Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007916.1 Hibiscus syriacus cultivar Beakdansim tig00110319_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: 3725575
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 16
Found at i:2405666 original size:191 final size:191
Alignment explanation
Indices: 2404652--2405771 Score: 1664
Period size: 189 Copynumber: 5.9 Consensus size: 191
2404642 TTAAATTAGC
2404652 ATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
1 ATCGACACAAACTAAAAAGTGTCGACAC---ATTTAGACATATTCTCTCATAAAACCGGTATACT
2404717 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCG
63 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATG-TTTTGGGATCG
*
2404782 ACACTTTT-TATATTGGATCGACACTTATGGTTGCACCATGTTTTCCATTCATCTGGACCAAAAA
127 ACACTTTTATATA-TGGATCGACACTTATGGTTGCACCCTGTTTTCCATTCATCTGGACCAAAAA
2404846 T
191 T
2404847 ATCGACACAAACT-AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-CGGTATACT
1 ATCGACACAAACTAAAAAGTGTCGACAC---ATTTAGACATATTCTCTCATAAAACCGGTATACT
* * *
2404910 TGTATCGGTTAGATT-AAAAA--ACA-ATTACATTATACTTTTGGTTTCGATGTTTTTGGATCGA
63 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTGGGATCGA
* * *
2404971 AACTTTTATATATGGATCGACACTT-TGGTTGCACCC-GTTTTCCATTCATTCGGGA-CTAAAAT
128 CACTTTTATATATGGATCGACACTTATGGTTGCACCCTGTTTTCCATTCA-TCTGGACCAAAAAT
* * *
2405033 ACCGACACAAACTAAAAAAGTGTCGACATATTTTAGACATA-T-TCTCATAAAAACCAGTATAC-
1 ATCGACACAAACT-AAAAAGTGTCGACACA-TTTAGACATATTCTCTCAT-AAAACCGGTATACT
2405095 -GTACCGGTTAGATTGAAAAATTACATA-TACA-T-TAC-TTTGGGTTCGATGTTTTAGGGATCG
63 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTT-GGGATCG
2405155 ACACTTTTATATATGGATCGACACTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAA
127 ACACTTTTATATATGGATCGACACTTATGGTTGCACCCTGTTTTCCATTCA-TCTGGACCAAAAA
2405220 T
191 T
*
2405221 ATCGACACAAACTAAAAAGTGTCGA-ACATTATTAGACATATTCTCTCATAAAATCGGTATACTT
1 ATCGACACAAACTAAAAAGTGTCGACACA-T-TTAGACATATTCTCTCATAAAACCGGTATACTT
2405285 GTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGA
64 GTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATG-TTTTGGGATCGA
*
2405350 CACTTTTATATATGGATCAACACTTATGGTTGCACCCTG-TTTCCATTCATCTGGACCAAAAAT
128 CACTTTTATATATGGATCGACACTTATGGTTGCACCCTGTTTTCCATTCATCTGGACCAAAAAT
*
2405413 ATCGACAC-TA--AAAAAGTGTCGACACATATTAGACATATTCTCTCATAAAACCGGTATACTTG
1 ATCGACACAAACTAAAAAGTGTCGACACAT-TTAGACATATTCTCTCATAAAACCGGTATACTTG
2405475 TA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGCTTTTGGGATCGA
65 TACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATG-TTTTGGGATCGA
* *
2405539 CACTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCAATCATCTGGAACAAAAAT
128 CACTTTTATATATGGATCGACAC-TTATGGTTGCACCCTGTTTTCCATTCATCTGGACCAAAAAT
2405604 ATCGACACAAACTAAAAAGTGTCGACACATTTAGACATA-T-TCTCATAAAACCGGTATACTTGT
1 ATCGACACAAACTAAAAAGTGTCGACACATTTAGACATATTCTCTCATAAAACCGGTATACTTGT
* *
2405667 ACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTTTGATGTTTTTGGATCGACA
66 ACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTGGGATCGAC-
* *
2405731 ATTTTTATATATGGTTCGACACTTTATGGTTGCACCCTGTT
129 ACTTTTATATATGGATCGACAC-TTATGGTTGCACCCTGTT
2405772 GGCCATATTG
Statistics
Matches: 859, Mismatches: 32, Indels: 72
0.89 0.03 0.07
Matches are distributed among these distances:
184 35 0.04
185 45 0.05
186 63 0.07
187 61 0.07
188 115 0.13
189 125 0.15
190 61 0.07
191 122 0.14
