Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011592.1 Kokia drynarioides strain JFW-HI SEQ_126582, 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: 190359
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:295 original size:17 final size:17
Alignment explanation
Indices: 248--313 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
238 ATATATATGG
**
248 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
265 AGATGCAGCT-ACAATAA
1 AAATGCA-ATGACAATAA
282 AAATGCAATGACAATAA
1 AAATGCAATGACAATAA
* *
299 TAATGCAAGGACAAT
1 AAATGCAATGACAAT
314 TATACTATAG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 1 0.03
17 37 0.95
18 1 0.03
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.20
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:313 original size:34 final size:34
Alignment explanation
Indices: 248--313 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
238 ATATATATGG
* *
248 AAATGCAATGACAATGTAGATGCAGCTACAATAA
1 AAATGCAATGACAATATAGATGCAGCGACAATAA
282 AAATGCAATGACAATAATA-ATGCAAG-GACAAT
1 AAATGCAATGACAAT-ATAGATGC-AGCGACAAT
314 TATACTATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGCAGCGACAATAA
Found at i:699 original size:18 final size:18
Alignment explanation
Indices: 676--714 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
666 TTGCATTGGA
676 TGCCCTCACATTTACGGG
1 TGCCCTCACATTTACGGG
694 TGCCCTCACATTTACGGG
1 TGCCCTCACATTTACGGG
712 TGC
1 TGC
715 TTCAACAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.23, T:0.28
Consensus pattern (18 bp):
TGCCCTCACATTTACGGG
Found at i:4412 original size:242 final size:242
Alignment explanation
Indices: 3987--4474 Score: 958
Period size: 242 Copynumber: 2.0 Consensus size: 242
3977 AAAATGTGAT
3987 GTTTAATTATAAATATGATAATTATGTGTGATTGAATGAAATTTAGTATAAAGAAGCATGAGAAA
1 GTTTAATTATAAATATGATAATTATGTGTGATTGAATGAAATTTAGTATAAAGAAGCATGAGAAA
*
4052 GGAATTAATCTCATTGAAACAGTTTCGACAGAACAGAGGACTAACTTCAAAAATTCATCAAAAAT
66 GGAATTAATCTCATTGAAACAGTTTCGACAGAACAGAGGACTAACTTCAAAAATTCACCAAAAAT
4117 TGTATAAAAATATTTAAAAGTTGAATTAAATATGTAATTAAATATTATTTAGTGTAGTTTCATAT
131 TGTATAAAAATATTTAAAAGTTGAATTAAATATGTAATTAAATATTATTTAGTGTAGTTTCATAT
4182 GGAAGAAACATTGAAATAAAAGGAATTTTATATTTTTAGATATACTA
196 GGAAGAAACATTGAAATAAAAGGAATTTTATATTTTTAGATATACTA
4229 GTTTAATTATAAATATGATAATTATGTGTGATTGAATGAAATTTAGTATAAAGAAGCATGAGAAA
1 GTTTAATTATAAATATGATAATTATGTGTGATTGAATGAAATTTAGTATAAAGAAGCATGAGAAA
4294 GGAATTAATCTCATTGAAACAGTTTCGACAGAACAGAGGACTAACTTCAAAAATTCACCAAAAAT
66 GGAATTAATCTCATTGAAACAGTTTCGACAGAACAGAGGACTAACTTCAAAAATTCACCAAAAAT
4359 TGTATAAAAATATTTAAAAGTTGAATTAAATATGTAATTAAATATTATTTAGTGTAGTTTCATAT
131 TGTATAAAAATATTTAAAAGTTGAATTAAATATGTAATTAAATATTATTTAGTGTAGTTTCATAT
*
4424 GGAGGAAACATTGAAATAAAAGGAATTTTATATTTTTAGATATACTA
196 GGAAGAAACATTGAAATAAAAGGAATTTTATATTTTTAGATATACTA
4471 GTTT
1 GTTT
4475 TTGTGTAACA
Statistics
Matches: 244, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
242 244 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (242 bp):
GTTTAATTATAAATATGATAATTATGTGTGATTGAATGAAATTTAGTATAAAGAAGCATGAGAAA
GGAATTAATCTCATTGAAACAGTTTCGACAGAACAGAGGACTAACTTCAAAAATTCACCAAAAAT
TGTATAAAAATATTTAAAAGTTGAATTAAATATGTAATTAAATATTATTTAGTGTAGTTTCATAT
GGAAGAAACATTGAAATAAAAGGAATTTTATATTTTTAGATATACTA
Found at i:5219 original size:6 final size:6
Alignment explanation
Indices: 5208--5246 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
5198 TGATCAAAAT
* * *
5208 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
5247 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:14752 original size:29 final size:25
Alignment explanation
Indices: 14711--14768 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
14701 CCATCACAGG
14711 ATAATTTATCATCCATTTACATATCAT
1 ATAATTTATCAT-C-TTTACATATCAT
*
14738 ATAAGTTTATTCATCTTTCCATATCAT
1 ATAA-TTTA-TCATCTTTACATATCAT
14765 ATAA
1 ATAA
14769 ACATTAAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 19 0.68
28 5 0.18
29 4 0.14
ACGTcount: A:0.36, C:0.17, G:0.02, T:0.45
Consensus pattern (25 bp):
ATAATTTATCATCTTTACATATCAT
Found at i:17596 original size:147 final size:145
Alignment explanation
Indices: 17108--17806 Score: 976
Period size: 146 Copynumber: 4.8 Consensus size: 145
17098 TTGTTAAAAA
* * * *
17108 TTTAAAATAACTAAAAAACA-ATTTTTTATTTTTAAACATCTAAACTTTTTCTTTTTTAAAGATA
1 TTTAAAATAACTAAAAAACAGA-TTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAA
* * *
17172 ATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAATCAAAACTTTGTTA
65 ATAACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAATCAAAACTTTGTTA
*
17237 AAATTTTAATTTTTTTC
130 AAATTTTAA-ATTTTTC
* **
17254 TTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATATAAACACTCTCTTTTTTAAAGAAAA
1 TTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAA
*
17319 TAATTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAATAAATCAAAACTTTGTTA
66 TAACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAA-AAATCAAAACTTTGTTA
17384 AAATTTTAAA-TTTT-
