATATATATAA
240215 CTAGCCCGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATATATATAATTT
Found at i:242639 original size:3 final size:3
Alignment explanation
Indices: 242623--242665 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
242613 TTTTTATTTA
* *
242623 TAT TATT TATT TAT TAT AAA TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
242666 AATAATAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 28 0.80
4 7 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:244002 original size:29 final size:29
Alignment explanation
Indices: 243944--244006 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
243934 AATACTTTCA
*
243944 TTATTTTTAACTACAAGTTTTATTACTTT
1 TTATTTTTAACTACAAGTTTTATTAATTT
* * *
243973 TTATATTTTAA-TACTATTTTTTTTAA-TT
1 TTAT-TTTTAACTACAAGTTTTATTAATTT
244001 TTATTT
1 TTATTT
244007 GTTTTAGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.07
28 6 0.21
29 15 0.52
30 6 0.21
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (29 bp):
TTATTTTTAACTACAAGTTTTATTAATTT
Found at i:244104 original size:11 final size:11
Alignment explanation
Indices: 244076--244109 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
244066 ATATGTTTAA
*
244076 ATTATTACTTTA
1 ATTATTA-TTTT
244088 ATTATTATTTT
1 ATTATTATTTT
244099 ATTATTATTTT
1 ATTATTATTTT
244110 CATCTTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:246370 original size:43 final size:44
Alignment explanation
Indices: 246304--246389 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 44
246294 GGCTTTAGAG
* *
246304 AAGTTAGGAGAGAAAGTTATCCCCTATATGT-AAAGTTTTGTTA
1 AAGTTAGGACAGAAAGTTATCCCCTACATGTAAAAGTTTTGTTA
* *
246347 AAGTTAGGACTGAAAGTTGTCCCCTACATGTAAAAGTTTTGTT
1 AAGTTAGGACAGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
246390 TGATGCACCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
43 27 0.71
44 11 0.29
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (44 bp):
AAGTTAGGACAGAAAGTTATCCCCTACATGTAAAAGTTTTGTTA
Found at i:246541 original size:14 final size:15
Alignment explanation
Indices: 246522--246559 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
246512 TATTACACAA
*
246522 TTTGCATTCT-TATT
1 TTTGCATTCTACATT
246536 TTTGCATTTCTACATT
1 TTTGCA-TTCTACATT
246552 TTTGCATT
1 TTTGCATT
246560 TTCATGTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 9 0.43
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.61
Consensus pattern (15 bp):
TTTGCATTCTACATT
Found at i:246636 original size:20 final size:20
Alignment explanation
Indices: 246599--246641 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
246589 TATTTGTATC
* *
246599 TTTACATTTTTACGTTTGTA
1 TTTACATTTTCACGTTTGCA
**
246619 TTTACATTTTCATTTTTGCA
1 TTTACATTTTCACGTTTGCA
246639 TTT
1 TTT
246642 GCATCTTTGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.63
Consensus pattern (20 bp):
TTTACATTTTCACGTTTGCA
Found at i:246936 original size:42 final size:42
Alignment explanation
Indices: 246867--246950 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
246857 AGATATGATT
* * * * * *
246867 GATCAAGTAAAAAAGTTCCAGGGTGATTGAAATGAACAAATG
1 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
*
246909 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAGCAAATG
1 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
246951 ACAAAACTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.19
Consensus pattern (42 bp):
GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
Found at i:250945 original size:75 final size:75
Alignment explanation
Indices: 250856--251027 Score: 254
Period size: 75 Copynumber: 2.3 Consensus size: 75
250846 AACAAGAAAA
* * *
250856 AAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAAATTGGAATTTTGACGCATTTTGAACGT
1 AAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAAATAGAAATATTGACGCATTTTGAACGT
