Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007943.1 Hibiscus syriacus cultivar Beakdansim tig00110365_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: 1187827
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:227309 original size:14 final size:14
Alignment explanation
Indices: 227290--227323 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
227280 AGTTTGTAAT
*
227290 ATAATAATAATATA
1 ATAATAATAAAATA
227304 ATAATAATAAAATA
1 ATAATAATAAAATA
*
227318 TTAATA
1 ATAATA
227324 TTATGGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATAATAAAATA
Found at i:227990 original size:20 final size:21
Alignment explanation
Indices: 227938--227995 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
227928 GGTCTTATGG
227938 ATGGCCCG-AAGTTCTTATTAT
1 ATGGCCCGAAAG-TCTTATTAT
* * *
227959 CTTGCTCGAAAGTCTTA-TAT
1 ATGGCCCGAAAGTCTTATTAT
*
227979 ATGGCCCGAAAGACTTA
1 ATGGCCCGAAAGTCTTA
227996 CACATCATGC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 16 0.55
21 10 0.34
22 3 0.10
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGGCCCGAAAGTCTTATTAT
Found at i:228025 original size:42 final size:42
Alignment explanation
Indices: 227961--228044 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
227951 CTTATTATCT
* *
227961 TGCTCGAAAGTCTTATATATGGCCCGAAAGACTTACACATCA
1 TGCTCGAAAGACTTATAGATGGCCCGAAAGACTTACACATCA
* * *
228003 TGCTCGAAAGACTTACT-GATGGCTCGAAGGACTTACTCATCA
1 TGCTCGAAAGACTTA-TAGATGGCCCGAAAGACTTACACATCA
228045 AGAAACCCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (42 bp):
TGCTCGAAAGACTTATAGATGGCCCGAAAGACTTACACATCA
Found at i:228282 original size:262 final size:259
Alignment explanation
Indices: 227611--228381 Score: 976
Period size: 262 Copynumber: 3.0 Consensus size: 259
227601 TAAGTGATGC
* * *
227611 GTTG-TGATTCAACTCCATATGTGATGAATCGAGTACCAGAAATGTTGAAAACATC-CTACAAAG
1 GTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCAGAAATGTTGAAAACATCTGTCCAAAG
* *
227674 GTCTTATGGATGGCCCAAAGGTCTTATCAT-TTGTTCGAAAGTCTA-AATGGCCCGAAGGATTTA
66 GTCTTATGGATGGCCCAAAGGTCTTATCATCTTCTTCGAAAGT-TATAATGGCCCGAAAGATTTA
* *
227737 CGCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA--C-TCAAGAAACCCTTGAAAAT
130 AGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAAT
* * * * *
227799 CAAGCTTAGTTTCTTAGTTGTCATTCAAGGAACCCCTACATATCAAGTTGGTCCCTCGAGTGAGG
195 CAAACCTAGTTTCTTAGTTGTCA-TCAAAGAACCCCTACATATCACGTTGGTCCCTTGAGTGAGG
227864 T
259 T
*** * * * *
227865 GGAACTGATTCAACTCCATATGTGATAAAT-GAGTATCAGAAATATTGAAAACATCATG-CCGAT
1 GTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCAGAAATGTTGAAAACATC-TGTCCAAA
* * *
227928 GGTCTTATGGATGGCCCGAAGTTCTTATTATCTTGC-TCGAAAGTCTTATATATGGCCCGAAAGA
65 GGTCTTATGGATGGCCCAAAGGTCTTATCATCTT-CTTCGAAAG--TTATA-ATGGCCCGAAAGA
* *
227992 CTTACA-CATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTACTCATCAAGAAACCCTTG
126 TTTA-AGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTG
* * *
228056 AAGATCAAACCTAGTTTCTTAGATGTTATCAAAGAACCCCTACATATCACGTTGGTCCCTTGAGT
190 AAAATCAAACCTAGTTTCTTAGTTGTCATCAAAGAACCCCTACATATCACGTTGGTCCCTTGAGT
228121 GAGGT
255 GAGGT
228126 GTTGCTGATTCAACTCCATATGTGATGAATCGAGTATC-GAAAATGTTGAAAACATCTTGTCCAA
1 GTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCAG-AAATGTTGAAAACATC-TGTCCAA
* * * * *
228190 AGGTTTTATGGATGGCCTAAAGGACTT-TCATCTTACTTCGAAAGATTATAGATGACCCGAATGA
64 AGGTCTTATGGATGGCCCAAAGGTCTTATCATCTT-CTTCGAAAG-TTATA-ATGGCCCGAAAGA
* * *
228254 TTTAAGCATCATACTGGAAAGACTTACTGATGGCCCGAAGGACTTTCTCATCAAGAAACCCTTGA
126 TTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGA
* * *
228319 AAATC-AAGCTACGTTTCTTAGTTGTCATCAAAGGACCTCTACATATCACGTTGGTCCCTTGAG
191 AAATCAAACCTA-GTTTCTTAGTTGTCATCAAAGAACCCCTACATATCACGTTGGTCCCTTGAG
228382 CTTAGTTTCT
Statistics
Matches: 441, Mismatches: 57, Indels: 30
0.84 0.11 0.06
Matches are distributed among these distances:
254 24 0.05
255 54 0.12
256 9 0.02
257 2 0.00
258 2 0.00
259 53 0.12
261 73 0.17
262 193 0.44
263 31 0.07
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (259 bp):
GTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCAGAAATGTTGAAAACATCTGTCCAAAG
GTCTTATGGATGGCCCAAAGGTCTTATCATCTTCTTCGAAAGTTATAATGGCCCGAAAGATTTAA
GCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAATC
AAACCTAGTTTCTTAGTTGTCATCAAAGAACCCCTACATATCACGTTGGTCCCTTGAGTGAGGT
Found at i:230491 original size:4 final size:4
Alignment explanation
Indices: 230478--230553 Score: 63
Period size: 4 Copynumber: 19.8 Consensus size: 4
230468 ATTGGTTTTA
* *
230478 TTTC -TTC TTTC TTTC TTTC TTTC TTTTC TTT- TCTC TATC TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC
* *
230524 TTTT TTTC TTTT TTTC TGTT- TTT- TTTC TTT
1 TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTT
230554 ATTTTATATT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
3 13 0.22
4 40 0.68
5 6 0.10
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:230536 original size:27 final size:28
Alignment explanation
Indices: 230506--230558 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
230496 CTTTCTTTTC
230506 TTTTCTCTATCTTTTTTCTTT-TTTTCT
1 TTTTCTCTATCTTTTTTCTTTATTTTCT
* * *
230533 TTTTTTCTGTTTTTTTTCTTTATTTT
1 TTTTCTCTATCTTTTTTCTTTATTTT
230559 ATATTTTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (28 bp):
TTTTCTCTATCTTTTTTCTTTATTTTCT
Found at i:230545 original size:23 final size:26
Alignment explanation
Indices: 230493--230558 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 26
230483 TCTTTCTTTC
*
230493 TTTCTTTCTTTTCTTTTCTCTATCTTT
1 TTTCTTT-TTTTCTTTTCTCTATCTGT
230520 TTTCTTTTTTTCTTTT-T-T-TCTGT
1 TTTCTTTTTTTCTTTTCTCTATCTGT
*
230543 TTT-TTTTCTTTATTTT
1 TTTCTTTT-TTTCTTTT
230559 ATATTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.11
23 14 0.39
24 1 0.03
25 1 0.03
26 9 0.25
27 7 0.19
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (26 bp):
TTTCTTTTTTTCTTTTCTCTATCTGT
Found at i:230565 original size:19 final size:19
Alignment explanation
Indices: 230524--230577 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
230514 ATCTTTTTTC
* *
230524 TTTTTTTCTTTTTTTCTGT
1 TTTTTTTCTTTTTTTATGA
230543 TTTTTTTCTTTATTTTAT-A
1 TTTTTTTCTTT-TTTTATGA
*
230562 TTTTATGTCTTTTTTT
1 TTTT-TTTCTTTTTTT
230578 GCTATATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.07, C:0.07, G:0.04, T:0.81
Consensus pattern (19 bp):
TTTTTTTCTTTTTTTATGA
Found at i:230565 original size:27 final size:28
Alignment explanation
Indices: 230517--230577 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
230507 TTTCTCTATC
* * *
230517 TTTTTTCTTTTTTTCTTTTTTTCTGT-T
1 TTTTTTCTTTTTTTCATATTTTATGTCT
230544 TTTTTTCTTTATTTT-ATATTTTATGTCT
1 TTTTTTCTTT-TTTTCATATTTTATGTCT
230572 TTTTTT
1 TTTTTT
230578 GCTATATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.07, C:0.08, G:0.03, T:0.82
Consensus pattern (28 bp):
TTTTTTCTTTTTTTCATATTTTATGTCT
Found at i:234069 original size:147 final size:147
Alignment explanation
Indices: 233802--234095 Score: 534
Period size: 147 Copynumber: 2.0 Consensus size: 147
233792 CCATCTTTCA
* *
233802 CGGCTTCTAATTCTTTGTTCATAATGTCTTTTTCGCTCTGCAACTGATGTATTTGAGCTTCTTAT
1 CGGCTTCTAATTCTTTGTTCATAATGTCTTTTTCACTCTGCAACTGATGTATTTGAGCTTCGTAT
* *
233867 TTCAGCAAATGCTCTTTAATTTCGTTATTCTCACTGATGTTTTTTTCCTTGGACTCCATTGGCTT
66 TTCAGCAAATGCTCTTTAATTTCGTTATTCTCACTGATGCTTTTGTCCTTGGACTCCATTGGCTT
233932 CACTTTAACTAGATGTT
131 CACTTTAACTAGATGTT
*
233949 CGGCTTCTAATTCTTTGTTCATAATGTCTTTTTCACTCTGCAGCTGATGTATTTGAGCTTCGTAT
1 CGGCTTCTAATTCTTTGTTCATAATGTCTTTTTCACTCTGCAACTGATGTATTTGAGCTTCGTAT
*
234014 TTCAGCAAATGCTCTTTAATTTGGTTATTCTCACTGATGCTTTTGTCCTTGGACTCCATTGGCTT
66 TTCAGCAAATGCTCTTTAATTTCGTTATTCTCACTGATGCTTTTGTCCTTGGACTCCATTGGCTT
234079 CACTTTAACTAGATGTT
131 CACTTTAACTAGATGTT
234096 TGGTTATTGA
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 141 1.00
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.46
Consensus pattern (147 bp):
CGGCTTCTAATTCTTTGTTCATAATGTCTTTTTCACTCTGCAACTGATGTATTTGAGCTTCGTAT
TTCAGCAAATGCTCTTTAATTTCGTTATTCTCACTGATGCTTTTGTCCTTGGACTCCATTGGCTT
CACTTTAACTAGATGTT
Found at i:234932 original size:17 final size:19
Alignment explanation
Indices: 234895--234933 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
234885 AGGCAAAAAG
234895 AAAACAAGTTAAGACGTATA
1 AAAACAAGTTAAGA-GTATA
234915 AAAACAAG-TAAG-GTATA
1 AAAACAAGTTAAGAGTATA
234932 AA
1 AA
234934 GGTAAATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.18
Consensus pattern (19 bp):
AAAACAAGTTAAGAGTATA
Found at i:235397 original size:149 final size:149
Alignment explanation
Indices: 235126--235418 Score: 379
Period size: 149 Copynumber: 2.0 Consensus size: 149
235116 TTCAAATCTT
* * *
235126 CTACTTCATCTCCTACTTCTAGAAATCTTTCGAGCTGGTTCACGATCTTCAACTATTGGTTTCGG
1 CTACTTCATCTCCTACTTCCAGAAATCTTTCGAGCTGGTTCACGATCTTCAACTATTGGCTTCAG
* * *
235191 CGTTGAATCATCTCGAGTCCGACTTGTTACCTCAGCAGACAAATGTTTGGATCGTCTCCTTAGAA
66 CATTGAATCATCTCGAGTCCAACTTGTTACCTCAGCAGACAAATGTCTGGATCGTCTCCTTAGAA
235256 GATAGACTCCCTCTAGCTC
131 GATAGACTCCCTCTAGCTC
* * ** *
235275 CTACTTTATCTCTTACTTCCAGAAATCTTTCGAGCTGGTTCGTGATCTTCAACTGTTGGCTTCAG
1 CTACTTCATCTCCTACTTCCAGAAATCTTTCGAGCTGGTTCACGATCTTCAACTATTGGCTTCAG
* * * *** * * * *
235340 TATTGAATCATCTCGAGTTCAACTTGTTACCTTAGCAGGTGAATGTCTGGCTTGTCTCTTTAGTA
66 CATTGAATCATCTCGAGTCCAACTTGTTACCTCAGCAGACAAATGTCTGGATCGTCTCCTTAGAA
* *
235405 GGTAGACTCTCTCT
131 GATAGACTCCCTCT
235419 TGAGCTTCTC
Statistics
Matches: 121, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
149 121 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.37
Consensus pattern (149 bp):
CTACTTCATCTCCTACTTCCAGAAATCTTTCGAGCTGGTTCACGATCTTCAACTATTGGCTTCAG
CATTGAATCATCTCGAGTCCAACTTGTTACCTCAGCAGACAAATGTCTGGATCGTCTCCTTAGAA
GATAGACTCCCTCTAGCTC
Found at i:237401 original size:22 final size:21
Alignment explanation
Indices: 237369--237414 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
237359 TGCAAAAATT
*
237369 AAAATAACAGTGGCTAAATCA
1 AAAATAACAGTGACTAAATCA
*
237390 AAAACTAACAGTGACTAAATTA
1 AAAA-TAACAGTGACTAAATCA
237412 AAA
1 AAA
237415 TAAAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.20
Consensus pattern (21 bp):
AAAATAACAGTGACTAAATCA
Found at i:237421 original size:22 final size:21
Alignment explanation