130 AAATTTTAAATTTTTC
* * ****
17398 TTTAAAATAACT-AAAAACAAATTTTTATTTTTAAAAATATAAACATTCTCTTTTTTTTTTAAAA
1 TTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAA
* *
17462 TAACTATTTTACCTAAAACTCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAATTTTGTT
66 TAACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTT--AAAAAATCAAAACTTTGTT
17527 AAAATTTTAAACTTTTTC
129 AAAATTTTAAA-TTTTTC
17545 TTTAAAATAACT-AAAAACAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAA
1 TTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAA
* * *
17609 TCACTATTTTACCTAAAAATTCAAACTTTTATTTCAAAATAGTTAAAAAATCAAAACTTTGTTAA
66 TAACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAATCAAAACTTTGTTAA
17674 AATTTTAAAATTTTTC
131 AATTTT-AAATTTTTC
* * * *
17690 TTTAAAACAACTAAAAAACATATTTTTATTTTTAAAAATCTAAATTTTCTCTTTTTTAAAGAAAA
1 TTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAA
* * * ** * *
17755 TCACTATTTTGCTTAAAAAATTAAAACTTTTATTTTGAAATTGTTTAAAAAA
66 TAACTATTTTACCT-AAAAATCCAAACTTTTATTTCGAAATAG-TTAAAAAA
17807 AAAAACAAAA
Statistics
Matches: 499, Mismatches: 43, Indels: 20
0.89 0.08 0.04
Matches are distributed among these distances:
143 87 0.17
144 38 0.08
145 50 0.10
146 167 0.33
147 149 0.30
148 8 0.02
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (145 bp):
TTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAA
TAACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAATCAAAACTTTGTTAA
AATTTTAAATTTTTC
Found at i:18251 original size:3 final size:3
Alignment explanation
Indices: 18243--18302 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
18233 AAAAAATTAA
* * * * * *
18243 AAT AAT AAT AAT AAG AAG AAT AAA AAT AAG AAT AAG AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
18291 GAT AAT AAT AAT
1 AAT AAT AAT AAT
18303 TTAGGCTCAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:25027 original size:56 final size:55
Alignment explanation
Indices: 24935--25148 Score: 250
Period size: 56 Copynumber: 3.8 Consensus size: 55
24925 AAAATCGAAG
* ** * *
24935 ACCATATAGTGTCAGAGATAGTCATGGTGACTATGGCATCATATGGACAATTGAAT
1 ACCATATAGTGTAAGACCTAG-CATGGTGGCTATGGCATCATATGGAGAATTGAAT
* *
24991 ACCATATAGTGTAAAACCTAGTCATGGTGGCAATGGCATCATAT-GAGGAATTGAAT
1 ACCATATAGTGTAAGACCTAG-CATGGTGGCTATGGCATCATATGGA-GAATTGAAT
* * * * *
25047 ATCATATAGTGCAAGACCTACGCATGGTGGCTATGGCATCATATGGGGAAATGAAG
1 ACCATATAGTGTAAGACCTA-GCATGGTGGCTATGGCATCATATGGAGAATTGAAT
* * *
25103 ACCACATAGTGTAAGACCTAGCCTGGTGGCTATGGCATCATGTGGA
1 ACCATATAGTGTAAGACCTAGCATGGTGGCTATGGCATCATATGGA
25149 AGAAGATGAA
Statistics
Matches: 135, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
55 25 0.19
56 108 0.80
57 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (55 bp):
ACCATATAGTGTAAGACCTAGCATGGTGGCTATGGCATCATATGGAGAATTGAAT
Found at i:25291 original size:29 final size:29
Alignment explanation
Indices: 25258--25413 Score: 163
Period size: 29 Copynumber: 5.4 Consensus size: 29
25248 TAAAAAAGGA
**
25258 AGCCTTTATGGCAGATTCTGTTATATGTG
1 AGCCTTTATGGTTGATTCTGTTATATGTG
*
25287 AGCCTTTATGGTTGATT-T-TTTTATGTG
1 AGCCTTTATGGTTGATTCTGTTATATGTG
* * *
25314 AGAGCTTTCGTGGTTGATTCTATTATATGTG
1 AG-CCTTT-ATGGTTGATTCTGTTATATGTG
* * * *
25345 AACTTTTTTGGTTGATTTTGTTATATGTG
1 AGCCTTTATGGTTGATTCTGTTATATGTG
* *
25374 AGCCGTTGTGGTTGATTCTGTTATATGTG
1 AGCCTTTATGGTTGATTCTGTTATATGTG
*
25403 AGCCTCTATGG
1 AGCCTTTATGG
25414 CTATCTATGT
Statistics
Matches: 103, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
27 10 0.10
28 5 0.05
29 75 0.73
30 4 0.04
31 9 0.09
ACGTcount: A:0.17, C:0.10, G:0.25, T:0.47
Consensus pattern (29 bp):
AGCCTTTATGGTTGATTCTGTTATATGTG
Found at i:25342 original size:58 final size:58
Alignment explanation
Indices: 25271--25413 Score: 191
Period size: 58 Copynumber: 2.5 Consensus size: 58
25261 CTTTATGGCA
* *
25271 GATTCTGTTATATGTGAGCCTTTATGGTTGATTTT-TT-TATGTGAGAGCTTTCGTGGTT
1 GATTCTGTTATATGTGAGCCTTTATGGTTGATTTTGTTATATGTGAG-CCGTT-GTGGTT
* * * *
25329 GATTCTATTATATGTGAACTTTTTTGGTTGATTTTGTTATATGTGAGCCGTTGTGGTT
1 GATTCTGTTATATGTGAGCCTTTATGGTTGATTTTGTTATATGTGAGCCGTTGTGGTT
*
25387 GATTCTGTTATATGTGAGCCTCTATGG
1 GATTCTGTTATATGTGAGCCTTTATGG
25414 CTATCTATGT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
58 59 0.82
59 5 0.07
60 8 0.11
ACGTcount: A:0.17, C:0.09, G:0.25, T:0.49
Consensus pattern (58 bp):
GATTCTGTTATATGTGAGCCTTTATGGTTGATTTTGTTATATGTGAGCCGTTGTGGTT
Found at i:40112 original size:158 final size:158
Alignment explanation
Indices: 39816--40295 Score: 547
Period size: 158 Copynumber: 3.0 Consensus size: 158
39806 CGATTTCGAG
* * ** * * * *
39816 ATTATAGGTTATATGGGTGCTGGTCTTAGATGTCCAACATATAGCTGAGATCCAAAAAATATTA-
1 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGATCCGATAATTA-TAG
* * **
39880 CGGATTCTCCACAGCT-TGTGTGTGAAGCATTGTGTAGCCCAACATCTCGACCCACAGCTCGTGT
65 TGGATTCTCCACAGCTCT-TGTGAGAAGCATCATGTAGCCCAACATCTCGACCCACAGCTCGTGT
* *
39944 AAGCAGGCCTATTTCACAGCTCGTCTGAGC
129 GAGCAGGCCTATTTCACAGCTCGTGTGAGC
* * *