*
250921 TTATATCAGC
66 TCATATCAGC
* * *
250931 AAATGCTGGGGCATGCTGGAAGCCCATTTCAATCAAAAATAGAAATATTGACGCATTTTGAACGT
1 AAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAAATAGAAATATTGACGCATTTTGAACGT
*
250996 TCGTATCAGC
66 TCATATCAGC
* *
251006 AATTGTTGGGGTATGTTGAAAG
1 AAATGTTGGGGCATGTTGAAAG
251028 TCTATATTAT
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 84 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (75 bp):
AAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAAATAGAAATATTGACGCATTTTGAACGT
TCATATCAGC
Found at i:252308 original size:22 final size:22
Alignment explanation
Indices: 252282--252427 Score: 256
Period size: 22 Copynumber: 6.6 Consensus size: 22
252272 TACATATACA
252282 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
252304 CTCTTCAAAGATGATAGATCCA
1 CTCTTCAAAGATGATAGATTCT
*
252326 CTCTTCAAAGATGATAGATCCT
1 CTCTTCAAAGATGATAGATTCT
252348 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
252370 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
252392 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
252414 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
252428 AAGCTTTATT
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:252967 original size:102 final size:102
Alignment explanation
Indices: 252791--252984 Score: 345
Period size: 102 Copynumber: 1.9 Consensus size: 102
252781 AATACGTCAC
252791 TCGATGGATCAACTTGTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAAAA
1 TCGATGGATCAACTTGTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAAAA
252856 GTTCATAATGAGAAGAACTTGTTCAACTTTAACTTGA
66 GTTCATAATGAGAAGAACTTGTTCAACTTTAACTTGA
* * *
252893 TCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGA
1 TCGATGGATCAACTTGTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAAA
252957 AGTTCATAATGAGAAGAACTTGTTCAAC
65 AGTTCATAATGAGAAGAACTTGTTCAAC
252985 CTTTTGCTCG
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
101 3 0.03
102 85 0.97
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.25
Consensus pattern (102 bp):
TCGATGGATCAACTTGTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAAAA
GTTCATAATGAGAAGAACTTGTTCAACTTTAACTTGA
Found at i:253219 original size:123 final size:122
Alignment explanation
Indices: 252900--253232 Score: 486
Period size: 122 Copynumber: 2.7 Consensus size: 122
252890 TGATCGATGG
*
252900 ATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * *
252965 ATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTTTCACAAAAGGAGATAGATTAAC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTGTAACAAAAGGAGATAGATCAAC
* * * * *
253023 ACCAACATTTCCAGAAGTGTTCATAATGAAAAGAACCCATCTGAAGAGGAAGAAGAAGTTTATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * *
253088 TGAGAAGAATTTGTTCAACCTTTTGCTTGACTCTGTAACAGAAGGAGATAGATCAAC
66 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTGTAACAAAAGGAGATAGATCAAC
* * *
253145 ATCAACATTTCCTGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
253210 ATGATAAGAACTTGTTCGACCTT
65 ATGAGAAGAACTTGTTCAACCTT
253233 AGCTTGATTC
Statistics
Matches: 185, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
122 109 0.59
123 76 0.41
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (122 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTGTAACAAAAGGAGATAGATCAAC
Found at i:253312 original size:137 final size:135
Alignment explanation
Indices: 253161--253502 Score: 449
Period size: 137 Copynumber: 2.5 Consensus size: 135
253151 ATTTCCTGAT
* *
253161 AAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGATAAGAACTTGTT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
253226 CGACCTTAG-CTTGATTCATCACCTATGGAGTTGAATAAAAGAAGAACCTCCCTT-GAGGATCAA
66 CAACCTT-GCCTTAATTCATCACATATGAAGTTGAATAAAAG-A-AACC-CCCTTCGAGGATCAA
253289 CATTTTC-AG
127 C-TTTTCTAG
*