192 53 0.06
193 45 0.05
194 117 0.14
195 17 0.02
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (191 bp):
ATCGACACAAACTAAAAAGTGTCGACACATTTAGACATATTCTCTCATAAAACCGGTATACTTGT
ACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTGGGATCGACAC
TTTTATATATGGATCGACACTTATGGTTGCACCCTGTTTTCCATTCATCTGGACCAAAAAT
Found at i:2405931 original size:19 final size:19
Alignment explanation
Indices: 2405885--2405933 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2405875 AATTATTCAC
*
2405885 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
2405904 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
2405923 ATACAAAATTA
1 ATACAAAATTA
2405934 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:2406231 original size:17 final size:18
Alignment explanation
Indices: 2406209--2406253 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
2406199 TTATATTCAC
*
2406209 ATACAAAA-ATATATCGT
1 ATACAAAATATAAATCGT
*
2406226 ATACAAAATTATAAATCTT
1 ATACAAAA-TATAAATCGT
2406245 ATACAAAAT
1 ATACAAAAT
2406254 TAACCCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.33
18 1 0.04
19 15 0.62
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (18 bp):
ATACAAAATATAAATCGT
Found at i:2406273 original size:322 final size:319
Alignment explanation
Indices: 2405671--2406316 Score: 1192
Period size: 322 Copynumber: 2.0 Consensus size: 319
2405661 ACTTGTACCG
2405671 GTTAGATTGAAAAATTACATATACATTATACTTTTGGGTTTTGATGTTTTTGGATCGACAATTTT
1 GTTAGATTGAAAAATTACATATACATTATACTTTTGGGTTTTGATGTTTTTGGATCGACAATTTT
2405736 TATATATGGTTCGACACTTTATGGTTGCACCCTGTTGGCCATATTGTAAATTTGCCTTTTACTTC
66 TATATATGGTTCGACACTTTATGGTTGCACCCTGTTGGCCATATTGTAAATTTGCCTTTTACTTC
2405801 AAAGATCAACATGACCCTTAATGTGTATAAGAAACATGTACAACACTACTACTAACTTTTCTCAT
131 AAAGATCAACATGACCCTTAATGTGTATAAGAAACATGTACAACACTACTACTAACTTTTCTCAT
2405866 CTCATTCATAATTATTCACATACAAAAATATAAATCGTATACAAAATTATAAATCTTATACAAAA
196 CTCATTCATAATTATTCACATACAAAAATAT-AATCGTATACAAAATTATAAATCTTATACAAAA
2405931 TTAACCCTACATTTACATCATTGCATCCTTTTGTTATTCTTATGT-A-ATGGCAGC-TTT
260 TTAACCCTACATTTACATCATTGCATCCTTTTGTTATTCTTATGTAATATGGCAGCTTTT
2405988 GTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTTGATGTTTTTGGGATCGACAATT
1 GTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTTTGATGTTTTT-GGATCGACAATT
2406053 TTTATATATGGTTCGACACTTTATGGTTGCACCCTGTTGGCCATATTGTAAATTTGCCTTTTACT
64 TTTATATATGGTTCGACACTTTATGGTTGCACCCTGTTGGCCATATTGTAAATTTGCCTTTTACT
2406118 TCAAAGTATCAACATGACCCTTAATGTGTATAAGAAACATGTACAACAGCATACTACTAACTTTT
129 TCAAAG-ATCAACATGACCCTTAATGTGTATAAGAAACATGTACAACA-C-TACTACTAACTTTT
2406183 CTCATCTCATTCATAATTATATTCACATACAAAAATAT-ATCGTATACAAAATTATAAATCTTAT
191 CTCATCTCATTCATAA-T-TATTCACATACAAAAATATAATCGTATACAAAATTATAAATCTTAT
2406247 ACAAAATTAACCCTACATTTACATCATTGCATCCTTTTGTTATTCTTATGTAATATGGCAGCTTT
254 ACAAAATTAACCCTACATTTACATCATTGCATCCTTTTGTTATTCTTATGTAATATGGCAGCTTT
2406312 T
319 T
2406313 GTTA
1 GTTA
2406317 TCTCCTGTTT
Statistics
Matches: 319, Mismatches: 0, Indels: 12
0.96 0.00 0.04
Matches are distributed among these distances:
317 21 0.07
318 30 0.09
319 83 0.26
320 41 0.13
321 1 0.00
322 107 0.34
323 2 0.01
324 27 0.08
325 7 0.02
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (319 bp):
GTTAGATTGAAAAATTACATATACATTATACTTTTGGGTTTTGATGTTTTTGGATCGACAATTTT
TATATATGGTTCGACACTTTATGGTTGCACCCTGTTGGCCATATTGTAAATTTGCCTTTTACTTC