39974 ATTACAGGTTATATAGGTGCTGGTCATAGATGTCCTACCGATGGTTGAGATCCGATAATTATAGT
1 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGATCCGATAATTATAGT
* * *
40039 GGATTCTCCACAGCTCTTGTGAGTAGCATCATGTAGCCCAACATCTCGACCCATAACTCGTGTGA
66 GGATTCTCCACAGCTCTTGTGAGAAGCATCATGTAGCCCAACATCTCGACCCACAGCTCGTGTGA
* * *
40104 -CTGAGCCTATTTCACAGCTTGTGTGAGA
131 GCAG-GCCTATTTCACAGCTCGTGTGAGC
* * * * * * * *
40132 ATTACAAGTTATATGGGTACTGGTCTTAAATGTCTTACCGATGGCTAAGATTCGGTAATTATTGT
1 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGATCCGATAATTATAGT
* * * * * *
40197 GGATTCTTCACAGCTCATGCGAGCAA-CATCTTATAGCCCAACATCTCGACCCACAGCTCATGTG
66 GGATTCTCCACAGCTCTTGTGAG-AAGCATCATGTAGCCCAACATCTCGACCCACAGCTCGTGTG
40261 AGCAGGTCC-ATTTCACAGCTCGTGTGAGC
130 AGCAGG-CCTATTTCACAGCTCGTGTGAGC
40290 ATTACA
1 ATTACA
40296 TGATATGGAA
Statistics
Matches: 270, Mismatches: 46, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
157 4 0.01
158 260 0.96
159 6 0.02
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (158 bp):
ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGATCCGATAATTATAGT
GGATTCTCCACAGCTCTTGTGAGAAGCATCATGTAGCCCAACATCTCGACCCACAGCTCGTGTGA
GCAGGCCTATTTCACAGCTCGTGTGAGC
Found at i:44234 original size:41 final size:41
Alignment explanation
Indices: 44140--44322 Score: 249
Period size: 41 Copynumber: 4.4 Consensus size: 41
44130 TTGTGCTCTT
* * * * * *
44140 TCGAGTCATAAGTCTTCCTTTAACCATATTCTCATTCTCAAC
1 TCGAGACATGAGTCTTCC-TTAATCAAAATCTCATTCTCATC
* *
44182 TCGAGATATGAGTCTTCCTTAATCAAAATCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
* *
44223 TCGATACATGAGTCTTCCTTATTCAAAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
*
44264 TCGAGACATGAGTCTTCCTTATTCAAAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
*
44305 TCAAGACATGAGTCTTCC
1 TCGAGACATGAGTCTTCC
44323 ATTTATACAA
Statistics
Matches: 127, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 112 0.88
42 15 0.12
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.37
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
Found at i:55311 original size:21 final size:21
Alignment explanation
Indices: 55285--55332 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
55275 ATGACTAGCT
55285 GAAGGAA-AAGGAAAAAAAAGA
1 GAAGGAAGAA-GAAAAAAAAGA
* *
55306 GAAGGAAGAAGAGAATAAAGA
1 GAAGGAAGAAGAAAAAAAAGA
55327 GAAGGA
1 GAAGGA
55333 CTCTGTGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (21 bp):
GAAGGAAGAAGAAAAAAAAGA
Found at i:56402 original size:16 final size:16
Alignment explanation
Indices: 56383--56413 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56373 ACAAAAAATG
56383 AGAAAAAGAAAGAAAA
1 AGAAAAAGAAAGAAAA
56399 AGAAAAAGAAAGAAA
1 AGAAAAAGAAAGAAA
56414 TTTTTGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAGAAAA
Found at i:63650 original size:158 final size:158
Alignment explanation
Indices: 63362--63841 Score: 674
Period size: 158 Copynumber: 3.0 Consensus size: 158
63352 CGATTTTAGG
* **
63362 ATTACAAGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGTTGAGATCCGACAATTATTGT
1 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGTTGAGATCCGACAATTATTAC
** * * * * * *
63427 GGTTTTTCCGCAGCTCGTGTGAGTAGCATCGTGTAGCCCAACATCTCAACCCACGGCTTAG-GTG
66 GAATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCCAACATCTCGACCCACAGC-TCGTGTG
63491 AGCAGGCTCATTTCACAGCTCGTGTGAGC
130 AGCAGGCTCATTTCACAGCTCGTGTGAGC
* * *
63520 ATTACAGGTTATATGGGTGTTGGTCTTAGATGTCCTACCGATGGCTGAGATCCGATAATTATTAC
1 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGTTGAGATCCGACAATTATTAC
* * *
63585 GAATTCTCCACAACTAGTGTGAGCAGCATCGTATAGCCCAACATCTCGACCCACAGCTCGTGTGA
66 GAATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCCAACATCTCGACCCACAGCTCGTGTGA
* *
63650 GCAAGCTCATTTCATAGCTCGTGTGAGC
131 GCAGGCTCATTTCACAGCTCGTGTGAGC
* * * * * ** *
63678 ATTACAGGTTATATAGGTGCTAGTCTAAGATGTTCTATCGATGGTTGAGATTTGGCAATTATTAC
1 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGTTGAGATCCGACAATTATTAC
* *
63743 GAATTCTTCACAGCTCGTGTGAGCAGCATCGTGTAGCCCAACATCTCGACCCACAACTCGTGTGA
66 GAATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCCAACATCTCGACCCACAGCTCGTGTGA
*
63808 GCAGGCCCATTTCACAGCTCGTGTGAGC
131 GCAGGCTCATTTCACAGCTCGTGTGAGC
63836 ATTACA
1 ATTACA
63842 TGATATGGAA
Statistics
Matches: 283, Mismatches: 38, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
157 2 0.01
158 281 0.99
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (158 bp):
ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGTTGAGATCCGACAATTATTAC
GAATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCCAACATCTCGACCCACAGCTCGTGTGA
GCAGGCTCATTTCACAGCTCGTGTGAGC
Found at i:66319 original size:34 final size:34
Alignment explanation
Indices: 66276--66342 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
66266 AACTTCCTGT
66276 GAAAAAAGTGAGCAAAGAATATGGCTTTAGTAAG
1 GAAAAAAGTGAGCAAAGAATATGGCTTTAGTAAG
*
66310 GAAAAAAGTGAGCAAAGAATATGGTTTTAGTAA
1 GAAAAAAGTGAGCAAAGAATATGGCTTTAGTAA