253298 AAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * ** *
253363 CAACCTTGCCTTAATTCATCACATATGAAGTTGAATCAATGACACCCTTTTCGAGGATCAGCTTT
66 CAACCTTGCCTTAATTCATCACATATGAAGTTGAATAAAAGAAACCCCCTTCGAGGATCAACTTT
253428 TCTAG
131 TCTAG
* * *
253433 AAGGAGTTCATAATGAGAAGAACTCATCTGACGAGGAAAAAG-AGTTCATAATGAGAAGAATTTG
1 AA--AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
253497 TTCAAC
64 TTCAAC
253503 TTTTTGCTAG
Statistics
Matches: 183, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
134 8 0.04
135 16 0.09
136 29 0.16
137 130 0.71
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (135 bp):
AAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTGCCTTAATTCATCACATATGAAGTTGAATAAAAGAAACCCCCTTCGAGGATCAACTTT
TCTAG
Found at i:253787 original size:19 final size:19
Alignment explanation
Indices: 253765--253802 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
253755 TATTTTATTT
253765 TATTA-TATTATAATAATAA
1 TATTATTATTA-AATAATAA
253784 TATTATTATTAAATAATAA
1 TATTATTATTAAATAATAA
253803 ATAATTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTATTATTAAATAATAA
Found at i:256263 original size:67 final size:67
Alignment explanation
Indices: 256155--256291 Score: 265
Period size: 67 Copynumber: 2.0 Consensus size: 67
256145 AATCATTGAG
256155 TAAGTTTTTGTTTTCTTATTAAAATTTTAAAACAAATAAATTAGTCAGTAACATTATCGATATAT
1 TAAGTTTTTGTTTTCTTATTAAAATTTTAAAACAAATAAATTAGTCAGTAACATTATCGATATAT
256220 AA
66 AA
*
256222 TAAGTTTTTGTTTTCTTATTAAAATTTTAAAACAAATAAATTAGTCAGTAACGTTATCGATATAT
1 TAAGTTTTTGTTTTCTTATTAAAATTTTAAAACAAATAAATTAGTCAGTAACATTATCGATATAT
256287 AA
66 AA
256289 TAA
1 TAA
256292 ATCGATCATT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (67 bp):
TAAGTTTTTGTTTTCTTATTAAAATTTTAAAACAAATAAATTAGTCAGTAACATTATCGATATAT
AA
Found at i:257426 original size:2 final size:2
Alignment explanation
Indices: 257419--257446 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
257409 TATAAGTATC
257419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
257447 TAGATAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:257633 original size:21 final size:23
Alignment explanation
Indices: 257608--257651 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
257598 AAAGATAAGA
257608 TTAAATATCCA-TAT-TATATAT
1 TTAAATATCCATTATATATATAT
257629 TTAAATATCCATTATATATATAT
1 TTAAATATCCATTATATATATAT
257652 ATATATATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.52
22 3 0.14
23 7 0.33
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAATATCCATTATATATATAT
Found at i:257657 original size:21 final size:21
Alignment explanation
Indices: 257609--257659 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 21
257599 AAGATAAGAT
*
257609 TAAATATCCATATTATATATT
1 TAAATATCCATATTATATATA
257630 TAAATATCCATTATATATATATA
1 TAAATATCCA-TAT-TATATATA
*
257653 TATATAT
1 TAAATAT
257660 GTATATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 3 0.12
23 13 0.50
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAATATCCATATTATATATA
Found at i:258006 original size:2 final size:2
Alignment explanation
Indices: 257999--258041 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
257989 CAATACATAC
257999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
258041 A
1 A
258042 GGTTTCTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:263891 original size:43 final size:43
Alignment explanation
Indices: 263797--263892 Score: 106
Period size: 43 Copynumber: 2.2 Consensus size: 43
263787 ATTGTTCAAC
**
263797 AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCAGTA
1 AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCACAA
* * * *
263840 AAATGCCGCAATA-GTCGTTGATGTTTAGCGGCGTTT-TCTACAA
1 AAACGCCGCAAAAGGT-ATTGATATTTAGCGGCGTTTATC-ACAA
263883 AAACGCCGCA
1 AAACGCCGCA
263893 GTATATTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
42 4 0.09