Indices: 237364--237418 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
237354 CAAAATGCAA
*
237364 AAATTAAAAT-AACAGTGGCT
1 AAATTAAAATAAACAGTGACT
*
237384 AAATCAAAA-ACTAACAGTGACT
1 AAATTAAAATA--AACAGTGACT
237406 AAATTAAAATAAA
1 AAATTAAAATAAA
237419 ACAAAACAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 8 0.29
21 2 0.07
22 17 0.61
23 1 0.04
ACGTcount: A:0.58, C:0.11, G:0.09, T:0.22
Consensus pattern (21 bp):
AAATTAAAATAAACAGTGACT
Found at i:237587 original size:13 final size:13
Alignment explanation
Indices: 237569--237594 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
237559 AATTTTGGTC
237569 TCTAAAGGGACCA
1 TCTAAAGGGACCA
237582 TCTAAAGGGACCA
1 TCTAAAGGGACCA
237595 AAATAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
TCTAAAGGGACCA
Found at i:244825 original size:18 final size:18
Alignment explanation
Indices: 244802--244837 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
244792 GAACAAAAAT
244802 CACAGGCAGTAACATGAC
1 CACAGGCAGTAACATGAC
244820 CACAGGCAGTAACATGAC
1 CACAGGCAGTAACATGAC
244838 GTGCAAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.22, T:0.11
Consensus pattern (18 bp):
CACAGGCAGTAACATGAC
Found at i:247114 original size:16 final size:16
Alignment explanation
Indices: 247093--247125 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
247083 TCAATTTTTA
*
247093 CAATAACGATTAGCAT
1 CAATAACGATGAGCAT
247109 CAATAACGATGAGCAT
1 CAATAACGATGAGCAT
247125 C
1 C
247126 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.21
Consensus pattern (16 bp):
CAATAACGATGAGCAT
Found at i:247290 original size:229 final size:229
Alignment explanation
Indices: 246869--247324 Score: 732
Period size: 229 Copynumber: 2.0 Consensus size: 229
246859 TCGGCGAGGG
* * *
246869 ACGATGAGCACCAATGACGATGAACATCGATAAATTAATTTGTAAAATGATAAAATTATAAGGTA
1 ACGATGAGCACCAATAACGATGAACATCGATAAATTAATTTATAAAACGATAAAATTATAAGGTA
* *
246934 CTGAACGTATAATTATATTTTAGTTAAAAATGTAATTGTAATTTTAAATAAATCACAATATTAAT
66 CTCAACGTATAATTATATTTTAGTTAAAAATGTAATTGTAATTATAAATAAATCACAATATTAAT
*
246999 TACATTGTGTTTTTAATATTTTTGGGTAAATTACAAGTTTAGTATCTAAAGTTTCTCTTTTAGTA
131 TACATTGTGTTTTTAATATTTTTGGGTAAATTACAAGTTTAGTATCTAAAGTTTCACTTTTAGTA
* * * *
247064 TGTTTTTGTACTTGAACTTTCAATTTTTACAATA
196 CGATTTAGTACTTAAACTTTCAATTTTTACAATA
* * * **
247098 ACGATTAGCATCAATAACGATGAGCATCTTTAAATTAATTTATAAAACGATAAAATTATAAGGTA
1 ACGATGAGCACCAATAACGATGAACATCGATAAATTAATTTATAAAACGATAAAATTATAAGGTA
* *
247163 CTCAACGTATACTTATATTTTAGTTAAAAATGTAATTGTAATTATAAATAAATCAGAATATTAAT
66 CTCAACGTATAATTATATTTTAGTTAAAAATGTAATTGTAATTATAAATAAATCACAATATTAAT
* *
247228 TACATTGTGTTTTTAATATTTTTGGGTAAATTACAAGTTTTGTATCTAAAGTTTGACTTTTAGTA
131 TACATTGTGTTTTTAATATTTTTGGGTAAATTACAAGTTTAGTATCTAAAGTTTCACTTTTAGTA
*
247293 CGATTTAGTACTTAAACTTTTAATTTTTACAA
196 CGATTTAGTACTTAAACTTTCAATTTTTACAA
247325 AATTATACCT
Statistics
Matches: 207, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
229 207 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (229 bp):
ACGATGAGCACCAATAACGATGAACATCGATAAATTAATTTATAAAACGATAAAATTATAAGGTA
CTCAACGTATAATTATATTTTAGTTAAAAATGTAATTGTAATTATAAATAAATCACAATATTAAT
TACATTGTGTTTTTAATATTTTTGGGTAAATTACAAGTTTAGTATCTAAAGTTTCACTTTTAGTA
CGATTTAGTACTTAAACTTTCAATTTTTACAATA
Found at i:247731 original size:23 final size:24
Alignment explanation
Indices: 247705--247781 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
247695 ATTTTATATA
* *
247705 ATTATTTAGTTAAAGA-CTAAAAT
1 ATTATTTAGTTAAAAATATAAAAT
*
247728 ATTAATTTATTTAAAAATATAAAAT
1 ATT-ATTTAGTTAAAAATATAAAAT
*
247753 ATT-TTTAGTATAAACTATATAAAAT
1 ATTATTTAGT-TAAA-AATATAAAAT
247778 ATTA
1 ATTA
247782 AATCATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.18
24 15 0.34
25 21 0.48
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.43
Consensus pattern (24 bp):
ATTATTTAGTTAAAAATATAAAAT
Found at i:247873 original size:22 final size:24
Alignment explanation
Indices: 247821--247865 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
247811 AATAAATATT
247821 TTAA-ATTGAATTTTAAAAAAAAA
1 TTAATATTGAATTTTAAAAAAAAA
*
247844 TTAATATTGATTTTTAAAAAAA
1 TTAATATTGAATTTTAAAAAAA
247866 CATATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TTAATATTGAATTTTAAAAAAAAA
Found at i:247941 original size:20 final size:20
Alignment explanation
Indices: 247903--247943 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
247893 AATAAAGCTG
*
247903 AAATAATTTAATTTTTAATT
1 AAATAATTTAATTTATAATT
**
247923 AAATAATTTGGTTTATAATT
1 AAATAATTTAATTTATAATT
247943 A
1 A
247944 TAAATGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
AAATAATTTAATTTATAATT
Found at i:256338 original size:21 final size:21
Alignment explanation
Indices: 256312--256351 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
256302 AAGTTTAAAG
*
256312 GGAGTATCGATACTCTCAAGA
1 GGAGTATCGATACTATCAAGA
256333 GGAGTATCGATACTATCAA
1 GGAGTATCGATACTATCAA
256352 TACCGGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (21 bp):
GGAGTATCGATACTATCAAGA
Found at i:257443 original size:14 final size:15
Alignment explanation
Indices: 257418--257446 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
257408 AGGAAATTAC
257418 TTTTATTATTAAAAT
1 TTTTATTATTAAAAT
257433 TTTTATT-TTAAAAT
1 TTTTATTATTAAAAT
257447 GGTCGTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTATTATTAAAAT
Found at i:263301 original size:20 final size:21
Alignment explanation
Indices: 263256--263295 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
263246 TACTATGCTG
263256 GAATTTAGATGTTAGAATGTT
1 GAATTTAGATGTTAGAATGTT
263277 GAATTTA-ATGTTAGAATGT
1 GAATTTAGATGTTAGAATGT
263296 GAAATTGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (21 bp):
GAATTTAGATGTTAGAATGTT
Found at i:264528 original size:66 final size:66
Alignment explanation
Indices: 264415--264562 Score: 172
Period size: 66 Copynumber: 2.2 Consensus size: 66
264405 GAGTCACTGA
* * **
264415 TGCACGAGGTGGAGTGATTACTAAATACTGTATAGATCACTCAATGAGACTTGTGCACCTTCGTG
1 TGCATGAGGTGGAGTGATAACTAAATACTGTATAGATCACTCAATGAGACTCATGCACCTTCGTG
264480 G
66 G
* ** * * *
264481 TGCATGAGGTGGAGTGATAACTGAATGTTGTACT-GATCACTCGATGAGACTCATGTACCTTTGT
1 TGCATGAGGTGGAGTGATAACTAAATACTGTA-TAGATCACTCAATGAGACTCATGCACCTTCGT
*
264545 TG
65 GG
*
264547 CGCATGAGGTGGAGTG
1 TGCATGAGGTGGAGTG
264563 GCTATATGAT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
66 68 0.99
67 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (66 bp):
TGCATGAGGTGGAGTGATAACTAAATACTGTATAGATCACTCAATGAGACTCATGCACCTTCGTG
G
Found at i:264977 original size:18 final size:17
Alignment explanation
Indices: 264930--265016 Score: 74
Period size: 18 Copynumber: 5.1 Consensus size: 17
264920 AAGATATAGT
264930 ACAGTAAA-AAAAAGAA
1 ACAGTAAAGAAAAAGAA
* * *
264946 ACGGTAAAGTAAAAGTA
1 ACAGTAAAGAAAAAGAA
264963 ACAGTATAAGAAAAA-AGA
1 ACAGTA-AAGAAAAAGA-A
264981 ACAGTACAA-AAAAGAGAA
1 ACAGTA-AAGAAAA-AGAA
264999 ACAGTAGAAG-AAAAGAA
1 ACAGTA-AAGAAAAAGAA
265016 A
1 A
265017 ACAATATAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
16 7 0.12
17 20 0.35
18 29 0.51
19 1 0.02
ACGTcount: A:0.66, C:0.07, G:0.18, T:0.09
Consensus pattern (17 bp):
ACAGTAAAGAAAAAGAA
Found at i:273313 original size:15 final size:15
Alignment explanation
Indices: 273293--273343 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
273283 ACTAGAAATA
273293 TGCTGTGGCTGCTGC
1 TGCTGTGGCTGCTGC
* *
273308 TGCTGTGACAG-TGC
1 TGCTGTGGCTGCTGC
*
273322 ATGCTGTGGCTGCTGT
1 -TGCTGTGGCTGCTGC
273338 TGCTGT
1 TGCTGT
273344 TGGTTTGTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 3 0.10
15 24 0.83
16 2 0.07
ACGTcount: A:0.06, C:0.22, G:0.37, T:0.35
Consensus pattern (15 bp):
TGCTGTGGCTGCTGC
Found at i:276365 original size:65 final size:66
Alignment explanation
Indices: 276261--276391 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 66
276251 CCCGTAACAT
276261 GGTGGGTTGCAAAAACGGGGGTAAAGAATCCGACTTTCCCAGGGATTTTCAATTATAAA-ACAGT
1 GGTGGGTTGCAAAAACGGGGGTAAAGAATCCGACTTTCCCAGGGATTTTCAATTATAAATACAGT
276325 A
66 A
276326 GGTGGGTTGCAAAAACGGGGGTAAAGAATCCGACTTTCCCAGGGATTTTCAATTATAAATACAGT
1 GGTGGGTTGCAAAAACGGGGGTAAAGAATCCGACTTTCCCAGGGATTTTCAATTATAAATACAGT
276391 A
66 A
276392 TAATGCATGT
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
65 59 0.91
66 6 0.09
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (66 bp):
GGTGGGTTGCAAAAACGGGGGTAAAGAATCCGACTTTCCCAGGGATTTTCAATTATAAATACAGT
A
Found at i:277436 original size:2 final size:2
Alignment explanation
Indices: 277429--277456 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
277419 TCTAATACTT
277429 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
277457 GAGAACAAAA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:280453 original size:2 final size:2
Alignment explanation
Indices: 280446--280470 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
280436 ATTTGGGTTG
280446 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
280471 ATCATCTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:280783 original size:18 final size:18
Alignment explanation
Indices: 280757--280791 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
280747 ACATTGATGA
*
280757 ATATTAATAAATAATATG
1 ATATAAATAAATAATATG
*
280775 ATATAAATAATTAATAT
1 ATATAAATAAATAATAT
280792 TGTATTGTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
ATATAAATAAATAATATG
Found at i:282063 original size:12 final size:12
Alignment explanation
Indices: 282046--282074 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
282036 CCAATTTATC
282046 TATCACATAGTA
1 TATCACATAGTA
282058 TATCACATAGTA
1 TATCACATAGTA
282070 TATCA
1 TATCA
282075 TTTATAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (12 bp):
TATCACATAGTA
Found at i:283658 original size:108 final size:107
Alignment explanation
Indices: 283365--283662 Score: 393
Period size: 107 Copynumber: 2.8 Consensus size: 107
283355 TGTCTGTTTA
* *
283365 AAGTTGATGGGGCCTTAGAAATCTGACGATAACAAAATAGATTAATTACTTAATTTGTTATCAAT
1 AAGTTGAT-GGGCCTTAGAAATCTGACGATAACAAAATAGATTAATTACTTATTTTGTTATAAAT
* * * *
283430 ATTATTAACATATTATGTATCACCTAAAATATTACTAAAATTT
65 ATTATTAACATACTAGGTAGCACCTAAAATATTACCAAAATTT
* * *
283473 AAGTTGATGAGCCTTAGAAATATGACGATAACAAAATAGATTAATTACTTATTTTGTTATTAATA
1 AAGTTGATGGGCCTTAGAAATCTGACGATAACAAAATAGATTAATTACTTATTTTGTTATAAATA
* *