66343 CCGCCCATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.48, C:0.04, G:0.25, T:0.22
Consensus pattern (34 bp):
GAAAAAAGTGAGCAAAGAATATGGCTTTAGTAAG
Found at i:71363 original size:2 final size:2
Alignment explanation
Indices: 71352--71395 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
71342 TACATATATA
* * *
71352 TG TG TA TG TG TG TG TA TG TG TG CG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
71394 TG
1 TG
71396 CATATATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.05, C:0.02, G:0.45, T:0.48
Consensus pattern (2 bp):
TG
Found at i:72601 original size:19 final size:19
Alignment explanation
Indices: 72577--72615 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
72567 TATAATTCAA
*
72577 TCTCAATTCTCTCTCAAAT
1 TCTCAAATCTCTCTCAAAT
72596 TCTCAAATCTCTCTCAAAT
1 TCTCAAATCTCTCTCAAAT
72615 T
1 T
72616 TTTTTGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (19 bp):
TCTCAAATCTCTCTCAAAT
Found at i:72745 original size:38 final size:39
Alignment explanation
Indices: 72667--72746 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
72657 TCTCTAAATT
*
72667 TTATTTTATTTATTAAAATTATCTTAATATTTTCGCAAA
1 TTATTTTATTTATTAAAATTATCATAATATTTTCGCAAA
72706 TTATTTT-TTCTATTAAAAATTATCGAT-AT-TTTTCG-AAA
1 TTATTTTATT-TATT-AAAATTATC-ATAATATTTTCGCAAA
72744 TTA
1 TTA
72747 ACAATAGTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
38 8 0.22
39 17 0.46
40 11 0.30
41 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (39 bp):
TTATTTTATTTATTAAAATTATCATAATATTTTCGCAAA
Found at i:76873 original size:40 final size:40
Alignment explanation
Indices: 76781--76875 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
76771 GGTATTTTCG
*
76781 AATAAATGAAAACGTTGAAAAGGATATTATCCGAAAGGAT
1 AATAAATGAAAAGGTTGAAAAGGATATTATCCGAAAGGAT
* *
76821 AATAAATGAAAAGGTT-AAATAGGATATTATCTGGAAGGAT
1 AATAAATGAAAAGGTTGAAA-AGGATATTATCCGAAAGGAT
76861 AATAAATGAAAAGGT
1 AATAAATGAAAAGGT
76876 CAAAAAGGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
39 3 0.06
40 48 0.94
ACGTcount: A:0.51, C:0.04, G:0.21, T:0.24
Consensus pattern (40 bp):
AATAAATGAAAAGGTTGAAAAGGATATTATCCGAAAGGAT
Found at i:77630 original size:26 final size:26
Alignment explanation
Indices: 77600--77652 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
77590 AATGTATCAA
77600 ATGAAATGGTAA-ATAGAAACGATTAT
1 ATGAAATGGTAATA-AGAAACGATTAT
* *
77626 ATGAAATGGTTATAAGAAACGGTTAT
1 ATGAAATGGTAATAAGAAACGATTAT
77652 A
1 A
77653 GGGAATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.21, T:0.28
Consensus pattern (26 bp):
ATGAAATGGTAATAAGAAACGATTAT
Found at i:77631 original size:13 final size:13
Alignment explanation
Indices: 77614--77652 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
77604 AATGGTAAAT
*
77614 AGAAACGATTATA
1 AGAAACGGTTATA
* *
77627 TGAAATGGTTATA
1 AGAAACGGTTATA
77640 AGAAACGGTTATA
1 AGAAACGGTTATA
77653 GGGAATGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (13 bp):
AGAAACGGTTATA
Found at i:79321 original size:14 final size:14
Alignment explanation
Indices: 79302--79354 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
79292 AATGTAATTA
79302 AAATTTGAAAACTT
1 AAATTTGAAAACTT
* *
79316 AAATTTTTAAAATTT
1 AAA-TTTGAAAACTT
* *
79331 GAATTTTAAAACTT
1 AAATTTGAAAACTT
79345 AAATTTGAAA
1 AAATTTGAAA
79355 GCTAAAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (14 bp):
AAATTTGAAAACTT
Found at i:79327 original size:15 final size:15
Alignment explanation
Indices: 79299--79350 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
79289 TGTAATGTAA
* *
79299 TTAAAATTTGAAAAC
1 TTAAATTTTTAAAAC
*
79314 TTAAATTTTTAAAAT
1 TTAAATTTTTAAAAC
*
79329 TTGAA-TTTTAAAAC
1 TTAAATTTTTAAAAC
79343 TTAAATTT
1 TTAAATTT
79351 GAAAGCTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (15 bp):
TTAAATTTTTAAAAC
Found at i:106799 original size:21 final size:21
Alignment explanation
Indices: 106755--106792 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
106745 TCATTTGTAA
106755 TAAATTATTAATAATATTATT
1 TAAATTATTAATAATATTATT
106776 TAAATTA-TAAT-ATATTA
1 TAAATTATTAATAATATTA
106793 ATATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTATTAATAATATTATT
Found at i:108076 original size:70 final size:71
Alignment explanation
Indices: 107933--108080 Score: 212
Period size: 70 Copynumber: 2.1 Consensus size: 71
107923 GTTCCATTTT
* * * *
107933 TCCA-ATTTAAATTGAAAGTAAGCAGAAACCTTGAAATCTTGATCTGTTCTCTTATTTTGTAGGG
1 TCCATATTTAAATTGAAAGTAAGAAAAAACCTTGAAATATTGATCTGTTCTCTTATTCTGTAGGG
*
107997 TTTTAA
66 TTCTAA
*
108003 TCCATATTTAAATTGATAA-TAAGAAAAAATCTTGAAATATTGATCT-TTCTCTTATTCTGTAGG
1 TCCATATTTAAATTGA-AAGTAAGAAAAAACCTTGAAATATTGATCTGTTCTCTTATTCTGTAGG
108066 GTTCTAA
65 GTTCTAA
108073 TCCATATT
1 TCCATATT
108081 AGTAATTAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
70 34 0.49
71 34 0.49
72 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (71 bp):
TCCATATTTAAATTGAAAGTAAGAAAAAACCTTGAAATATTGATCTGTTCTCTTATTCTGTAGGG
TTCTAA
Found at i:112317 original size:31 final size:32