43 40 0.91
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCACAA
Found at i:264380 original size:21 final size:21
Alignment explanation
Indices: 264316--264424 Score: 103
Period size: 21 Copynumber: 5.2 Consensus size: 21
264306 TGATATATTA
* * *
264316 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * *
264337 CCTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
264358 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* **
264379 CTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* *
264400 CTGCTCTCTCTGTTTCC-CTTG
1 CTTCTCTCTCTGCTTCCGC-TG
264421 CTTC
1 CTTC
264425 ATTTTCCGCT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
20 1 0.01
21 74 0.99
ACGTcount: A:0.01, C:0.40, G:0.18, T:0.40
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:268479 original size:42 final size:42
Alignment explanation
Indices: 268433--268623 Score: 119
Period size: 41 Copynumber: 4.6 Consensus size: 42
268423 AAACACCGCC
* *
268433 AATTTACCGCTCTATTGCGGCGTTTTGACTCAATCGCCGCAA
1 AATTTACCACTCTATTGCGGCGTTTTGACTAAATCGCCGCAA
* * * * * *
268475 AATTTA-TACTCTATTGTGGCGTTTGTG-GTAAAAACGCTGC-C
1 AATTTACCACTCTATTGCGGCGTTT-TGACT-AAATCGCCGCAA
* *
268516 AGTTTACCACTATATTGCGGCGTTTT-AGCTAAATCGCCGCAA
1 AATTTACCACTCTATTGCGGCGTTTTGA-CTAAATCGCCGCAA
* * ** * *
268558 AATTTA-TAATCTATTGAAGCGTTTGTGA-TATAAACGCCGC-T
1 AATTTACCACTCTATTGCGGCGTTT-TGACTA-AATCGCCGCAA
* *
268599 AA-TTAACACACTATTGCGGCGTTTT
1 AATTTACCACTCTATTGCGGCGTTTT
268624 TAGAAAAACG
Statistics
Matches: 110, Mismatches: 29, Indels: 22
0.68 0.18 0.14
Matches are distributed among these distances:
40 4 0.04
41 60 0.55
42 45 0.41
43 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (42 bp):
AATTTACCACTCTATTGCGGCGTTTTGACTAAATCGCCGCAA
Found at i:268522 original size:83 final size:83
Alignment explanation
Indices: 268398--268623 Score: 251
Period size: 83 Copynumber: 2.7 Consensus size: 83
268388 ACTATATGTG
* * * * * * * *
268398 TAATATATTGCGGCGTTTTTTGTCAAAACACCGCCAATTTACCGCTCTATTGCGGCGTTTT-GAC
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTATATTGCGGCGTTTTAG-C
*
268462 TCAATCGCCGCAAAATTTA
65 TAAATCGCCGCAAAATTTA
* * * *
268481 TACTCTATTGTGGCGTTTGTGGTAAAAACGCTGCCAGTTTACCACTATATTGCGGCGTTTTAGCT
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTATATTGCGGCGTTTTAGCT
268546 AAATCGCCGCAAAATTTA
66 AAATCGCCGCAAAATTTA
* * * * *
268564 TAATCTATTGAAGCGTTTGTGATATAAACGCCGCTAA-TTAACAC-ACTATTGCGGCGTTTT
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTA-TATTGCGGCGTTTT
268624 TAGAAAAACG
Statistics
Matches: 120, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
81 1 0.01
82 20 0.17
83 98 0.82
84 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (83 bp):
TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTATATTGCGGCGTTTTAGCT
AAATCGCCGCAAAATTTA
Found at i:274087 original size:109 final size:110
Alignment explanation
Indices: 273911--274159 Score: 271
Period size: 109 Copynumber: 2.3 Consensus size: 110
273901 TCCCCCTAGG
* * * * *
273911 TTTATCGTAGTTTTACATTTTAGTCACATGT-AGGGAC-CAAATCTGTTATTTTCACTTTTCTTC
1 TTTAGCGTATTTTTACACTTTAGTCATATGTGA-GGACTGAAATCTGTTATTTTCACTTTTCTTC
* *
273974 GCATGTTAT-ATAATT-TTTGGTATATTCACTATTCAGTCCCTCTAAC
65 GCATGTTATAAT-ATTATTAGGT-TATTCACTATTCAGTCCCTATAAC
* * *
274020 TTTAGCGTGTTTTTGCA-TTCTGGTCATATGTGAGGACTGAAAT-TGTTATTTTTC-CTTTTCCT
1 TTTAGCGTATTTTTACACTT-TAGTCATATGTGAGGACTGAAATCTGTTA-TTTTCACTTTT-CT
* * *
274082 T-GCATGTTATAATATTATTAGGTTATTTACTATTTAGTCCCTATAAG
63 TCGCATGTTATAATATTATTAGGTTATTCACTATTCAGTCCCTATAAC
274129 TTTAGCGTATTTTTACACTTTAGTCATATGT
1 TTTAGCGTATTTTTACACTTTAGTCATATGT
274160 AGTGACTTTT
Statistics
Matches: 117, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
108 2 0.02
109 93 0.79
110 22 0.19
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.48
Consensus pattern (110 bp):