283538 TTATTAACATACTAGGTAGCACTTAAAATGTTACCAAAATTT
66 TTATTAACATACTAGGTAGCACCTAAAATATTACCAAAATTT
* * * * *
283580 AAGTTGATGGGACCTTTGAAATCTGACAACAACAAAAAATG-TTAATTTCTTATTTTGTTATAAA
1 AAGTTGATGGG-CCTTAGAAATCTGACGATAACAAAATA-GATTAATTACTTATTTTGTTATAAA
*
283644 TAAATATTAA-ATACTAGGT
64 T-ATTATTAACATACTAGGT
283663 TGCATCCAAT
Statistics
Matches: 168, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
107 99 0.59
108 61 0.36
109 8 0.05
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (107 bp):
AAGTTGATGGGCCTTAGAAATCTGACGATAACAAAATAGATTAATTACTTATTTTGTTATAAATA
TTATTAACATACTAGGTAGCACCTAAAATATTACCAAAATTT
Found at i:284368 original size:23 final size:23
Alignment explanation
Indices: 284299--284370 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
284289 CGGTAGTTAG
284299 TTTAACGTAATAGGTAGC-ACTTA
1 TTTAACGTAATAGGTAGCGAC-TA
* * *
284322 TTTAACGTATTAGGTAGTGCCTA
1 TTTAACGTAATAGGTAGCGACTA
* *
284345 TTTAACATAATAGGTAGCGTCTA
1 TTTAACGTAATAGGTAGCGACTA
284368 TTT
1 TTT
284371 TATTTTACCG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (23 bp):
TTTAACGTAATAGGTAGCGACTA
Found at i:284446 original size:23 final size:23
Alignment explanation
Indices: 284420--284491 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
284410 CGGTAGCTAG
*
284420 TTTAACCTAATAGGTATCGCCTA
1 TTTAACCTAATAGGTAACGCCTA
*
284443 TTT-ACCGTAATAGGTAACACCTA
1 TTTAACC-TAATAGGTAACGCCTA
* * *
284466 TTTAACATAATAGGTAGCGTCTA
1 TTTAACCTAATAGGTAACGCCTA
284489 TTT
1 TTT
284492 TATTTTACCG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 3 0.07
23 36 0.88
24 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (23 bp):
TTTAACCTAATAGGTAACGCCTA
Found at i:284466 original size:121 final size:121
Alignment explanation
Indices: 284250--284566 Score: 481
Period size: 121 Copynumber: 2.6 Consensus size: 121
284240 AAATTGTATA
*
284250 TATTTTACCGTTTACATTATTATTAACATTTAAACAAACCGGTAGTTAGTTTAACGTAATAGGTA
1 TATTTTACCGTTTACATTATTATTAACATTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGTA
* * ***
284315 GCACTTATTTAACGTATTAGGTAGTGCCTATTTAACATAATAGGTAGCGTCTATTT
66 GCACCTATTTAACGTAATAGGTAACACCTATTTAACATAATAGGTAGCGTCTATTT
* *
284371 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGGTAGCTAGTTTAACCTAATAGGTA
1 TATTTTACCGTTTACATTATTATTAACATTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGTA
* * *
284436 TCGCCTATTTACCGTAATAGGTAACACCTATTTAACATAATAGGTAGCGTCTATTT
66 GCACCTATTTAACGTAATAGGTAACACCTATTTAACATAATAGGTAGCGTCTATTT
* * * *
284492 TATTTTACCGTTTACATTATTATTAACATTTAAACAAACTGATAGCTAGATTAACGTAATATGTA
1 TATTTTACCGTTTACATTATTATTAACATTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGTA
* *
284557 ACACATATTT
66 GCACCTATTT
284567 TATTTTACTG
Statistics
Matches: 176, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 176 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (121 bp):
TATTTTACCGTTTACATTATTATTAACATTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGTA
GCACCTATTTAACGTAATAGGTAACACCTATTTAACATAATAGGTAGCGTCTATTT
Found at i:285768 original size:75 final size:75
Alignment explanation
Indices: 285645--285828 Score: 253
Period size: 75 Copynumber: 2.5 Consensus size: 75
285635 ACATAGATAG
* * *
285645 TTAACGTAATATGTAGTGCATATTTTATTTTACCGTTTACATTATTAGTAATCTTTAAACAAACC
1 TTAACGTAATATGTAATGCATATTTTATTTTAACGTTTACATTATTAGTAATCTTCAAACAAACC
*
285710 AGTAGGTATT
66 AGTAGGTAGT
* * *
285720 TTAACGTAACATGTAATGTC-TATTTTATTTTAACGTTTATATTATTAGTAATCTTCGAACAAAC
1 TTAACGTAATATGTAATG-CATATTTTATTTTAACGTTTACATTATTAGTAATCTTCAAACAAAC
* *
285784 CGGTATGTAGT
65 CAGTAGGTAGT
* *
285795 TTAACATAATATATAATGCATATTTTATTTTAAC
1 TTAACGTAATATGTAATGCATATTTTATTTTAAC
285829 TGGTTAAATT
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
74 1 0.01
75 93 0.98
76 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (75 bp):
TTAACGTAATATGTAATGCATATTTTATTTTAACGTTTACATTATTAGTAATCTTCAAACAAACC
AGTAGGTAGT
Found at i:286248 original size:20 final size:20
Alignment explanation
Indices: 286204--286541 Score: 187
Period size: 20 Copynumber: 16.6 Consensus size: 20
286194 AATGACCAAT
*
286204 AAAATCGCAACGCGATATA-
1 AAAATCGCAACGCGATTTAG
286223 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
286243 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
286263 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
286283 AAAATCGCAACGCGAGCTTCT
1 AAAATCGCAACGCGA-TTTAG
**
286304 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
286327 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
286347 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
286367 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * *
286387 AGAGTCGCAACGCGATCTAG
1 AAAATCGCAACGCGATTTAG
* * *
286407 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* * * *
286430 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
286450 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
286470 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
286490 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
286510 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
286530 AAAATCGCAACG
1 AAAATCGCAACG
286542 TTAAAAAGAT
Statistics
Matches: 261, Mismatches: 46, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
19 18 0.07
20 200 0.77
21 15 0.06
22 1 0.00
23 27 0.10
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:286382 original size:40 final size:40
Alignment explanation
Indices: 286308--286539 Score: 293
Period size: 40 Copynumber: 5.7 Consensus size: 40
286298 GCTTCTAAGT
* *
286308 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAATGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* *
286351 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* * *
286391 TCGCAACGCGATCTAGAAGAGAATCGCAATGCGACTGAGAGAA
1 TCGCAATGCGAT-T--TAGAGAATCGCAATGCGATTGAGAGAA
* * *
286434 TCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAA
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
286474 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAA
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* *
286514 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAATGCGATTTAGAGAATCGCAA
286540 CGTTAAAAAG
Statistics
Matches: 167, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
40 116 0.69
41 1 0.01
42 3 0.02
43 47 0.28
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:286637 original size:6 final size:6
Alignment explanation
Indices: 286628--286695 Score: 120
Period size: 6 Copynumber: 11.5 Consensus size: 6
286618 CATTACCATT
286628 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
286676 ACCACG ACCCCG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
286696 CGAGACGAGA
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
5 5 0.08
6 56 0.92
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:287425 original size:6 final size:6
Alignment explanation
Indices: 287383--287457 Score: 108
Period size: 6 Copynumber: 13.5 Consensus size: 6
287373 TCTCGTCTCG
287383 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT -GTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
287425 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
287458 AATACGTGTC
Statistics
Matches: 68, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
5 30 0.44
6 38 0.56
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:287560 original size:20 final size:20
Alignment explanation
Indices: 287535--287578 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
287525 TTTTTAACTA
*
287535 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
287555 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
287575 TTCT
1 TTCT
287579 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:287588 original size:20 final size:20
Alignment explanation
Indices: 287565--287779 Score: 130
Period size: 20 Copynumber: 10.6 Consensus size: 20
287555 TTCTTTTTAA
287565 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
287585 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
287605 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
287625 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
287645 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
287668 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
287689 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
* *** **
287707 ACCATTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
287729 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
287749 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
287768 CGTTGCGATTTT
1 CGTTGCGATTTT
287780 ATTGGTCATT
Statistics
Matches: 155, Mismatches: 32, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.11
20 105 0.68
21 13 0.08
22 4 0.03
23 14 0.09
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:287611 original size:40 final size:40
Alignment explanation
Indices: 287567--287675 Score: 155
Period size: 40 Copynumber: 2.6 Consensus size: 40
287557 CTTTTTAACG
*
287567 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTATCAATCGCA
* * *
287607 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTATCAATCGCA
287647 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
287676 ACTTGGAAGC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 42 0.71
42 2 0.03
43 15 0.25
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTATCAATCGCA
Found at i:287769 original size:19 final size:20
Alignment explanation
Indices: 287729--287779 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
287719 TTCTTTTTAA
*
287729 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
287749 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
287768 CGTTGCGATTTT
1 CGTTGCGATTTT
287780 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:290225 original size:22 final size:23
Alignment explanation
Indices: 290182--290228 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
290172 ACGCTAATTT
*
290182 ATGACTTGCAAAAACTGTGTGTC
1 ATGACTTACAAAAACTGTGTGTC
*
290205 ATGACTTACAATAA-TGTGTGTC
1 ATGACTTACAAAAACTGTGTGTC
290227 AT
1 AT
290229 ATTTAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (23 bp):
ATGACTTACAAAAACTGTGTGTC
Found at i:291036 original size:2 final size:2
Alignment explanation
Indices: 291031--291058 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