Alignment explanation
Indices: 112277--112336 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
112267 CAAATCAATG
*
112277 ACTTGAATAAAAACTTTCGAATA-TTTTAGTA
1 ACTTAAATAAAAACTTTCGAATAGTTTTAGTA
112308 ACTTAAATAAAAACTTTCGAATAGTTTTA
1 ACTTAAATAAAAACTTTCGAATAGTTTTA
112337 TGACCCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.38
Consensus pattern (32 bp):
ACTTAAATAAAAACTTTCGAATAGTTTTAGTA
Found at i:112968 original size:19 final size:20
Alignment explanation
Indices: 112944--112984 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
112934 TATGTATTTT
112944 ATATTT-TATATTATTTA-AA
1 ATATTTATATATT-TTTACAA
112963 ATATTTATATATTTTTACAA
1 ATATTTATATATTTTTACAA
112983 AT
1 AT
112985 CTAATGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTATATATTTTTACAA
Found at i:123151 original size:15 final size:16
Alignment explanation
Indices: 123125--123155 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
123115 ATTTTTAGGT
123125 TAATAGTTATATATTA
1 TAATAGTTATATATTA
123141 TAATA-TTATATATTA
1 TAATAGTTATATATTA
123156 AATTCGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TAATAGTTATATATTA
Found at i:125555 original size:30 final size:31
Alignment explanation
Indices: 125520--125675 Score: 128
Period size: 30 Copynumber: 5.2 Consensus size: 31
125510 AATAAAACCA
* *
125520 GGTCAATTTTGAATTTTTGGAAACTTTAGA-
1 GGTCAAATTTGAATTTTTGGAAAATTTAGAG
** * *
125550 GGTCAAA-TCAACATTTTTGG-AAAGTTCGAG
1 GGTCAAATTTGA-ATTTTTGGAAAATTTAGAG
* ** *
125580 GGTCAAATTTGAATTTTTAGAATGTTCA-AG
1 GGTCAAATTTGAATTTTTGGAAAATTTAGAG
*
125610 GGTCAAATTTGTATTTTTGGAAAATTTA-AG
1 GGTCAAATTTGAATTTTTGGAAAATTTAGAG
* * *
125640 GGTTAATTTTGAATTTTTGAAAAATTT--AG
1 GGTCAAATTTGAATTTTTGGAAAATTTAGAG
125669 GGTCAAA
1 GGTCAAA
125676 ACTAGTTTTA
Statistics
Matches: 97, Mismatches: 25, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
29 15 0.15
30 78 0.80
31 4 0.04
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (31 bp):
GGTCAAATTTGAATTTTTGGAAAATTTAGAG
Found at i:127403 original size:39 final size:39
Alignment explanation
Indices: 127280--127568 Score: 253
Period size: 39 Copynumber: 7.3 Consensus size: 39
127270 TATAGCTTTA
* * * *
127280 GGGGTAAAAGATTAGATTGTTTCAATTTGCCCCATGGTC
1 GGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTT
* * *
127319 GGGGTAAGAGATCT-GATGGTCTTCAATTTGCCCTC-TGGTT
1 GGGGTAAAAGAT-TGGATTG-CTTCAATCTGCCC-CATGGTT
* * * *
127359 AGGGTAAAAGATTGAATTGCTTCAATCTACCCCATGGTC
1 GGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTT
* * *
127398 GGGGTAAGAGATCGGA-TGATCTTCAATCTGCCCTC-TTGTT
1 GGGGTAAAAGATTGGATTG--CTTCAATCTGCCC-CATGGTT
* * * *
127438 AGGGTAAAATATTGGATTGCTTCAATCTGCCCTATGGTC
1 GGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTT
* * * * ***
127477 GAGGTAAGAGATTTGATGGTCTTCAATCTGCCTTTTGGTT
1 GGGGTAAAAGATTGGATTG-CTTCAATCTGCCCCATGGTT
*
127517 AGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTT
1 GGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTT
127556 GGGGTAAAAGATT
1 GGGGTAAAAGATT
127569 CGAGGTTATA
Statistics
Matches: 196, Mismatches: 43, Indels: 22
0.75 0.16 0.08
Matches are distributed among these distances:
38 3 0.02
39 101 0.52
40 88 0.45
41 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (39 bp):
GGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTT
Found at i:127568 original size:79 final size:79
Alignment explanation
Indices: 127281--127567 Score: 405
Period size: 79 Copynumber: 3.6 Consensus size: 79
127271 ATAGCTTTAG
* * *
127281 GGGTAAAAGATTAGATTGTTTCAATTTGCCCCATGGTCGGGGTAAGAGATCTGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCTGATGGTCTTCAAT
* * *
127346 TTGCCCTCTGGTTA
66 CTGCCTTTTGGTTA
* * * *
127360 GGGTAAAAGATTGAATTGCTTCAATCTACCCCATGGTCGGGGTAAGAGATCGGATGATCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCTGATGGTCTTCAAT
*
127425 CTGCCCTCTT-GTTA
66 CTG-CCTTTTGGTTA
* * * *
127439 GGGTAAAATATTGGATTGCTTCAATCTGCCCTATGGTCGAGGTAAGAGATTTGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCTGATGGTCTTCAAT
127504 CTGCCTTTTGGTTA
66 CTGCCTTTTGGTTA
* *
127518 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTGGGGTAAAAGAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGAT
127568 TCGAGGTTAT
Statistics
Matches: 181, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
78 5 0.03
79 173 0.96
80 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCTGATGGTCTTCAAT
CTGCCTTTTGGTTA
Found at i:127703 original size:50 final size:51
Alignment explanation
Indices: 127625--127722 Score: 162
Period size: 50 Copynumber: 1.9 Consensus size: 51
127615 ATCCTTGCAA
*
127625 CTTCAATTTGCCCCCTCTACAGCTTTAGGTGAATGAGATTCGCCATTGGAG
1 CTTCAATTTGACCCCTCTACAGCTTTAGGTGAATGAGATTCGCCATTGGAG
* *
127676 CTTCAATTT-ACCCCTCTACAGCTTTAGGTGTATGAGATTTGCCATTG
1 CTTCAATTTGACCCCTCTACAGCTTTAGGTGAATGAGATTCGCCATTG
127723 CGGCCTTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 35 0.80
51 9 0.20
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.35
Consensus pattern (51 bp):