AAAGATCAACATGACCCTTAATGTGTATAAGAAACATGTACAACACTACTACTAACTTTTCTCAT
CTCATTCATAATTATTCACATACAAAAATATAATCGTATACAAAATTATAAATCTTATACAAAAT
TAACCCTACATTTACATCATTGCATCCTTTTGTTATTCTTATGTAATATGGCAGCTTTT
Found at i:2408149 original size:21 final size:21
Alignment explanation
Indices: 2408124--2408167 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2408114 CCCCTTATGC
2408124 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
2408145 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
2408166 CT
1 CT
2408168 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:2410090 original size:20 final size:20
Alignment explanation
Indices: 2410061--2410120 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
2410051 CGGTAACGTT
*
2410061 TTACCAGTTTTATCATTTTG
1 TTACCGGTTTTATCATTTTG
2410081 TTACCGGTTTTATCATATTT-
1 TTACCGGTTTTATCAT-TTTG
*
2410101 TTACCTGG-TATATCATTTTG
1 TTACC-GGTTTTATCATTTTG
2410121 GATCGATACA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.09
20 27 0.77
21 5 0.14
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (20 bp):
TTACCGGTTTTATCATTTTG
Found at i:2410200 original size:180 final size:181
Alignment explanation
Indices: 2409865--2410318 Score: 651
Period size: 181 Copynumber: 2.5 Consensus size: 181
2409855 CGAAAGTACA
* * * *
2409865 ATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCAGTTTTATCATATTTTTACATGTTA
1 ATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATATTTTTACCTGTTA
* * *
2409930 TATCGTTGTGGATCGATATATATTTTTAAAGTATCGACACATTATAGGAGCTAAAACTGCTTCTC
66 TATCGTTTTGGATCGATACAT-TTTTAAAAGTATCGACACATTATAGGAGCTAAAACTGCTTCTC
* *
2409995 TTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAGTATCGACACTTTCAAT
130 TTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTACCGACACTTTAAAT
* * *
2410046 ATATCCGGTAACGTTTTACCAGTTTTATCATTTTGTTACCGGTTTTATCATATTTTTACCTGGTA
1 ATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATATTTTTACCTGTTA
* * ** *
2410111 TATCATTTTGGATCGATACATTTTTAAAAGTATCGACACTTTATAGGATTTAAAACTGTTTCTCT
66 TATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATAGGAGCTAAAACTGCTTCTCT
*
2410176 TTTAAATTCACGAAGTGTCGATCCTTATATTAAAGTACCGACACTTTAAAT
131 TTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTACCGACACTTTAAAT
* * * * * *
2410227 GTATCTGGTAGCGCTTTACCGGTTTTATCATTTCT-ATACCGGTTTTGTCATAGTTTTACCTGTT
1 ATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTTTTATCATATTTTTACCTGTT
*
2410291 ATATCGTTTTGGATCGACACATTTTTAA
65 ATATCGTTTTGGATCGATACATTTTTAA
2410319 TTTGGATCGA
Statistics
Matches: 242, Mismatches: 29, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
180 67 0.28
181 174 0.72
182 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (181 bp):
ATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATATTTTTACCTGTTA
TATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATAGGAGCTAAAACTGCTTCTCT
TTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTACCGACACTTTAAAT
Found at i:2415454 original size:17 final size:18
Alignment explanation
Indices: 2415429--2415475 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
2415419 TATGGAATTG
*
2415429 GATTTCAATTCC-TGACA
1 GATTTCAATTCCTTCACA
*
2415446 GATTCCAATTCCTTCACA
1 GATTTCAATTCCTTCACA
2415464 GATTTCAATTCC
1 GATTTCAATTCC
2415476 CTCAGAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:2418196 original size:24 final size:23
Alignment explanation