291021 AGACACACAC
291031 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
291059 GATTTCATTT
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:291425 original size:17 final size:17
Alignment explanation
Indices: 291403--291439 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
291393 TCATTTATCT
291403 TTCACATTAATCTATAC
1 TTCACATTAATCTATAC
291420 TTCACATTAATCTATAC
1 TTCACATTAATCTATAC
291437 TTC
1 TTC
291440 TATTGGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.43
Consensus pattern (17 bp):
TTCACATTAATCTATAC
Found at i:296451 original size:25 final size:25
Alignment explanation
Indices: 296423--296499 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
296413 TGGTGAAAGA
296423 TTTTGTAGGTTAAAGTGGTTTAGGG
1 TTTTGTAGGTTAAAGTGGTTTAGGG
* * * * **
296448 TTTTTTAAGGTGAGAGTGCTCAAGGG
1 TTTTGT-AGGTTAAAGTGGTTTAGGG
*
296474 TTGTGTAGGTTAAAGTGGTTTAGGG
1 TTTTGTAGGTTAAAGTGGTTTAGGG
296499 T
1 T
296500 AAAGTTCGAT
Statistics
Matches: 38, Mismatches: 13, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
25 20 0.53
26 18 0.47
ACGTcount: A:0.21, C:0.03, G:0.36, T:0.40
Consensus pattern (25 bp):
TTTTGTAGGTTAAAGTGGTTTAGGG
Found at i:301044 original size:20 final size:20
Alignment explanation
Indices: 301007--301045 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
300997 ATTGAAGGGT
* *
301007 AGTATCGATACTCTCATACC
1 AGTATCGATAATCCCATACC
301027 AGTATCGATAATCCCATAC
1 AGTATCGATAATCCCATAC
301046 TATAATATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTATCGATAATCCCATACC
Found at i:316467 original size:21 final size:21
Alignment explanation
Indices: 316426--316473 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
316416 AAAAAATGAT
* *
316426 TAAAATATATACATAATAAAA
1 TAAAATATATAAACAATAAAA
316447 TAAAATATA-AAACAATGAAAA
1 TAAAATATATAAACAAT-AAAA
316468 TGAAAA
1 T-AAAA
316474 AAAAATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 14 0.61
22 4 0.17
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (21 bp):
TAAAATATATAAACAATAAAA
Found at i:316566 original size:13 final size:13
Alignment explanation
Indices: 316533--316571 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
316523 ATCTAGTAAT
*
316533 AAAATAATAATGATG
1 AAAATAATAA--ATA
316548 AAAATAATAAATA
1 AAAATAATAAATA
316561 AAAATAATAAA
1 AAAATAATAAA
316572 GAAATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 13 0.57
15 10 0.43
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (13 bp):
AAAATAATAAATA
Found at i:316600 original size:18 final size:17
Alignment explanation
Indices: 316579--316628 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
316569 AAAGAAATAT
316579 ATGTATATAAATAAAAA
1 ATGTATATAAATAAAAA
*
316596 GATGTACATAAGA-AAAAA
1 -ATGTATATAA-ATAAAAA
*
316614 ATATATAT-AATAAAA
1 ATGTATATAAATAAAA
316629 GAAAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
15 1 0.04
16 5 0.19
17 6 0.22
18 14 0.52
19 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.26
Consensus pattern (17 bp):
ATGTATATAAATAAAAA
Found at i:316665 original size:2 final size:2
Alignment explanation
Indices: 316658--316686 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
316648 AATAGGTAAG
316658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
316687 AAATAAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:317865 original size:2 final size:2
Alignment explanation
Indices: 317858--317916 Score: 58
Period size: 2 Copynumber: 32.0 Consensus size: 2
317848 GTAAATAAAC
*
317858 AT AT AT AT AT AT AT -T AT A- AT TT AT A- AT AT CAT AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
317896 AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
317917 GTTATAATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
1 6 0.12
2 40 0.83
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:318079 original size:17 final size:19
Alignment explanation
Indices: 318057--318107 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 19
318047 AGCAATACTG
318057 GTAGTATCGATACTA-AT-
1 GTAGTATCGATACTACATA
*
318074 GTAGTATCGATACTACCTA
1 GTAGTATCGATACTACATA
318093 GTGAGTATCGATACT
1 GT-AGTATCGATACT
318108 TACCTTACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 15 0.50
18 1 0.03
19 2 0.07
20 12 0.40
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (19 bp):
GTAGTATCGATACTACATA
Found at i:319281 original size:62 final size:62
Alignment explanation
Indices: 319199--319336 Score: 240
Period size: 62 Copynumber: 2.2 Consensus size: 62
319189 TACCTTAGGG
* *
319199 TCAAGTATCGATACCCCTATGAGTGCTGGTACCAAAAATGTATTCTGTTGTGAAATTGGGGCC
1 TCAA-TATCGATACCCCTATGAGTACTAGTACCAAAAATGTATTCTGTTGTGAAATTGGGGCC
*
319262 TCAATATCGATACCTCTATGAGTACTAGTACCAAAAATGTATTCTGTTGTGAAATTGGGGCC
1 TCAATATCGATACCCCTATGAGTACTAGTACCAAAAATGTATTCTGTTGTGAAATTGGGGCC
319324 TCAATATCGATAC
1 TCAATATCGATAC
319337 TTTCACCCTA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
62 68 0.94
63 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (62 bp):
TCAATATCGATACCCCTATGAGTACTAGTACCAAAAATGTATTCTGTTGTGAAATTGGGGCC
Found at i:319372 original size:20 final size:20
Alignment explanation
Indices: 319347--319396 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
319337 TTTCACCCTA
*
319347 AGTATCGATACTATAGGGGT
1 AGTATCGATACTACAGGGGT
319367 AGTATCGATACTACAGGGGT
1 AGTATCGATACTACAGGGGT
*
319387 AGTATTGATA
1 AGTATCGATA
319397 TTGCCGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTACAGGGGT
Found at i:333470 original size:31 final size:31
Alignment explanation
Indices: 333407--333470 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
333397 ACTTTTGATT
* * * *
333407 AAATTTAAAGGTCAAATTGATATTTTATCTA
1 AAATTTAAAGGTCAAAATGACATTTCACCTA
*
333438 AAATTTAAGGGTCAAAATGACATTTCACCTA
1 AAATTTAAAGGTCAAAATGACATTTCACCTA
333469 AA
1 AA
333471 GTTTGGTGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (31 bp):
AAATTTAAAGGTCAAAATGACATTTCACCTA
Found at i:351280 original size:54 final size:54
Alignment explanation
Indices: 351191--351463 Score: 365
Period size: 54 Copynumber: 5.1 Consensus size: 54
351181 TTACATTTTC
* ** * * *
351191 TGACAGGCATCCTATGTTATTACAAGATAGGCATGATTTTCAAGTGTGC-A-AGCG
1 TGACAGGTATCCTACATTATTACAAGACAGACATGATTTTCAA--GTGCAAGAGAG
** *
351245 TGACAGGTATCAGACATTATTACAAGACAGACATGATTTTCAACTGCAAGAGAG
1 TGACAGGTATCCTACATTATTACAAGACAGACATGATTTTCAAGTGCAAGAGAG
*
351299 TGACAGGTATCCTACATTGA-TACAAGACAGACATGATCTTCAAGTGCAAGAGAG
1 TGACAGGTATCCTACATT-ATTACAAGACAGACATGATTTTCAAGTGCAAGAGAG
* * *
351353 TGACAGGTATCTTACATCATTACAAGACAGACACGATTTTCAACG-GCAAGAGAG
1 TGACAGGTATCCTACATTATTACAAGACAGACATGATTTTCAA-GTGCAAGAGAG
351407 TGACAGGTATCCTACATTATTACAAGACAGACATGATTTTCAAGTGCAAGAGAG
1 TGACAGGTATCCTACATTATTACAAGACAGACATGATTTTCAAGTGCAAGAGAG
351461 TGA
1 TGA
351464 AAATGATGCA
Statistics
Matches: 193, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
52 3 0.02
53 3 0.02
54 185 0.96
55 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (54 bp):
TGACAGGTATCCTACATTATTACAAGACAGACATGATTTTCAAGTGCAAGAGAG
Found at i:353006 original size:129 final size:130
Alignment explanation
Indices: 352798--353381 Score: 661
Period size: 138 Copynumber: 4.3 Consensus size: 130
352788 GTTCACGATG
* *
352798 TTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGACCGAGATGATGTGAGCCACCATACT
1 TTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGATCGAGATGATGTGAGCCACCATTCT
* * *
352863 ACTCACGAGTCATCT-AAAAGAATCTGCAAAGAC-GGAGTTGCAAAGAGGGAATTTGTTTACTGT
66 ACTCACGAGTCATCTCAAAA-AACCTGCAAAGACGGGAGTTGCAAAGAGCGAATTTGTTTACGGT
352926 A
130 A
* * *
352927 TAGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGATCAAGATGATGTGAGCCGCCATTCT
1 TTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGATCGAGATGATGTGAGCCACCATTCT
*
352992 ATTCACGAGTCATCTCAAAAAACCTGCAAAGACAATGATGGTGGAGTTGCAAAGAGCGAATTTGT
66 ACTCACGAGTCATCTCAAAAAACCTGCAAAGAC-------G-GGAGTTGCAAAGAGCGAATTTGT
*
353057 TTATGGTA
123 TTACGGTA
* * *
353065 TTGAACAGATGAATGACTTGACTCCCGGATTGTTTCAAGATCGAGATGATGGGAGCCACCATTCT
1 TTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGATCGAGATGATGTGAGCCACCATTCT
* * * *
353130 ACTCCCGAGTCATCTCAGAAAACCTGCAAAGACAATGATGGGGGAGTTGCAAAGAGAGAATTTTT
66 ACTCACGAGTCATCTCAAAAAACCTGCAAAGAC--------GGGAGTTGCAAAGAGCGAATTTGT
*
353195 TTGCGGTA
123 TTACGGTA
* * * *
353203 TTGGACAGGTG-ATAGACTTGACTCCTGGATTGTCTCAAGATCGAGATGATATGAGCCACCATCC
1 TTGAACAGATGAAT-GACTTGACTCCTGGATTGTCTCAAGATCGAGATGATGTGAGCCACCATTC
* *
353267 TACTCACGAGACATCTCAAAAAATCTGCAAAGATGACGATGGTGGAGTTGCAAAGAGCGAATTTG
65 TACTCACGAGTCATCTCAAAAAACCTGC-AA-A-GAC----G-GGAGTTGCAAAGAGCGAATTTG
** *
353332 TCGACGGTC
122 TTTACGGTA
*
353341 TTGAACAGATGAATGACTTGACTCCTGGATTGTCTCTAGAT
1 TTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGAT
353382 GAGTCATCTT
Statistics
Matches: 387, Mismatches: 51, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
129 86 0.22
130 4 0.01
137 4 0.01
138 282 0.73
139 7 0.02
140 1 0.00
141 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (130 bp):
TTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGATCGAGATGATGTGAGCCACCATTCT
ACTCACGAGTCATCTCAAAAAACCTGCAAAGACGGGAGTTGCAAAGAGCGAATTTGTTTACGGTA
Found at i:353123 original size:267 final size:268
Alignment explanation
Indices: 352623--353376 Score: 913
Period size: 276 Copynumber: 2.8 Consensus size: 268
352613 TGATGATGAT
* * * * * *
352623 GGAGTTGCAAAGAGCGAGTTCATTCACAGTATCGAACAGATGAATGAATTGACTCCTGGATTGTC
1 GGAGTTGCAAAGAGAGAATTTATTTACAGTATAGAACAGATGAATGACTTGACTCCTGGATTGTC
* * * *
352688 TCAAGAAGATCAAGATGATATGAGCCACCATTCTGCTCATGAGTCATCTCAAACAATCTGCAAAA
66 TC---AAGATCAAGATGATATGAGCCACCATTCTACTCACGAGTCATCTCAAAAAATCTGCAAAG
* * * * * *
352753 ACAATGATGGTGATGGAGCTGCGAAGAGCGAGTTCGTTCACGATGTTGAACAGATGAATGACTTG
128 ACAATGAT-G-G-TGGAGTTGCAAAGAGCGAATTTGTTCACGGTATTGAACAGATGAATGACTTG
*
352818 ACTCCTGGATTGTCTCAAGACCGAGATGATGTGAGCCACCATACTACTCACGAGTCATCT-AAAA
190 ACTCCTGGATTGTCTCAAGACCGAGATGATGGGAGCCACCATACTACTCACGAGTCATCTCAAAA
*
352882 GAATCTGCAAAGAC-
255 -AACCTGCAAAGACG
* * *
352896 GGAGTTGCAAAGAGGGAATTTGTTTACTGTATAGAACAGATGAATGACTTGACTCCTGGATTGTC
1 GGAGTTGCAAAGAGAGAATTTATTTACAGTATAGAACAGATGAATGACTTGACTCCTGGATTGTC
* * * *
352961 TCAAGATCAAGATGATGTGAGCCGCCATTCTATTCACGAGTCATCTCAAAAAACCTGCAAAGACA
66 TCAAGATCAAGATGATATGAGCCACCATTCTACTCACGAGTCATCTCAAAAAATCTGCAAAGACA