CTTCAATTTGACCCCTCTACAGCTTTAGGTGAATGAGATTCGCCATTGGAG
Found at i:139337 original size:30 final size:30
Alignment explanation
Indices: 139303--139486 Score: 135
Period size: 30 Copynumber: 6.2 Consensus size: 30
139293 TTAAAATCGT
* * *
139303 GTCAATTTTGAATTTTTGGAAACTTTAGGG
1 GTCAAATTAGAATTTTTGGAAAATTTAGGG
* * * *
139333 GTCAAATAAAAAATTTT-GAAAGTTT-GAGG
1 GTCAAATTAGAATTTTTGGAAAATTTAG-GG
139362 GTCAAATTAGAATTTTTGGAAAATTT-GAGG
1 GTCAAATTAGAATTTTTGGAAAATTTAG-GG
* * * * * * *
139392 GCCAAATCAGAATTTTTAGTAAGTTCATGG
1 GTCAAATTAGAATTTTTGGAAAATTTAGGG
*
139422 GTCAAAATT-GGATTTTTGGAAAATTTAGGG
1 GTC-AAATTAGAATTTTTGGAAAATTTAGGG
* * * *
139452 GTCAATTTTGAATTTTTTGAAAATTT-TGG
1 GTCAAATTAGAATTTTTGGAAAATTTAGGG
139481 GTCAAA
1 GTCAAA
139487 AATTATTTTA
Statistics
Matches: 119, Mismatches: 30, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
28 1 0.01
29 34 0.29
30 80 0.67
31 4 0.03
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (30 bp):
GTCAAATTAGAATTTTTGGAAAATTTAGGG
Found at i:139364 original size:29 final size:30
Alignment explanation
Indices: 139316--139398 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 30
139306 AATTTTGAAT
*
139316 TTTTGGAAACTTT-AGGGGTCAAATAAAAAA
1 TTTTGGAAAATTTGA-GGGTCAAATAAAAAA
* * * *
139346 TTTT-GAAAGTTTGAGGGTCAAATTAGAAT
1 TTTTGGAAAATTTGAGGGTCAAATAAAAAA
*
139375 TTTTGGAAAATTTGAGGGCCAAAT
1 TTTTGGAAAATTTGAGGGTCAAAT
139399 CAGAATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 23 0.51
30 22 0.49
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (30 bp):
TTTTGGAAAATTTGAGGGTCAAATAAAAAA
Found at i:139375 original size:59 final size:59
Alignment explanation
Indices: 139310--139456 Score: 165
Period size: 59 Copynumber: 2.5 Consensus size: 59
139300 CGTGTCAATT
* *
139310 TTGAATTTTTGGAAACTTTAGGGGTCAAATAAAAAATTTT-GAAAGTTTGA-GGGTCAAA
1 TTGAATTTTTGGAAAATTTAGGGGTCAAATAAAAAATTTTAGAAAG-TTCATGGGTCAAA
* * * * *
139368 TTAGAATTTTTGGAAAATTT-GAGGGCCAAATCAGAATTTTTAGTAAGTTCATGGGTCAAAA
1 TT-GAATTTTTGGAAAATTTAG-GGGTCAAATAAAAAATTTTAGAAAGTTCATGGGTC-AAA
*
139429 TTGGATTTTTGGAAAATTTAGGGGTCAA
1 TTGAATTTTTGGAAAATTTAGGGGTCAA
139457 TTTTGAATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
58 3 0.04
59 34 0.46
60 31 0.42
61 6 0.08
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35
Consensus pattern (59 bp):
TTGAATTTTTGGAAAATTTAGGGGTCAAATAAAAAATTTTAGAAAGTTCATGGGTCAAA
Found at i:145697 original size:49 final size:49
Alignment explanation
Indices: 145615--145948 Score: 303
Period size: 49 Copynumber: 6.8 Consensus size: 49
145605 GCTTTTTTCA
*
145615 GCTTCAATCTGCCCCT-TTCCATCTTTAGGGTATAAGATTCGCCTTTGCG
1 GCTTTAATCTGCCCCTCTT-CATCTTTAGGGTATAAGATTCGCCTTTGCG
* * * ** * *
145664 ACTTAAATCTACCTTTCTTCATCTTTAGCGTATAAGATTCGCCTTTGTG
1 GCTTTAATCTGCCCCTCTTCATCTTTAGGGTATAAGATTCGCCTTTGCG
* *
145713 GCTTTAATTTGCCCCTCTTCATCTTTAGGATATAAGATTCGCCTTTGCG
1 GCTTTAATCTGCCCCTCTTCATCTTTAGGGTATAAGATTCGCCTTTGCG
* * * *
145762 GCTTTAATTTGCCCCTCTTCATCTTTAGGGTATAATATTCTCCTTTGTG
1 GCTTTAATCTGCCCCTCTTCATCTTTAGGGTATAAGATTCGCCTTTGCG
** ** * **
145811 GCTTTAATCTTTCCCTCCACATCTCTAGGGTATAAGATTCGCCTTTGTT
1 GCTTTAATCTGCCCCTCTTCATCTTTAGGGTATAAGATTCGCCTTTGCG
* ** * ** * * * *
145860 GCTTCAATCTTTCCTTCCACATCTCTATGGTATAAGATTCACATTTAG-G
1 GCTTTAATCTGCCCCTCTTCATCTTTAGGGTATAAGATTCGCCTTT-GCG
* * ** **
145909 ACTTCAATCTTTCCCTCCACATCTTTAGGGTATAAGATTC
1 GCTTTAATCTGCCCCTCTTCATCTTTAGGGTATAAGATTC
145949 ATCTTTGAGG
Statistics
Matches: 244, Mismatches: 39, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
49 241 0.99
50 3 0.01
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (49 bp):
GCTTTAATCTGCCCCTCTTCATCTTTAGGGTATAAGATTCGCCTTTGCG
Found at i:145883 original size:98 final size:97
Alignment explanation
Indices: 145634--145998 Score: 351
Period size: 98 Copynumber: 3.7 Consensus size: 97
145624 TGCCCCTTTC
* * * * ** *
145634 CATCTTTAGGGTATAAGATTCGCCTTTGCGACTTAAATC-TACCTTTCTTCATCTTTAGCGTATA
1 CATCTTTAGGGTATAAGATTCGCCTTTG-GGCTTCAATCTTTCC-CTCCACATCTTTAGGGTATA
* * **
145698 AGATTCGCCTTTGTGGCTTTAAT-TTGCCCCTCTT
64 AGATTCACCTTTGTGGCTTTAATCTT-TCCCTCCA
* * * **
145732 CATCTTTAGGATATAAGATTCGCCTTTGCGGCTTTAAT-TTGCCCCTCTTCATCTTTAGGGTATA
1 CATCTTTAGGGTATAAGATTCGCCTTTG-GGCTTCAATCTT-TCCCTCCACATCTTTAGGGTATA
* *
145796 ATATTCTCCTTTGTGGCTTTAATCTTTCCCTCCA
64 AGATTCACCTTTGTGGCTTTAATCTTTCCCTCCA
* * * * *
145830 CATCTCTAGGGTATAAGATTCGCCTTTGTTGCTTCAATCTTTCCTTCCACATCTCTATGGTATAA
1 CATCTTTAGGGTATAAGATTCGCCTTTG-GGCTTCAATCTTTCCCTCCACATCTTTAGGGTATAA
* * *
145895 GATTCACATTTAG-GACTTCAATCTTTCCCTCCA
65 GATTCACCTTT-GTGGCTTTAATCTTTCCCTCCA
** * * *
145928 CATCTTTAGGGTATAAGATTCATCTTTGAGGCTTCAATATTTCCCTCCACGTCTTTAGGGTATAG
1 CATCTTTAGGGTATAAGATTCGCCTTTG-GGCTTCAATCTTTCCCTCCACATCTTTAGGGTATAA
145993 GATTCA
65 GATTCA
145999 ATGTTTCCTC
Statistics
Matches: 224, Mismatches: 38, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
98 217 0.97
99 7 0.03
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (97 bp):
CATCTTTAGGGTATAAGATTCGCCTTTGGGCTTCAATCTTTCCCTCCACATCTTTAGGGTATAAG