Indices: 2418159--2418203 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2418149 TAATTAGTTA
*
2418159 TAATTAATTTAATATATAAAATT
1 TAATTAAGTTAATATATAAAATT
*
2418182 TAATTATAGTTAATATTTAAAA
1 TAATTA-AGTTAATATATAAAA
2418204 AATATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TAATTAAGTTAATATATAAAATT
Found at i:2423480 original size:186 final size:187
Alignment explanation
Indices: 2423251--2423623 Score: 739
Period size: 187 Copynumber: 2.0 Consensus size: 187
2423241 TCTTTGATCT
2423251 CAAAATGATTCCTTAACAGACTTATAGTATCTTATACAAACCCTTTTAGGGTT-AAAAACCAATT
1 CAAAATGATTCCTTAACAGACTTATAGTATCTTATACAAACCCTTTTAGGGTTAAAAAACCAATT
2423315 ATCCAAATTTTCTAAGCAAAACTAGCATTTCTTATGCACATCTGTAATTATATCAGATCAATATG
66 ATCCAAATTTTCTAAGCAAAACTAGCATTTCTTATGCACATCTGTAATTATATCAGATCAATATG
2423380 TCTTTTCATAGTTATTAACCAACTTCCAGGGATAATTCTTGTCATCAACAAACATAA
131 TCTTTTCATAGTTATTAACCAACTTCCAGGGATAATTCTTGTCATCAACAAACATAA
2423437 CAAAATGATTCCTTAACAGACTTATAGTATCTTATACAAACCCTTTTAGGGTTAAAAAACCAATT
1 CAAAATGATTCCTTAACAGACTTATAGTATCTTATACAAACCCTTTTAGGGTTAAAAAACCAATT
2423502 ATCCAAATTTTCTAAGCAAAACTAGCATTTCTTATGCACATCTGTAATTATATCAGATCAATATG
66 ATCCAAATTTTCTAAGCAAAACTAGCATTTCTTATGCACATCTGTAATTATATCAGATCAATATG
2423567 TCTTTTCATAGTTATTAACCAACTTCCAGGGATAATTCTTGTCATCAACAAACATAA
131 TCTTTTCATAGTTATTAACCAACTTCCAGGGATAATTCTTGTCATCAACAAACATAA
2423624 GGGTATTTTT
Statistics
Matches: 186, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
186 53 0.28
187 133 0.72
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (187 bp):
CAAAATGATTCCTTAACAGACTTATAGTATCTTATACAAACCCTTTTAGGGTTAAAAAACCAATT
ATCCAAATTTTCTAAGCAAAACTAGCATTTCTTATGCACATCTGTAATTATATCAGATCAATATG
TCTTTTCATAGTTATTAACCAACTTCCAGGGATAATTCTTGTCATCAACAAACATAA
Found at i:2430449 original size:12 final size:14
Alignment explanation
Indices: 2430432--2430464 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2430422 TAAAATTCAT
2430432 AAATAATT-A-TTA
1 AAATAATTAATTTA
2430444 AAATAATTAATTTA
1 AAATAATTAATTTA
2430458 AAATAAT
1 AAATAAT
2430465 CTTTTAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 1 0.05
14 10 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATAATTAATTTA
Found at i:2435552 original size:21 final size:21
Alignment explanation
Indices: 2435528--2435567 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2435518 TGATCAAATG
2435528 ATAT-TATTTTAGTAATTTTAT
1 ATATATATTTT-GTAATTTTAT
*
2435549 ATATATATTTTGTGATTTT
1 ATATATATTTTGTAATTTT
2435568 TAGGTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (21 bp):
ATATATATTTTGTAATTTTAT
Found at i:2435987 original size:18 final size:17
Alignment explanation
Indices: 2435964--2435999 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2435954 AACAAAAAGT
*
2435964 AATTTTAATGGCTTCAAA
1 AATTTTAAGGGCTT-AAA
2435982 AATTTTAAGGGCTTAAA
1 AATTTTAAGGGCTTAAA
2435999 A
1 A
2436000 TACAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (17 bp):
AATTTTAAGGGCTTAAA
Found at i:2437058 original size:15 final size:15
Alignment explanation
Indices: 2437028--2437097 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
2437018 TATTTTTTGC
* *
2437028 AAATTTTACATGTTT
1 AAATTTTATATTTTT
*
2437043 AAGTTTTATATTTTT
1 AAATTTTATATTTTT
*
2437058 AAATATTTTATATTTTC
1 -AA-ATTTTATATTTTT
*
2437075 CAATTTT-TAATTTTT
1 AAATTTTAT-ATTTTT
2437090 AAAATTTT
1 -AAATTTT