TTTAGCGTATTTTTACACTTTAGTCATATGTGAGGACTGAAATCTGTTATTTTCACTTTTCTTCG
CATGTTATAATATTATTAGGTTATTCACTATTCAGTCCCTATAAC
Found at i:276078 original size:2 final size:2
Alignment explanation
Indices: 276071--276098 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
276061 TAATATTTGA
276071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
276099 TAAAGTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:277639 original size:20 final size:21
Alignment explanation
Indices: 277614--277656 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
277604 ATATTCTTAT
*
277614 AATTTTAAAATT-TTTATTTA
1 AATTTTAAAATTATATATTTA
277634 AATTTTAAAATTATATATTTA
1 AATTTTAAAATTATATATTTA
277655 AA
1 AA
277657 AAAAACACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTTTAAAATTATATATTTA
Found at i:279043 original size:17 final size:17
Alignment explanation
Indices: 279005--279039 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
278995 TAATAATGAG
279005 TTATTATAAAATATATT
1 TTATTATAAAATATATT
*
279022 TTATTAT-AATTATATT
1 TTATTATAAAATATATT
279038 TT
1 TT
279040 TATTTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTATAAAATATATT
Found at i:282556 original size:34 final size:34
Alignment explanation
Indices: 282513--282589 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
282503 TGCACCTGGG
282513 GCTTCCGGTGGATGGAGGTGTGATATAAGGGATA
1 GCTTCCGGTGGATGGAGGTGTGATATAAGGGATA
282547 GCTTCCGGTGGATGGAGGTGTGATATAAGGGATA
1 GCTTCCGGTGGATGGAGGTGTGATATAAGGGATA
282581 GCTTCCGGT
1 GCTTCCGGT
282590 TCTTGGACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.21, C:0.12, G:0.40, T:0.27
Consensus pattern (34 bp):
GCTTCCGGTGGATGGAGGTGTGATATAAGGGATA
Found at i:282899 original size:3 final size:3
Alignment explanation
Indices: 282891--282925 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
282881 ACCTACTCAG
* *
282891 GAC GAC GAC AAC GAC GAA GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
282926 TGATGGTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.40, C:0.29, G:0.31, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:283200 original size:35 final size:33
Alignment explanation
Indices: 283160--283244 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
283150 GTATTTAAGT
283160 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
283195 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
283230 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
283245 TAAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:291323 original size:50 final size:50
Alignment explanation
Indices: 291200--291323 Score: 176
Period size: 50 Copynumber: 2.5 Consensus size: 50
291190 TTCCATATTC
* * *
291200 TTCCATACTCTTCCATAAGGTTCCACACATCTCCAAAATATTCCAAAGGA
1 TTCCACACTCTTCCATAAGCTTCTACACATCTCCAAAATATTCCAAAGGA
* * * *
291250 GTCCACACTCTTCCATAAGCTTCTACACATCTCTAGAATATTCCAGAGGA
1 TTCCACACTCTTCCATAAGCTTCTACACATCTCCAAAATATTCCAAAGGA
*
291300 TTCCACACTCTTCCAAAAGCTTCT
1 TTCCACACTCTTCCATAAGCTTCT
291324 GGAGAGTTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.29
Consensus pattern (50 bp):
TTCCACACTCTTCCATAAGCTTCTACACATCTCCAAAATATTCCAAAGGA
Found at i:299129 original size:50 final size:50
Alignment explanation
Indices: 299065--299186 Score: 138
Period size: 50 Copynumber: 2.4 Consensus size: 50
299055 TCCACTCCCT
* *
299065 TCCATACTCTTCCATAATG-TTCCACACATCTCCAGAATATTCCAAAGGAG
1 TCCACACTCTTCCATAA-GCTTCCACACATCTCCAAAATATTCCAAAGGAG
* ** * * * *
299115 TCCACACTCTTCCATAAGCTTCTACGTATCTTCAAAATATTCTAGAGGAT
1 TCCACACTCTTCCATAAGCTTCCACACATCTCCAAAATATTCCAAAGGAG
*
299165 TCCACACTCTTCCACAAGCTTC
1 TCCACACTCTTCCATAAGCTTC
299187 TAGAGAGTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
49 1 0.02
50 60 0.98
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (50 bp):
TCCACACTCTTCCATAAGCTTCCACACATCTCCAAAATATTCCAAAGGAG
Done.