ATTCACCTTTGTGGCTTTAATCTTTCCCTCCA
Found at i:145894 original size:147 final size:147
Alignment explanation
Indices: 145615--145997 Score: 375
Period size: 147 Copynumber: 2.6 Consensus size: 147
145605 GCTTTTTTCA
* * * * *
145615 GCTTCAATCTGCCCCT-TTCCATCTTTAGGGTATAAGATTCGCCTTTGCGACTTAAATC-TACCT
1 GCTTCAATTTGCCCCTCTT-CATCTTTAGGGTATAAGATTCTCCTTTGAGGCTTAAATCTTTCC-
* ** * * ** *
145678 TTCTTCATCTTTAGCGTATAAGATTCGCCTTTGTGGCTTTAATTTGCCCCTCTTCATCTTTAGGA
64 CTCCACATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAATTTGCCCCTCCACATCTCTAGGA
* *
145743 TATAAGATTCGCCTTT-GCG
129 TATAAGATTCACATTTAG-G
* * * *
145762 GCTTTAATTTGCCCCTCTTCATCTTTAGGGTATAATATTCTCCTTTGTGGCTTTAATCTTTCCCT
1 GCTTCAATTTGCCCCTCTTCATCTTTAGGGTATAAGATTCTCCTTTGAGGCTTAAATCTTTCCCT
* * * *
145827 CCACATCTCTAGGGTATAAGATTCGCCTTTGTTGCTTCAATCTT-TCCTTCCACATCTCTATGG-
66 CCACATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAAT-TTGCCCCTCCACATCTCTA-GGA
145890 TATAAGATTCACATTTAGG
129 TATAAGATTCACATTTAGG
* * ** * *
145909 ACTTCAATCTT-TCCCTCCACATCTTTAGGGTATAAGATTCAT-CTTTGAGGCTTCAATATTTCC
1 GCTTCAAT-TTGCCCCTCTTCATCTTTAGGGTATAAGATTC-TCCTTTGAGGCTTAAATCTTTCC
* *
145972 CTCCACGTCTTTAGGGTATAGGATTC
64 CTCCACATCTTTAGGGTATAAGATTC
145998 AATGTTTCCT
Statistics
Matches: 195, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
147 182 0.93
148 13 0.07
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (147 bp):
GCTTCAATTTGCCCCTCTTCATCTTTAGGGTATAAGATTCTCCTTTGAGGCTTAAATCTTTCCCT
CCACATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAATTTGCCCCTCCACATCTCTAGGATA
TAAGATTCACATTTAGG
Found at i:145949 original size:49 final size:48
Alignment explanation
Indices: 145634--145998 Score: 297
Period size: 49 Copynumber: 7.5 Consensus size: 48
145624 TGCCCCTTTC
* * * * * **
145634 CATCTTTAGGGTATAAGATTCGCCTTTGCGACTTAAATC-TACCTTTCTT
1 CATCTTTAGGGTATAAGATTCACCTTTGTG-CTTCAATCTTTCC-CTCCA
* * * * **
145683 CATCTTTAGCGTATAAGATTCGCCTTTGTGGCTTTAAT-TTGCCCCTCTT
1 CATCTTTAGGGTATAAGATTCACCTTTGT-GCTTCAATCTT-TCCCTCCA
* * * * * **
145732 CATCTTTAGGATATAAGATTCGCCTTTGCGGCTTTAAT-TTGCCCCTCTT
1 CATCTTTAGGGTATAAGATTCACCTTTG-TGCTTCAATCTT-TCCCTCCA
* * *
145781 CATCTTTAGGGTATAATATTCTCCTTTGTGGCTTTAATCTTTCCCTCCA
1 CATCTTTAGGGTATAAGATTCACCTTTGT-GCTTCAATCTTTCCCTCCA
* * *
145830 CATCTCTAGGGTATAAGATTCGCCTTTGTTGCTTCAATCTTTCCTTCCA
1 CATCTTTAGGGTATAAGATTCACCTTTG-TGCTTCAATCTTTCCCTCCA
* * *
145879 CATCTCTATGGTATAAGATTCACATTTAG-GACTTCAATCTTTCCCTCCA
1 CATCTTTAGGGTATAAGATTCACCTTT-GTG-CTTCAATCTTTCCCTCCA
* * *
145928 CATCTTTAGGGTATAAGATTCATCTTTGAGGCTTCAATATTTCCCTCCA
1 CATCTTTAGGGTATAAGATTCACCTTTG-TGCTTCAATCTTTCCCTCCA
* *
145977 CGTCTTTAGGGTATAGGATTCA
1 CATCTTTAGGGTATAAGATTCA
145999 ATGTTTCCTC
Statistics
Matches: 274, Mismatches: 31, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
48 2 0.01
49 264 0.96
50 8 0.03
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (48 bp):
CATCTTTAGGGTATAAGATTCACCTTTGTGCTTCAATCTTTCCCTCCA
Found at i:146197 original size:83 final size:83
Alignment explanation
Indices: 146058--146226 Score: 302
Period size: 83 Copynumber: 2.0 Consensus size: 83
146048 TATGCTTCTA
*
146058 TGGACCTCTATGTAGGCCAAATTATTAGGATGCCCTAATCGAAATGAGTCAAATGCTCCTAACTA
1 TGGACCTCTATGGAGGCCAAATTATTAGGATGCCCTAATCGAAATGAGTCAAATGCTCCTAACTA
146123 AATGAGTGTGCATGATAT
66 AATGAGTGTGCATGATAT
* * *
146141 TGGACCTCTATGGAGGCCAAATTATTAGGATGCCCTGATCGGAATGATTCAAATGCTCCTAACTA
1 TGGACCTCTATGGAGGCCAAATTATTAGGATGCCCTAATCGAAATGAGTCAAATGCTCCTAACTA
146206 AATGAGTGTGCATGATAT
66 AATGAGTGTGCATGATAT
146224 TGG
1 TGG
146227 CATGAATATC
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (83 bp):
TGGACCTCTATGGAGGCCAAATTATTAGGATGCCCTAATCGAAATGAGTCAAATGCTCCTAACTA
AATGAGTGTGCATGATAT
Found at i:159753 original size:20 final size:21
Alignment explanation
Indices: 159711--159755 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
159701 TACAAATGAT
*
159711 TGTTCTTTTGTTTTTTGCTTC
1 TGTTCTTTTGTTTATTGCTTC
159732 TGTTC-TTTGTTTATTG-TCTC
1 TGTTCTTTTGTTTATTGCT-TC
159752 TGTT
1 TGTT
159756 TTCTTCTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 16 0.73
21 5 0.23
ACGTcount: A:0.02, C:0.13, G:0.16, T:0.69
Consensus pattern (21 bp):
TGTTCTTTTGTTTATTGCTTC
Found at i:162215 original size:25 final size:25
Alignment explanation
Indices: 162187--162255 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
162177 TTGATATGAT
* *
162187 ATGATATGTTAAGATATGACCCGAC
1 ATGATATGTTATGATATGACACGAC
**
162212 ATGATATACTATGAT-TCGACACGAC
1 ATGATATGTTATGATAT-GACACGAC
*
162237 ATAATATGTTATGATATGA
1 ATGATATGTTATGATATGA
162256 TGATCCATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.03
25 33 0.94
26 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (25 bp):
ATGATATGTTATGATATGACACGAC
Found at i:162217 original size:35 final size:35
Alignment explanation
Indices: 162149--162226 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
162139 ATGAGGGTAG
* ** **
162149 GATATGATATGTTAAGTTATGATTCGATTTGATAT