* * *
353026 ATGATGGTGGAGTTGCAAAGAGCGAATTTGTTTATGGTATTGAACAGATGAATGACTTGACTCCC
131 ATGATGGTGGAGTTGCAAAGAGCGAATTTGTTCACGGTATTGAACAGATGAATGACTTGACTCCT
* * * * *
353091 GGATTGTTTCAAGATCGAGATGATGGGAGCCACCATTCTACTCCCGAGTCATCTCAGAAAACCTG
196 GGATTGTCTCAAGACCGAGATGATGGGAGCCACCATACTACTCACGAGTCATCTCAAAAAACCTG
353156 CAAAGACAATGATGGG
261 CAAAGAC--------G
* * * * * *
353172 GGAGTTGCAAAGAGAGAATTTTTTTGCGGTATTGGACAGGTG-ATAGACTTGACTCCTGGATTGT
1 GGAGTTGCAAAGAGAGAATTTATTTACAGTATAGAACAGATGAAT-GACTTGACTCCTGGATTGT
* * * *
353236 CTCAAGATCGAGATGATATGAGCCACCATCCTACTCACGAGACATCTCAAAAAATCTGCAAAGAT
65 CTCAAGATCAAGATGATATGAGCCACCATTCTACTCACGAGTCATCTCAAAAAATCTGCAAAGAC
* * *
353301 GACGATGGTGGAGTTGCAAAGAGCGAATTTG-TCGACGGTCTTGAACAGATGAATGACTTGACTC
130 AATGATGGTGGAGTTGCAAAGAGCGAATTTGTTC-ACGGTATTGAACAGATGAATGACTTGACTC
353365 CTGGATTGTCTC
194 CTGGATTGTCTC
353377 TAGATGAGTC
Statistics
Matches: 415, Mismatches: 54, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
267 110 0.27
268 4 0.01
269 1 0.00
270 60 0.14
273 59 0.14
275 3 0.01
276 178 0.43
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (268 bp):
GGAGTTGCAAAGAGAGAATTTATTTACAGTATAGAACAGATGAATGACTTGACTCCTGGATTGTC
TCAAGATCAAGATGATATGAGCCACCATTCTACTCACGAGTCATCTCAAAAAATCTGCAAAGACA
ATGATGGTGGAGTTGCAAAGAGCGAATTTGTTCACGGTATTGAACAGATGAATGACTTGACTCCT
GGATTGTCTCAAGACCGAGATGATGGGAGCCACCATACTACTCACGAGTCATCTCAAAAAACCTG
CAAAGACG
Found at i:353144 original size:138 final size:138
Alignment explanation
Indices: 352896--353381 Score: 695
Period size: 138 Copynumber: 3.5 Consensus size: 138
352886 CTGCAAAGAC
* * *
352896 GGAGTTGCAAAGAGGGAATTTGTTTACTGTATAGAACAGATGAATGACTTGACTCCTGGATTGTC
1 GGAGTTGCAAAGAGCGAATTTGTTTACGGTATTGAACAGATGAATGACTTGACTCCTGGATTGTC
* * *
352961 TCAAGATCAAGATGATGTGAGCCGCCATTCTATTCACGAGTCATCTCAAAAAACCTGCAAAGACA
66 TCAAGATCGAGATGATGTGAGCCACCATTCTACTCACGAGTCATCTCAAAAAACCTGCAAAGACA
353026 ATGATGGT
131 ATGATGGT
* * *
353034 GGAGTTGCAAAGAGCGAATTTGTTTATGGTATTGAACAGATGAATGACTTGACTCCCGGATTGTT
1 GGAGTTGCAAAGAGCGAATTTGTTTACGGTATTGAACAGATGAATGACTTGACTCCTGGATTGTC
* * *
353099 TCAAGATCGAGATGATGGGAGCCACCATTCTACTCCCGAGTCATCTCAGAAAACCTGCAAAGACA
66 TCAAGATCGAGATGATGTGAGCCACCATTCTACTCACGAGTCATCTCAAAAAACCTGCAAAGACA
*
353164 ATGATGGG
131 ATGATGGT
* * * * *
353172 GGAGTTGCAAAGAGAGAATTTTTTTGCGGTATTGGACAGGTG-ATAGACTTGACTCCTGGATTGT
1 GGAGTTGCAAAGAGCGAATTTGTTTACGGTATTGAACAGATGAAT-GACTTGACTCCTGGATTGT
* * * * *
353236 CTCAAGATCGAGATGATATGAGCCACCATCCTACTCACGAGACATCTCAAAAAATCTGCAAAGAT
65 CTCAAGATCGAGATGATGTGAGCCACCATTCTACTCACGAGTCATCTCAAAAAACCTGCAAAGAC
* *
353301 GACGATGGT
130 AATGATGGT
** *
353310 GGAGTTGCAAAGAGCGAATTTGTCGACGGTCTTGAACAGATGAATGACTTGACTCCTGGATTGTC
1 GGAGTTGCAAAGAGCGAATTTGTTTACGGTATTGAACAGATGAATGACTTGACTCCTGGATTGTC
*
353375 TCTAGAT
66 TCAAGAT
353382 GAGTCATCTT
Statistics
Matches: 305, Mismatches: 41, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
137 2 0.01
138 301 0.99
139 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (138 bp):
GGAGTTGCAAAGAGCGAATTTGTTTACGGTATTGAACAGATGAATGACTTGACTCCTGGATTGTC
TCAAGATCGAGATGATGTGAGCCACCATTCTACTCACGAGTCATCTCAAAAAACCTGCAAAGACA
ATGATGGT
Found at i:353298 original size:405 final size:412
Alignment explanation
Indices: 352615--353381 Score: 987
Period size: 405 Copynumber: 1.9 Consensus size: 412
352605 GAAGACCATG
* *
352615 ATGATGATGGAGTTGCAAAGAGCGAGTTCATTCACAGTATCGAACAGATGAATGAATTGACTCCT
1 ATGATGATGGAGTTGCAAAGAGCGAATTCATTCACAGTATCGAACAGATGAATGAATTGACTCCC
* * * *
352680 GGATTGTCTCAAGAAGATCAAGATGATATGAGCCACCATTCTGCTCATGAGTCATCTCAAACAAT
66 GGATTGTCTC-A-AAGATCAAGATGATAGGAGCCACCATTCTACTCACGAGTCATCTCAAACAAC
* * * *
352745 CTGCAAAAACAATGATGGTGATGGAGCTGCGAAGAGCGAGTTCGTTCACGATGTTGAACAGATGA
129 CTGCAAAAACAATGATGGTGA-GGAGCTGCAAAGAGAGAATTCGTTCACGATATTGAACAGATGA
* *
352810 ATGACTTGACTCCTGGATTGTCTCAAGACCGAGATGATGTGAGCCACCATACTACTCACGAGTCA
193 ATGACTTGACTCCTGGATTGTCTCAAGACCGAGATGATATGAGCCACCATACTACTCACGAGACA
* ** *
352875 TCTAAAAGAATCTGC-AA-A-GAC-GGAGTTGCAAAGAGGGAATTTGTTTACTGTATAGAACAGA
258 TCTAAAAGAATCTGCAAAGATGACGGGAGTTGCAAAGAGCGAATTTGTCGACGGTATAGAACAGA
352936 TGAATGACTTGACTCCTGGATTGTCTCAAGATCAAGATGATGTGAGCCGCCATTCTATTCACGAG
323 TGAATGACTTGACTCCTGGATTGTCTCAAGATCAAGATGATGTGAGCCGCCATTCTATTCACGAG
353001 TCATCTCAAAAAACCTGCAAAGACA
388 TCATCTCAAAAAACCTGCAAAGACA
* ** * ** * *
353026 ATGATGGTGGAGTTGCAAAGAGCGAATTTGTTTATGGTATTGAACAGATGAATGACTTGACTCCC
1 ATGATGATGGAGTTGCAAAGAGCGAATTCATTCACAGTATCGAACAGATGAATGAATTGACTCCC
* * * *
353091 GGATTGTTTC-AAGATCGAGATGATGGGAGCCACCATTCTACTCCCGAGTCATCTCAGAA-AACC
66 GGATTGTCTCAAAGATCAAGATGATAGGAGCCACCATTCTACTCACGAGTCATCTCA-AACAACC
* * ** ** * * *
353154 TGCAAAGACAATGATGG-G-GGAGTTGCAAAGAGAGAATTTTTTTGCGGTATTGGACAGGTG-AT
130 TGCAAAAACAATGATGGTGAGGAGCTGCAAAGAGAGAATTCGTTCACGATATTGAACAGATGAAT
* *
353216 AGACTTGACTCCTGGATTGTCTCAAGATCGAGATGATATGAGCCACCATCCTACTCACGAGACAT
195 -GACTTGACTCCTGGATTGTCTCAAGACCGAGATGATATGAGCCACCATACTACTCACGAGACAT
* *
353281 CTCAAAA-AATCTGCAAAGATGACGATGGTGGAGTTGCAAAGAGCGAATTTGTCGACGGTCTTGA
259 CT-AAAAGAATCTGCAAAGATGAC----G-GGAGTTGCAAAGAGCGAATTTGTCGACGGTATAGA
*
353345 ACAGATGAATGACTTGACTCCTGGATTGTCTCTAGAT
318 ACAGATGAATGACTTGACTCCTGGATTGTCTCAAGAT
353382 GAGTCATCTT
Statistics
Matches: 302, Mismatches: 42, Indels: 21
0.83 0.12 0.06
Matches are distributed among these distances:
404 2 0.01
405 99 0.33
406 6 0.02
407 2 0.01
408 62 0.21
409 2 0.01
411 64 0.21
414 65 0.22
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (412 bp):
ATGATGATGGAGTTGCAAAGAGCGAATTCATTCACAGTATCGAACAGATGAATGAATTGACTCCC
GGATTGTCTCAAAGATCAAGATGATAGGAGCCACCATTCTACTCACGAGTCATCTCAAACAACCT
GCAAAAACAATGATGGTGAGGAGCTGCAAAGAGAGAATTCGTTCACGATATTGAACAGATGAATG
ACTTGACTCCTGGATTGTCTCAAGACCGAGATGATATGAGCCACCATACTACTCACGAGACATCT
AAAAGAATCTGCAAAGATGACGGGAGTTGCAAAGAGCGAATTTGTCGACGGTATAGAACAGATGA
ATGACTTGACTCCTGGATTGTCTCAAGATCAAGATGATGTGAGCCGCCATTCTATTCACGAGTCA
TCTCAAAAAACCTGCAAAGACA
Found at i:355391 original size:23 final size:24
Alignment explanation
Indices: 355346--355391 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
355336 AGTCAGCAAC
*
355346 AGAAGGATAAGGAACTGAAGAAGA
1 AGAAGGATAAGGAACTCAAGAAGA
355370 AGAA-GATAAGGAA-TCAATGAAG
1 AGAAGGATAAGGAACTCAA-GAAG
355392 TCCCTTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 13 0.65
24 4 0.20
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.11
Consensus pattern (24 bp):
AGAAGGATAAGGAACTCAAGAAGA
Found at i:360230 original size:245 final size:243
Alignment explanation
Indices: 359752--360343 Score: 695
Period size: 245 Copynumber: 2.4 Consensus size: 243
359742 CTCGAGCTTG
** * * * * *
359752 ATATCCTTTATCGTGAAGTTAAAACCCAAC-TCAAAATCTAGGATGAAAAATAGCTCCTCGTTGA
1 ATATCCTTTATCGTGAAGTTAAAATTCAACTTGAAGATCTTGGTTG-AAAATAGCTCCTCGCT-A
* * * * * *
359816 -TGAGTTAAGCTAAATTTTGGTTGACTCCTTCATCGTGAAGTTGATTCGATCATGCATGACTTAA
64 TTGAGTTAAGCTAAATTATGGATGACTCATTCGTCGTGAAATTGATTCAATCATGCATGACTTAA
* * *
359880 GCATGATATCCTTCGCCTTGAAGTTGAAATCTAGCTCGGAATATAGACTGGGAAATAACTCAACG
129 GCATGATATCCTTCACCGTGAAGTTGAAATCTAGCTCGAAATATAGACTGGGAAATAACTCAACG
* * *
359945 TTGTTGAGTTAAGCTAAATCGCAATTGATTTTGAGTCTTCTTTTAGTCCA
194 TTGTTGAGTTAAGCTAAATCGCAAGTGATCTTGAGTCTTCTTCTAGTCCA
* *
359995 ATATCCTTTGTCGTGAAGTTAAAATTCAACTTGAAGACCTTGGTTGAAAATAGCTCCTCGCTATT
1 ATATCCTTTATCGTGAAGTTAAAATTCAACTTGAAGATCTTGGTTGAAAATAGCTCCTCGCTATT
* ** * * *
360060 GAGTTAAGCTAAATTATGGATGATTCATTCGTTTTGAAATTGATTCAATC-TCGGATGACTTGAT
66 GAGTTAAGCTAAATTATGGATGACTCATTCGTCGTGAAATTGATTCAATCAT-GCATGACTTAAG
* * * * * * *
360124 CATGATGTGTCCTTCATCGTGAAGTTGAAATTTAGCTCGAAATTTGGACTGGGAAGTAACTCATC
130 CATGA--TATCCTTCACCGTGAAGTTGAAATCTAGCTCGAAATATAGACTGGGAAATAACTCAAC
* * *
360189 GTTGTTGAGTTAAGCTAAATCGCAGGTGATCTTGGGTCTTCTTCTAGTCTA
193 GTTGTTGAGTTAAGCTAAATCGCAAGTGATCTTGAGTCTTCTTCTAGTCCA
* * * * *
360240 ATATCATTTATCGTGAAGTTGAAATTCGACTTGAAGATCTTGGTTTGAAAATAGCTCATCGCTGT
1 ATATCCTTTATCGTGAAGTTAAAATTCAACTTGAAGATCTTGG-TTGAAAATAGCTCCTCGCTAT
* ** *
360305 TGAGTTGAGCTATGTTATGGATGACTCTTTCGTCGTGAA
65 TGAGTTAAGCTAAATTATGGATGACTCATTCGTCGTGAA
360344 GTTTAGTCGA
Statistics
Matches: 292, Mismatches: 51, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
242 2 0.01
243 98 0.34
244 10 0.03
245 131 0.45
246 51 0.17
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (243 bp):
ATATCCTTTATCGTGAAGTTAAAATTCAACTTGAAGATCTTGGTTGAAAATAGCTCCTCGCTATT
GAGTTAAGCTAAATTATGGATGACTCATTCGTCGTGAAATTGATTCAATCATGCATGACTTAAGC
ATGATATCCTTCACCGTGAAGTTGAAATCTAGCTCGAAATATAGACTGGGAAATAACTCAACGTT
GTTGAGTTAAGCTAAATCGCAAGTGATCTTGAGTCTTCTTCTAGTCCA
Found at i:360538 original size:20 final size:20
Alignment explanation
Indices: 360513--360565 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
360503 CTCAAAGAGA
360513 AATCTTGATCTTCTTCTTCC
1 AATCTTGATCTTCTTCTTCC
360533 AATCTTGATCTTCTTCTTCC
1 AATCTTGATCTTCTTCTTCC
360553 AATCTTGATCTTC
1 AATCTTGATCTTC
360566 CTCCACTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.28, G:0.06, T:0.49
Consensus pattern (20 bp):
AATCTTGATCTTCTTCTTCC
Found at i:365303 original size:5 final size:5
Alignment explanation
Indices: 365295--365320 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
365285 AAATTAAATG
365295 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
365321 TTCAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:365336 original size:20 final size:20
Alignment explanation
Indices: 365284--365343 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
365274 CAATGATTTA
** *
365284 AAAATTAAATGAATAAAAT-
1 AAAATTAAAAAAATAAATTC
*
365303 AAAATAAAATAAAATAAATTC
1 AAAATTAAA-AAAATAAATTC
*
365324 AAAATTAAAAAAAGAAATTC
1 AAAATTAAAAAAATAAATTC
365344 TTATTATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 8 0.24
20 17 0.52
21 8 0.24
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAATTAAAAAAATAAATTC
Found at i:368802 original size:11 final size:11
Alignment explanation
Indices: 368788--368817 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
368778 TTAATATATT
*
368788 ATTTTAATAAC
1 ATTTTAATAAA
368799 ATTTTAATAAA
1 ATTTTAATAAA
368810 ATTTTAAT
1 ATTTTAAT
368818 TATTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTTAATAAA
Found at i:368953 original size:30 final size:28
Alignment explanation
Indices: 368912--368979 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 28
368902 TACTTTCATT
*
368912 TTAATAATATTTAAAAATTGTGAATAAAAA
1 TTAATATTATTTAAAAATT-T-AATAAAAA
** *
368942 TTAATATTATTTATTAATTTCATAAAAA
1 TTAATATTATTTAAAAATTTAATAAAAA
368970 -TAATATTATT
1 TTAATATTATT
368980 GAATTGTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.29
28 7 0.21
29 1 0.03
30 16 0.47
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (28 bp):
TTAATATTATTTAAAAATTTAATAAAAA
Found at i:369052 original size:15 final size:15
Alignment explanation
Indices: 369021--369061 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
369011 AAATATAATA
*
369021 TAATATTATTA-TTT
1 TAATATTATAATTTT
369035 TAATATTATAATTTT
1 TAATATTATAATTTT
*
369050 TAATATTGTAAT
1 TAATATTATAAT
369062 AATAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TAATATTATAATTTT
Found at i:369078 original size:14 final size:14
Alignment explanation
Indices: 369021--369081 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
369011 AAATATAATA
*
369021 TAATATTATTATTT
1 TAATAATATTATTT
* *
369035 TAATATTATAATTT
1 TAATAATATTATTT
* **
369049 T--TAATATTGTAA
1 TAATAATATTATTT
369061 TAATAATATTATTT
1 TAATAATATTATTT
369075 TAATAAT
1 TAATAAT
369082 TAATTAATAA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
12 7 0.19
14 29 0.81
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TAATAATATTATTT
Found at i:369089 original size:25 final size:25
Alignment explanation
Indices: 369047--369094 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
369037 ATATTATAAT
*
369047 TTTTAATATTGTAATAATAATATTA
1 TTTTAATAATGTAATAATAATATTA
369072 TTTTAATAAT-TAATTAATAATAT
1 TTTTAATAATGTAA-TAATAATAT
369095 ATTATTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTTAATAATGTAATAATAATATTA
Found at i:369145 original size:37 final size:32
Alignment explanation
Indices: 369058--369177 Score: 93
Period size: 33 Copynumber: 3.6 Consensus size: 32
369048 TTTAATATTG
* *
369058 TAATA-ATAATATTATTTTAATAATTAATTAA
1 TAATATATAATTTTATTTTAATAAATAATTAA
* *
369089 TAATATATTATTCTCATTTTAATAAATAATTAATA
1 TAATATATAATT-TTATTTTAATAAATAATT-A-A
369124 TAATTTATACTAATTTTATTTTAATGAAAT-A-TAA
1 TAA--TATA-TAATTTTATTTTAAT-AAATAATTAA
*
369158 TAATCATAATATTTTTATTT
1 TAAT-AT-ATAATTTTATTT
369178 ATAAAATTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
31 5 0.07
32 5 0.07
33 28 0.39
34 6 0.08
35 5 0.07
36 1 0.01
37 14 0.19
38 8 0.11
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (32 bp):
TAATATATAATTTTATTTTAATAAATAATTAA
Found at i:369213 original size:70 final size:70
Alignment explanation
Indices: 369015--369213 Score: 158
Period size: 70 Copynumber: 2.8 Consensus size: 70
369005 TCTTTAAAAT
* * * **
369015 ATAATATAATATTATTATTTTAATATTATAATTTTTA-ATATTGTAATAATAATATTATTTTAAT
1 ATAATATAATATTCTCATTTTAATA-AATAATTAATATA-ATT-T-ATAATAATATTATTTTAAT
*
369079 AATTAATTA
62 AAATAATTA
* * *
369088 ATAATATATTATTCTCATTTTAATAAATAATTAATATAATTTATACTAATTTTATTTTAATGAAA
1 ATAATATAATATTCTCATTTTAATAAATAATTAATATAATTTATAATAATATTATTTTAAT-AAA
369153 T-A-TA
65 TAATTA
* * * *
369157 ATAATCATAATATTTTTA-TTT-ATAAA-ATTATAGATATAATATTTTAATAATATTATT
1 ATAAT-ATAATATTCTCATTTTAATAAATAAT-TA-ATATAAT-TTATAATAATATTATT
369214 AAATTATTAT
Statistics
Matches: 104, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
67 2 0.02
68 7 0.07
69 17 0.16
70 40 0.38
71 4 0.04
72 11 0.11
73 23 0.22
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (70 bp):
ATAATATAATATTCTCATTTTAATAAATAATTAATATAATTTATAATAATATTATTTTAATAAAT
AATTA
Found at i:369360 original size:14 final size:14
Alignment explanation
Indices: 369341--369372 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
369331 AATATTGTAA
*
369341 AATAATTTTTAAAT
1 AATAATTTTCAAAT
369355 AATAATTTTCAAAT
1 AATAATTTTCAAAT
369369 AATA
1 AATA
369373 TGATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
AATAATTTTCAAAT
Found at i:371679 original size:5 final size:5
Alignment explanation
Indices: 371657--371710 Score: 54
Period size: 5 Copynumber: 9.6 Consensus size: 5
371647 TCTTTTAAAT
371657 TTTTA TTTTGA TTGTTTA TTTTA TTTTA TTTTA TTTTA TTCTAATA TTTTA
1 TTTTA TTTT-A -T-TTTA TTTTA TTTTA TTTTA TTTTA TT-T--TA TTTTA
371708 TTT
1 TTT
371711 ATACATTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
5 30 0.70
6 3 0.07
7 3 0.07
8 7 0.16
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:371899 original size:20 final size:17
Alignment explanation
Indices: 371858--371900 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
371848 TGTTTCTTTA
*
371858 TTTTTTGTTTTTATTTG
1 TTTTATGTTTTTATTTG
371875 TTTTATGTTCTTTATCTTCG
1 TTTTATGTT-TTTAT-TT-G
371895 TTTTAT
1 TTTTAT
371901 TTATTCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 5 0.23
19 2 0.09
20 7 0.32
ACGTcount: A:0.09, C:0.07, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTATGTTTTTATTTG
Found at i:371949 original size:63 final size:59
Alignment explanation
Indices: 371837--371952 Score: 135
Period size: 63 Copynumber: 1.9 Consensus size: 59
371827 ATATATTTTC
* *
371837 TTTATTTTATTTGTTTCTTTATTTTTTGTTTTTATTTGTTTTATGTTCTTTATCTTCGT
1 TTTATTTTATTTGTTTCTTTATTTTTTGTTTTTATTTATTTCATGTTCTTTATCTTCGT
* * *
371896 TTTA-TTTATTCTGTTTACTTTTTTATCTTTGTTTTATCTTTATTTCATTTTCTTTAT
1 TTTATTTTATT-TGTTT-CTTTATT-T-TTTGTTTT-TATTTATTTCATGTTCTTTAT
371953 TTCATTTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
58 6 0.13
59 9 0.19
60 6 0.13
61 1 0.02
62 8 0.17
63 17 0.36
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.73
Consensus pattern (59 bp):
TTTATTTTATTTGTTTCTTTATTTTTTGTTTTTATTTATTTCATGTTCTTTATCTTCGT
Found at i:371951 original size:14 final size:14
Alignment explanation
Indices: 371932--371959 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
371922 CTTTGTTTTA
371932 TCTTTATTTCATTT
1 TCTTTATTTCATTT
371946 TCTTTATTTCATTT
1 TCTTTATTTCATTT
371960 GTTTTTTCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TCTTTATTTCATTT
Found at i:373050 original size:20 final size:21
Alignment explanation
Indices: 373022--373066 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
373012 TCTCACTAAC
*
373022 TTTTCTTTTCATT-GTTTTAT
1 TTTTCTTTTCATTCATTTTAT
* *
373042 TTTTGTTTTCTTTCATTTTAT
1 TTTTCTTTTCATTCATTTTAT
373063 TTTT
1 TTTT
373067 ATCATTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTCATTCATTTTAT
Found at i:377083 original size:85 final size:85
Alignment explanation
Indices: 376879--378006 Score: 1146
Period size: 85 Copynumber: 13.3 Consensus size: 85
376869 AAAAGCACCT
* * * * * * * *
376879 TCAACGAAAGACCTTTGAGTTCAATTACATTCAACTCAAAGGCGCATCAAATTTG-TAGCATAGT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAA-TTGACAGCATAGC
* *
376943 TCAAGACGAGAAGGGCTATCTG
64 TCAAGGCGAGAAGGGTTATCTG
* * * ** * *
376965 CCAACAAAAGACCTTCGAGTTCGATTATACTCAGCTTAAAGGCATGTCCAATTGACAACATAACT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCATAGCT
377030 CAAGGCGAGAAGGGTTATCTG
65 CAAGGCGAGAAGGGTTATCTG
* * * * *
377051 TCAGCCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCGCATCAAATATG-CAGAATAGCT
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAAT-TGACAGCATAGCT
* *
377115 CAAGGAGAGAAGGGTTATATG
65 CAAGGCGAGAAGGGTTATCTG
* * * * * *
377136 -CTAACAAAAGACCTTTGAGTTCGATTACACTCAACTCAAAGACACATCCAATTGATAGTATAAC
1 TC-AAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCATAGC
377200 TCAAGGCGAGAAGGGTTATCTG
64 TCAAGGCGAGAAGGGTTATCTG
* * * * *
377222 TCAGCCAAGACCATCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CATTTG-CAGCATAGCTA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCATAGCTC
* *
377285 AAGGCGAGTAGGGCTATCCT-
66 AAGGCGAGAAGGGTTAT-CTG
* * * *
377305 CCAACAAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCCAATCGACAGCATAACT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCATAGCT
*
377370 CAAGGAGAGAAGGGTTATCTG
65 CAAGGCGAGAAGGGTTATCTG
* * * *
377391 TCAGCCAAGACCTTCGAGTTCGATTACACTCAGCTGAAAGGCACAT-CATTTG-CAGCATAGCTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCATAGCTC
* *
377454 AAGGCGAGAAGGGCTATCTA
66 AAGGCGAGAAGGGTTATCTG
* * * *
377474 CCAATAAAAGACCTTCGTGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAAG-
1 TCAA-CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCAT-AGC
* *
377538 TCAAGGCAAGAAGGGTTATCTA
64 TCAAGGCGAGAAGGGTTATCTG
* * *
377560 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CATTTG-CAGCATAGCTT
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCATAGCTC
* **
377623 AAGGCGAGAAAGACTATCTG
66 AAGGCGAGAAGGGTTATCTG
* * * * * * * * *
377643 CCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAATGTATAT-TAATTTACAACATAACT
1 TCAA-CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCATAGCT
377707 CAAGGCGAGAAGGGTTATCTG
65 CAAGGCGAGAAGGGTTATCTG
* * * * * * * *
377728 TCAACTAAGTCCTTCGAATTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCATAGCTC
*
377793 AAGGCGAGAAGGGCTATCTG
66 AAGGCGAGAAGGGTTATCTG
* * ** * *
377813 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATTAAATTTACAGCATAGCTT
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCATAGCTC
*
377878 AAGGCAAGAAGGGTTATCTG
66 AAGGCGAGAAGGGTTATCTG
* * * * * * ** * * * *
377898 TCAACAAATACCTTCGAGTTCGATTCCATTCAACTCAAGGGTATGTCAAATTCACAGTATAGCTT
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCATAGCTC
* ** *
377963 AAGTCGAGAAAAGCTATCTG
66 AAGGCGAGAAGGGTTATCTG
* *
377983 TCAACAAAAACTTTCGAGTTCGAT
1 TCAACAAAGACCTTCGAGTTCGAT
378007 CCCATTCAGT
Statistics
Matches: 868, Mismatches: 155, Indels: 39
0.82 0.15 0.04
Matches are distributed among these distances:
82 2 0.00
83 79 0.09
84 167 0.19
85 425 0.49
86 192 0.22
87 3 0.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (85 bp):
TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTGACAGCATAGCTC
AAGGCGAGAAGGGTTATCTG
Found at i:377386 original size:169 final size:170
Alignment explanation
Indices: 376886--378006 Score: 1342
Period size: 169 Copynumber: 6.6 Consensus size: 170
376876 CCTTCAACGA
* * * * * * * *
376886 AAGACCTTTGAGTTCAATTACATTCAACTCAAAGGCGCATCAAATTTGTAGCATAGTTCAAGACG
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-AATTTGCAGCATAGCTCAAGGCG
* * **
376951 AGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTATACTCAGCTTAAAGGCATGTCCAA
65 AGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAA
* * *
377016 TTGACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAGCC
130 TTGACAGCATAACTCAAGGAGAGAAGGGTTATCTGTCAACC
* * * *
377057 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCGCATCAAATATGCAGAATAGCTCAAGGAG
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-AATTTGCAGCATAGCTCAAGGCG
* * * * * *
377122 AGAAGGGTTATATGCTAACAAAAGACCTTTGAGTTCGATTACACTCAACTCAAAGACACATCCAA
65 AGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAA
* * * *
377187 TTGATAGTATAACTCAAGGCGAGAAGGGTTATCTGTCAGCC
130 TTGACAGCATAACTCAAGGAGAGAAGGGTTATCTGTCAACC
* *
377228 AAGACCATCGAGTTCGATTACACTCAGCTCAAAGGCACATC-ATTTGCAGCATAGCTAAAGGCGA
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTGCAGCATAGCTCAAGGCGA
* *
377292 GTAGGGCTATCCT-CCAACAAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCCAA
66 GAAGGGCTAT-CTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAA
* *
377356 TCGACAGCATAACTCAAGGAGAGAAGGGTTATCTGTCAGCC
130 TTGACAGCATAACTCAAGGAGAGAAGGGTTATCTGTCAACC
*
377397 AAGACCTTCGAGTTCGATTACACTCAGCTGAAAGGCACATC-ATTTGCAGCATAGCTCAAGGCGA
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTGCAGCATAGCTCAAGGCGA
* * *
377461 GAAGGGCTATCTACCAATAAAAGACCTTCGTGTTCGATTACACTCAGCTCAAAGGCACATCCAAT
66 GAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAAT
* * *
377526 TTACAGCATAAGTCAAGGCA-AGAAGGGTTATCTATCAACC
131 TGACAGCATAACTCAAGG-AGAGAAGGGTTATCTGTCAACC
*
377566 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-ATTTGCAGCATAGCTTAAGGCGA
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTGCAGCATAGCTCAAGGCGA
* * * * * * *
377630 GAAAGACTATCTGCCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAATGTATAT-TAAT
66 GAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAAT
* * * *
377694 TTACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACT
131 TGACAGCATAACTCAAGGAGAGAAGGGTTATCTGTCAACC
* * * * * *
377734 AAGTCCTTCGAATTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCG
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-AATTTGCAGCATAGCTCAAGGCG
* * * **
377799 AGAAGGGCTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATTAAA
65 AGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAA
* * * *
377863 TTTACAGCATAGCTTAAGGCA-AGAAGGGTTATCTGTCAACA
130 TTGACAGCATAACTCAAGG-AGAGAAGGGTTATCTGTCAACC
* * * * * * ** ** * * *
377904 AATACCTTCGAGTTCGATTCCATTCAACTCAAGGGTATGTCAAATTCACAGTATAGCTTAAGTCG
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-AATTTGCAGCATAGCTCAAGGCG
** * *
377969 AGAAAAGCTATCTGTCAACAAAA-ACTTTCGAGTTCGAT
65 AGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGAT
378007 CCCATTCAGT
Statistics
Matches: 836, Mismatches: 105, Indels: 19
0.87 0.11 0.02
Matches are distributed among these distances:
168 76 0.09
169 415 0.50
170 156 0.19
171 189 0.23
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (170 bp):
AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTGCAGCATAGCTCAAGGCGA
GAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAAT
TGACAGCATAACTCAAGGAGAGAAGGGTTATCTGTCAACC
Found at i:379933 original size:13 final size:13
Alignment explanation
Indices: 379917--379966 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
379907 TATTTTGGTC
*
379917 TTTTAAATTTTTA
1 TTTTATATTTTTA
379930 TTTT-TATTGTTTA
1 TTTTATATT-TTTA
*
379943 TTTTATTTTTTTA
1 TTTTATATTTTTA
379956 TTTTAT-TTTTT
1 TTTTATATTTTT
379967 TCTAATGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 8 0.24
13 22 0.67
14 3 0.09
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTATATTTTTA
Found at i:379933 original size:26 final size:24
Alignment explanation
Indices: 379899--379981 Score: 62
Period size: 26 Copynumber: 3.3 Consensus size: 24
379889 CTTGTTTTTA
* *
379899 TTTTGTTTTATTTTGGTCTTTTAAAT
1 TTTTATTTTATTTT--TATTTTAAAT
**
379925 TTTTATTTTTATTGTTTATTTTATTT
1 TTTTA-TTTTATT-TTTATTTTAAAT
*
379951 TTTTATTTTATTTTT-TTCT-AAT
1 TTTTATTTTATTTTTATTTTAAAT
379973 GTTTTATTT
1 -TTTTATTT
379982 ATACATTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
22 1 0.02
23 11 0.23
24 3 0.06
25 7 0.15
26 16 0.34
27 7 0.15
28 2 0.04
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76
Consensus pattern (24 bp):
TTTTATTTTATTTTTATTTTAAAT
Found at i:379967 original size:13 final size:13
Alignment explanation
Indices: 379924--379967 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
379914 GTCTTTTAAA
379924 TTTTTATTTT-TAT
1 TTTTTATTTTAT-T
*
379937 TGTTTATTTTATT
1 TTTTTATTTTATT
379950 TTTTTATTTTATT
1 TTTTTATTTTATT
379963 TTTTT
1 TTTTT
379968 CTAATGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 27 0.96
14 1 0.04
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:380054 original size:17 final size:16
Alignment explanation
Indices: 380030--380088 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
380020 ATTCTCTTTC
380030 TTTTTATTTTTTTCTT
1 TTTTTATTTTTTTCTT
*
380046 TTCTTTATTTTTTTC-C
1 TT-TTTATTTTTTTCTT
*
380062 TTTATATTTTTTTCTT
1 TTTTTATTTTTTTCTT
*
380078 TATTTAGTTTT
1 TTTTTA-TTTT
380089 ATTTTATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.31
16 8 0.23
17 16 0.46
ACGTcount: A:0.10, C:0.08, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTTATTTTTTTCTT
Found at i:380079 original size:14 final size:13
Alignment explanation
Indices: 380030--380082 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
380020 ATTCTCTTTC
*
380030 TTTTTATTT-TTT
1 TTTTTCTTTATTT
380042 TCTTTTCTTTATTT
1 T-TTTTCTTTATTT
*
380056 TTTTCCTTTATATT
1 TTTTTCTTTAT-TT
380070 TTTTTCTTTATTT
1 TTTTTCTTTATTT
380083 AGTTTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 1 0.03
13 18 0.51
14 16 0.46
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTCTTTATTT
Found at i:380083 original size:18 final size:18
Alignment explanation
Indices: 380024--380083 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 18
380014 ACTATTATTC
*
380024 TCTTTCTTTTTATTTTTT
1 TCTTTCTTTATATTTTTT
380042 TCTTT-TCTT-TATTTTTT
1 TCTTTCT-TTATATTTTTT
380059 TC---CTTTATATTTTTT
1 TCTTTCTTTATATTTTTT
*
380074 TCTTTATTTA
1 TCTTTCTTTA
380084 GTTTTATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 2 0.06
15 11 0.31
17 11 0.31
18 11 0.31
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (18 bp):
TCTTTCTTTATATTTTTT
Found at i:380112 original size:18 final size:17
Alignment explanation
Indices: 380068--380113 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
380058 TTCCTTTATA
*
380068 TTTTTTTCTTTATTTAG
1 TTTTTATCTTTATTTAG
*
380085 -TTTTAT-TTTATTATTG
1 TTTTTATCTTTATT-TAG
380101 TTTTTATCTTTAT
1 TTTTTATCTTTAT
380114 ATATATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 6 0.25
18 5 0.21
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTTTATCTTTATTTAG
Found at i:380118 original size:2 final size:2
Alignment explanation
Indices: 380111--380153 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
380101 TTTTTATCTT
380111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
380153 T
1 T
380154 TTTCTTTATT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:381443 original size:2 final size:2
Alignment explanation
Indices: 381436--381464 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
381426 TGTAAATTCA
381436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
381465 ACAAAGCTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:381601 original size:18 final size:18
Alignment explanation
Indices: 381580--381623 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
381570 AACATTTCAC
381580 ATTTAAAATATAATAATG
1 ATTTAAAATATAATAATG
381598 ATTTAAAATATAATAATG
1 ATTTAAAATATAATAATG
*
381616 ATGTAAAA
1 ATTTAAAA
381624 CGTAAACGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (18 bp):
ATTTAAAATATAATAATG
Found at i:385237 original size:12 final size:12
Alignment explanation
Indices: 385220--385245 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
385210 ACTTGATCCC
385220 AATATCAAACTA
1 AATATCAAACTA
385232 AATATCAAACTA
1 AATATCAAACTA
385244 AA
1 AA
385246 AGTCTTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (12 bp):
AATATCAAACTA
Found at i:387910 original size:22 final size:22
Alignment explanation
Indices: 387885--387936 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
387875 TAATCTCTTG
387885 AAGATAAGGAACCAAAATCCTA
1 AAGATAAGGAACCAAAATCCTA
* *
387907 AAGATAATGAACCAAAATCTTA
1 AAGATAAGGAACCAAAATCCTA
387929 AAGATAAG
1 AAGATAAG
387937 ATATTGCCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.56, C:0.13, G:0.13, T:0.17
Consensus pattern (22 bp):
AAGATAAGGAACCAAAATCCTA
Found at i:388326 original size:20 final size:21
Alignment explanation
Indices: 388290--388331 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
388280 AGATAAAACC
388290 ACTATTAAAGACTAAGGTAGT
1 ACTATTAAAGACTAAGGTAGT
*
388311 ACTATT-AAGGCTAAGGTAGT
1 ACTATTAAAGACTAAGGTAGT
388331 A
1 A
388332 ATGTCAGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (21 bp):
ACTATTAAAGACTAAGGTAGT
Found at i:392769 original size:6 final size:6
Alignment explanation
Indices: 392758--392837 Score: 53
Period size: 6 Copynumber: 13.3 Consensus size: 6
392748 ACTATTTATA
392758 ATTAAT ATTAAT A-TAA- ATTATAT ATT-AT AATTAAT ATTAAT A-TAA-
1 ATTAAT ATTAAT ATTAAT ATTA-AT ATTAAT -ATTAAT ATTAAT ATTAAT
* * *
392803 AATACAGT CTATAAA ATTAAT ATTAAT ATTAAT AT
1 ATTA-A-T AT-TAAT ATTAAT ATTAAT ATTAAT AT
392838 AAATTGTATT
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
4 2 0.03
5 12 0.20
6 36 0.61
7 6 0.10
8 1 0.02
9 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
ATTAAT
Found at i:392781 original size:24 final size:23
Alignment explanation
Indices: 392728--392794 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 23
392718 ATTTCATCCC
392728 TTTATAATTTATATTAATA-AACTA
1 TTTATAA-TTATATTAATATAAC-A
392752 TTTATAATTAATATTAATATAA-A
1 TTTATAATT-ATATTAATATAACA
392775 -TTATATATTATAATTAATAT
1 TTTATA-ATTAT-ATTAATAT
392795 TAATATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
22 7 0.18
23 14 0.36
24 16 0.41
25 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTATAATTATATTAATATAACA
Found at i:392786 original size:29 final size:30
Alignment explanation
Indices: 392753--392831 Score: 106
Period size: 29 Copynumber: 2.6 Consensus size: 30
392743 AATAAACTAT
* *
392753 TTATAATTAATATTAATATAAATTATA-TA
1 TTATAATTAATATTAATATAAAATACAGTA
*
392782 TTATAATTAATATTAATATAAAATACAGTC