1 GATATGATATGTTAAGATATGACCCGACATGATAT
162184 GATATGATATGTTAAGATATGACCCGACATGATAT
1 GATATGATATGTTAAGATATGACCCGACATGATAT
162219 -ACTATGAT
1 GA-TATGAT
162227 TCGACACGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 1 0.03
35 36 0.97
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (35 bp):
GATATGATATGTTAAGATATGACCCGACATGATAT
Found at i:168802 original size:7 final size:7
Alignment explanation
Indices: 168771--168809 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
168761 TAGGGAGACA
168771 AAAATTCT
1 AAAATT-T
168779 AAAA-TT
1 AAAATTT
168785 AAAATTTT
1 AAAA-TTT
168793 AAAATTT
1 AAAATTT
168800 AAAATTT
1 AAAATTT
168807 AAA
1 AAA
168810 TCTTGGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.17
7 14 0.48
8 10 0.34
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (7 bp):
AAAATTT
Found at i:172806 original size:25 final size:25
Alignment explanation
Indices: 172774--172822 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
172764 CTATTCTCTC
*
172774 AGAGATGAACGCTCTTGAAAAAAAG
1 AGAGATGAACGCTCATGAAAAAAAG
*
172799 AGAGATGAACTCTCATGAAAAAAA
1 AGAGATGAACGCTCATGAAAAAAA
172823 CAATAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.12, G:0.20, T:0.16
Consensus pattern (25 bp):
AGAGATGAACGCTCATGAAAAAAAG
Found at i:178462 original size:25 final size:25
Alignment explanation
Indices: 178424--178471 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
178414 CTAGGAATAA
* *
178424 AACTTTATTTGCAA-GAAAGCCTAGT
1 AACTTTACTGGCAAGGAAA-CCTAGT
178449 AACTTTACTGGCAAGGAAACCTA
1 AACTTTACTGGCAAGGAAACCTA
178472 TTATGAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (25 bp):
AACTTTACTGGCAAGGAAACCTAGT
Found at i:180717 original size:30 final size:30
Alignment explanation
Indices: 180678--180749 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
180668 TGTTTACATG
180678 AACTTTAATTTGGTGC-AAT-TATACATATAA
1 AACTTTAATTTGGTGCAAATATATAC-T-TAA
* *
180708 AACTCTAATTGTGGTTCAAATATATACTTAA
1 AACTTTAATT-TGGTGCAAATATATACTTAA
180739 AACTTTAATTT
1 AACTTTAATTT
180750 TGATTTAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 10 0.28
31 17 0.47
32 4 0.11
33 5 0.14
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (30 bp):
AACTTTAATTTGGTGCAAATATATACTTAA
Found at i:183032 original size:15 final size:16
Alignment explanation
Indices: 183004--183046 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
182994 ATAATGTGTA
* *
183004 AAAAGTAAAGTAAAGT
1 AAAAGTAAAATAAAAT
183020 AAAA-TAAAATAAAAT
1 AAAAGTAAAATAAAAT
183035 AAATAGTAAAAT
1 AAA-AGTAAAAT
183047 GAATGCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.52
16 5 0.22
17 6 0.26
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
AAAAGTAAAATAAAAT
Found at i:184235 original size:21 final size:21
Alignment explanation
Indices: 184197--184236 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
184187 ACCCTGCAAC
* * *
184197 TTCTACTGATACATGTATGAG
1 TTCTACCGAAACAAGTATGAG
184218 TTCTACCGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
184237 CAGATTTCAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGAG
Found at i:189213 original size:26 final size:26
Alignment explanation
Indices: 189184--189267 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
189174 AGCTCATATA
* * *
189184 AGCCAGTTCAGCATATCGCTCTTTCG
1 AGCCAGTTCAGAATATTGCTCTTACG
* *
189210 AGCCAGTGCAGTATATTGCTC-TACCG
1 AGCCAGTTCAGAATATTGCTCTTA-CG
* *
189236 AACTAGTTCAGAATATTGCTCTTACG
1 AGCCAGTTCAGAATATTGCTCTTACG
189262 AGCCAG
1 AGCCAG
189268 ATGACATATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
25 1 0.02
26 43 0.93
27 2 0.04
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (26 bp):
AGCCAGTTCAGAATATTGCTCTTACG
Found at i:190224 original size:23 final size:22
Alignment explanation
Indices: 190192--190271 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
190182 GCTTGGGAAA
*
190192 CAGTAAGCACACACAATGCAAT
1 CAGTAGGCACACACAATGCAAT
*
190214 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAATGCAAT
* * *
190237 CAGTAGGCGCACATAACGCAAAT
1 CAGTAGGCACACACAATGC-AAT
190260 CAGTAGGCACAC
1 CAGTAGGCACAC
190272 GAGATGCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
22 15 0.31
23 34 0.69
ACGTcount: A:0.39, C:0.29, G:0.20, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAATGCAAT
Found at i:190286 original size:23 final size:23
Alignment explanation
Indices: 190260--190359 Score: 143
Period size: 23 Copynumber: 4.3 Consensus size: 23
190250 TAACGCAAAT
*
190260 CAGTAGGCACACG-AGATGCGAAA
1 CAGTAAGCACACGAAG-TGCGAAA
190283 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
190306 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
190329 CAGTAAGCACAC-ACAGTGCTG-AA
1 CAGTAAGCACACGA-AGTGC-GAAA
190352 CAGTAAGC
1 CAGTAAGC
Statistics
Matches: 73, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
22 1 0.01
23 69 0.95
24 3 0.04
ACGTcount: A:0.41, C:0.23, G:0.26, T:0.10
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Done.