1 TTATAATTAATATTAATATAAAATACAGTA
*
392812 TATAAAATTAATATTAATAT
1 T-TATAATTAATATTAATAT
392832 TAATATAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.57
30 2 0.05
31 17 0.39
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (30 bp):
TTATAATTAATATTAATATAAAATACAGTA
Found at i:392956 original size:20 final size:21
Alignment explanation
Indices: 392916--392957 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
392906 AAGATAATTA
392916 ACATTAATATAAACTCTATAGT
1 ACATTAATATAAAC-CTATAGT
392938 ACATTAATATAAA-CTATAGT
1 ACATTAATATAAACCTATAGT
392958 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACCTATAGT
Found at i:392975 original size:20 final size:20
Alignment explanation
Indices: 392952--392989 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
392942 TAATATAAAC
* *
392952 TATAGTTTATAAATTATATA
1 TATAGGTTATAAAGTATATA
392972 TATAGGTTATAAAGTATA
1 TATAGGTTATAAAGTATA
392990 AACTATATAG
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:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (20 bp):
TATAGGTTATAAAGTATATA
Found at i:393086 original size:24 final size:23
Alignment explanation
Indices: 393045--393098 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
393035 TACATATATT
*
393045 TATATA-ACATATAAATAGATTG
1 TATATATACATATAAATAGATTA
* *
393067 TATATATACATATACTATAGGTTA
1 TATATATACATATA-AATAGATTA
393091 TATATATA
1 TATATATA
393099 TAGTTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 6 0.22
23 7 0.26
24 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (23 bp):
TATATATACATATAAATAGATTA
Found at i:393100 original size:15 final size:16
Alignment explanation
Indices: 393076--393116 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
393066 GTATATATAC
393076 ATATACTATAGGTTAT
1 ATATACTATAGGTTAT
*
393092 ATATA-TATAGTTTAT
1 ATATACTATAGGTTAT
393107 ATATACTATA
1 ATATACTATA
393117 CATAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (16 bp):
ATATACTATAGGTTAT
Found at i:393116 original size:20 final size:20
Alignment explanation
Indices: 393043--393132 Score: 66
Period size: 20 Copynumber: 4.5 Consensus size: 20
393033 GTTACATATA
*
393043 TTTATATA-ACATATAAATAG
1 TTTATATATAC-TATACATAG
393063 ATTGTATATATACATATACTATAG
1 -TT-TATATATAC-TATAC-ATAG
*
393087 -GT-TATATA-TAT--ATAG
1 TTTATATATACTATACATAG
393102 TTTATATATACTATACATAG
1 TTTATATATACTATACATAG
*
393122 TTTATACATAC
1 TTTATATATAC
393133 ATGTACTATA
Statistics
Matches: 57, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
15 4 0.07
16 1 0.02
17 6 0.11
18 6 0.11
20 20 0.35
21 3 0.05
22 6 0.11
23 7 0.12
24 4 0.07
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (20 bp):
TTTATATATACTATACATAG
Found at i:393553 original size:20 final size:20
Alignment explanation
Indices: 393525--393562 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
393515 CAGGGGTTAG
393525 AGTTGAGGGTTTAGGTTTAT
1 AGTTGAGGGTTTAGGTTTAT
*
393545 AGTTTAGGGTTTAGGTTT
1 AGTTGAGGGTTTAGGTTT
393563 CACAATTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.47
Consensus pattern (20 bp):
AGTTGAGGGTTTAGGTTTAT
Found at i:393573 original size:21 final size:20
Alignment explanation
Indices: 393530--393580 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
393520 GTTAGAGTTG
* *
393530 AGGGTTTAGGTTTATAGTTT
1 AGGGTTTAGGTTTACAATTT
393550 AGGGTTTAGGTTTCACAATTT
1 AGGGTTTAGGTTT-ACAATTT
*
393571 AGGGTATAGG
1 AGGGTTTAGG
393581 GTTTTATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.24, C:0.04, G:0.31, T:0.41
Consensus pattern (20 bp):
AGGGTTTAGGTTTACAATTT
Found at i:393750 original size:15 final size:15
Alignment explanation
Indices: 393677--393750 Score: 60
Period size: 15 Copynumber: 4.8 Consensus size: 15
393667 TATACATACA
393677 TATATATAATATA-TT
1 TATATAT-ATATAGTT
* * *
393692 AATATAAATTATAATT
1 TATATATA-TATAGTT
*
393708 TATAAAATATATAGTT
1 TAT-ATATATATAGTT
* *
393724 TATACATTTATAGTT
1 TATATATATATAGTT
393739 TATATATATATA
1 TATATATATATA
393751 TATAGAAAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
14 1 0.02
15 29 0.63
16 13 0.28
17 3 0.07
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (15 bp):
TATATATATATAGTT
Found at i:393986 original size:18 final size:19
Alignment explanation
Indices: 393965--394000 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
393955 AAATTTTCTA
393965 TTCCATCTAAATT-TCAAT
1 TTCCATCTAAATTCTCAAT
*
393983 TTCCCTCTAAATTCTCAA
1 TTCCATCTAAATTCTCAA
394001 ATAAAATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.42
Consensus pattern (19 bp):
TTCCATCTAAATTCTCAAT
Found at i:394136 original size:25 final size:25
Alignment explanation
Indices: 394088--394145 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
394078 TTAATATAAA
*
394088 TTATAGTTTATAAACTCTATATTTT
1 TTATAGTTTATAAACTATATATTTT
* *
394113 TTATAGTTTATACA-TATATAATTT
1 TTATAGTTTATAAACTATATATTTT
*
394137 ATATA-TTTA
1 TTATAGTTTA
394146 GTTCATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 4 0.14
24 12 0.41
25 13 0.45
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.55
Consensus pattern (25 bp):
TTATAGTTTATAAACTATATATTTT
Found at i:394206 original size:15 final size:15
Alignment explanation
Indices: 394114--394217 Score: 90
Period size: 15 Copynumber: 7.0 Consensus size: 15
394104 CTATATTTTT
*
394114 TATAGTTTATACATA
1 TATAGTTTATATATA
*
394129 TATAATTTATATAT-
1 TATAGTTTATATATA
* *
394143 T-TAGTTCATATAAA
1 TATAGTTTATATATA
* *
394157 CAT-GATT-TATATA
1 TATAGTTTATATATA
*
394170 TATAGCTTATAATAATTA
1 TATAGTTTAT-AT-A-TA
394188 TATAGTTTATATATA
1 TATAGTTTATATATA
394203 TATAGTTTATATATA
1 TATAGTTTATATATA
394218 AACTTATATT
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
13 16 0.23
14 6 0.09
15 31 0.44
16 3 0.04
17 3 0.04
18 11 0.16
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (15 bp):
TATAGTTTATATATA
Found at i:394229 original size:17 final size:16
Alignment explanation
Indices: 394209--394243 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
394199 TATATATAGT
394209 TTATATATAAACTTATA
1 TTATATATAAA-TTATA
*
394226 TTATATATATATTATA
1 TTATATATAAATTATA
394242 TT
1 TT
394244 TTTTCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATATAAATTATA
Found at i:394236 original size:11 final size:11
Alignment explanation
Indices: 394163--394242 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
394153 TAAACATGAT
394163 TTATATATATA
1 TTATATATATA
394174 GCTTATA-ATA-A
1 --TTATATATATA
*
394185 TTATATAGTTTA
1 TTATATA-TATA
394197 -TATATATATA
1 TTATATATATA
394207 GTT-TATATATA
1 -TTATATATATA
394218 --A-ACT-TATA
1 TTATA-TATATA
394226 TTATATATATA
1 TTATATATATA
394237 TTATAT
1 TTATAT
394243 TTTTTCAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 24
0.68 0.03 0.30
Matches are distributed among these distances:
8 5 0.09
9 6 0.11
10 6 0.11
11 27 0.50
12 5 0.09
13 5 0.09
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (11 bp):
TTATATATATA
Found at i:394241 original size:61 final size:58
Alignment explanation
Indices: 394127--394241 Score: 135
Period size: 61 Copynumber: 1.9 Consensus size: 58
394117 AGTTTATACA
394127 TATATAATTTATATATTTAGTTCATATAAACATGATTTATATATATAGCTTATAATAAT
1 TATATAATTTATATATTTAGTTCATATAAACATGATTTATATATATA-CTTATAATAAT
* * *
394186 TATATAGTTTATATATATATAGTTTATATATAA-ACTTATATTATATATATA-TTATA
1 TATATAATTTATATAT-T-TAGTTCATATA-AACA-TGAT-TTATATATATACTTATA
394242 TTTTTTCAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
59 15 0.31
60 1 0.02
61 16 0.33
62 5 0.10
63 11 0.23
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (58 bp):
TATATAATTTATATATTTAGTTCATATAAACATGATTTATATATATACTTATAATAAT
Found at i:399475 original size:13 final size:12
Alignment explanation
Indices: 399456--399488 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
399446 GTAACTTTTT
399456 ATTTTTTTATTA
1 ATTTTTTTATTA
399468 ATTTTTTTATTA
1 ATTTTTTTATTA
399480 ATTTTTTTA
1 ATTTTTTTA
399489 AATTATTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTTTTATTA
Found at i:399611 original size:39 final size:39
Alignment explanation
Indices: 399557--399638 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
399547 TCCGGATGTG
*
399557 CTAACCACTAACCGCTAACTTTTTTAACAGCTAACATTT
1 CTAACCACTAACCGCTAACTTTTCTAACAGCTAACATTT
* * *
399596 CTAACTACTAACCGCTAACTTTTCTAACAGTTAACCTTT
1 CTAACCACTAACCGCTAACTTTTCTAACAGCTAACATTT
399635 CTAA
1 CTAA
399639 TTGCTAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (39 bp):
CTAACCACTAACCGCTAACTTTTCTAACAGCTAACATTT
Found at i:399630 original size:23 final size:23
Alignment explanation
Indices: 399580--399631 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
399570 GCTAACTTTT
*
399580 TTAACAGCTAACATTTCTAACTA
1 TTAACCGCTAACATTTCTAACTA
* *
399603 CTAACCGCTAACTTTTCTAAC-A
1 TTAACCGCTAACATTTCTAACTA
399625 GTTAACC
1 -TTAACC
399632 TTTCTAATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.33
Consensus pattern (23 bp):
TTAACCGCTAACATTTCTAACTA
Found at i:402001 original size:2 final size:2
Alignment explanation
Indices: 401994--402021 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
401984 GTAAAATCTA
401994 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
402022 TCTAATCATT
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:402572 original size:18 final size:18
Alignment explanation
Indices: 402549--402606 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
402539 CAGTGGGTTC
402549 CACTACTTGTGTCACGGT
1 CACTACTTGTGTCACGGT
*
402567 CACTACTTGGGT--C---
1 CACTACTTGTGTCACGGT
402580 CACTACTTGTGTCACGGT
1 CACTACTTGTGTCACGGT
*
402598 TACTACTTG
1 CACTACTTG
402607 GGTCCACTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
13 11 0.34
15 1 0.03
16 1 0.03
18 19 0.59
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (18 bp):
CACTACTTGTGTCACGGT
Found at i:402585 original size:13 final size:13
Alignment explanation
Indices: 402567--402620 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
402557 GTGTCACGGT
402567 CACTACTTGGGTC
1 CACTACTTGGGTC
*
402580 CACTACTTGTGTC
1 CACTACTTGGGTC
402593 ACGGTTACTACTTGGGTC
1 -C----ACTACTTGGGTC
402611 CACTACTTGG
1 CACTACTTGG
402621 ATCACGATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
13 21 0.62
14 1 0.03
17 1 0.03
18 11 0.32
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (13 bp):
CACTACTTGGGTC
Done.