2437098 CACATTCATA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
14 1 0.02
15 22 0.51
16 9 0.21
17 11 0.26
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (15 bp):
AAATTTTATATTTTT
Found at i:2437066 original size:32 final size:30
Alignment explanation
Indices: 2437028--2437103 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 30
2437018 TATTTTTTGC
2437028 AAATTTTACATGTTT-AAGTTTTATATTTTTA
1 AAATTTTACAT-TTTCAAGTTTTA-ATTTTTA
* *
2437059 AATATTTTATATTTTCCAATTTTTAATTTTTA
1 AA-ATTTTACATTTT-CAAGTTTTAATTTTTA
2437091 AAATTTTCACATT
1 AAATTTT-ACATT
2437104 CATAAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
31 10 0.26
32 21 0.55
33 7 0.18
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.58
Consensus pattern (30 bp):
AAATTTTACATTTTCAAGTTTTAATTTTTA
Found at i:2437068 original size:17 final size:17
Alignment explanation
Indices: 2437046--2437097 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
2437036 CATGTTTAAG
2437046 TTTTATATTTTTAAATA
1 TTTTATATTTTTAAATA
**
2437063 TTTTATATTTTCCAAT-
1 TTTTATATTTTTAAATA
2437079 TTTTA-ATTTTTAAA-A
1 TTTTATATTTTTAAATA
2437094 TTTT
1 TTTT
2437098 CACATTCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 11 0.37
16 5 0.17
17 14 0.47
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTATATTTTTAAATA
Found at i:2438116 original size:58 final size:61
Alignment explanation
Indices: 2438040--2438179 Score: 196
Period size: 59 Copynumber: 2.3 Consensus size: 61
2438030 AAATTTTTTT
* ** *
2438040 ACTATTAAAAGTTACAAAATGATC-ATTTGACAATAGGGAGTTATTTTGTTGAGT-CCC-A
1 ACTATTAAAAGTTACAAAATGATCTATTTAACAATAACGAGTTATTTTGTCGAGTCCCCTA
* * *
2438098 ACTATTAAAAGTTACAAAATAATCTTTTTAACAATAACGAGTTGTTTTGTCGAGTCCCCTA
1 ACTATTAAAAGTTACAAAATGATCTATTTAACAATAACGAGTTATTTTGTCGAGTCCCCTA
2438159 ACTATTAAAAGTTACAAAATG
1 ACTATTAAAAGTTACAAAATG
2438180 TCACCCGACT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
58 23 0.32
59 24 0.34
60 3 0.04
61 21 0.30
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (61 bp):
ACTATTAAAAGTTACAAAATGATCTATTTAACAATAACGAGTTATTTTGTCGAGTCCCCTA
Found at i:2438581 original size:3 final size:3
Alignment explanation
Indices: 2438555--2438614 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
2438545 TTTTGCCCAT
* *
2438555 TTA TTT TTA TTTA TGA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2438600 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
2438615 AATTTATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2440898 original size:64 final size:63
Alignment explanation
Indices: 2440781--2440905 Score: 162
Period size: 64 Copynumber: 2.0 Consensus size: 63
2440771 CGATGCACAG
* * *
2440781 GGAGTGCATCGATGCACCCATATTAATGGAAACATCGAATATAATTGGTGCATCAATGCATAA
1 GGAGTGCATCGATGCACCCATATAAATGAAAACATCGAAGATAATTGGTGCATCAATGCATAA
* * * *
2440844 GGAGTGCATCGATGCATCCCCT-TAAAATGAAAACATCGAAGGTGATTGGTGCATCGATGCAT
1 GGAGTGCATCGATGCA-CCCATAT-AAATGAAAACATCGAAGATAATTGGTGCATCAATGCAT
2440906 TGTTGAATGA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
63 17 0.32
64 36 0.68
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (63 bp):
GGAGTGCATCGATGCACCCATATAAATGAAAACATCGAAGATAATTGGTGCATCAATGCATAA
Found at i:2441984 original size:151 final size:149
Alignment explanation
Indices: 2441769--2442069 Score: 550
Period size: 151 Copynumber: 2.0 Consensus size: 149
2441759 TATATGTGTG
2441769 TTAATGATTATTGTATATGTTATAAGATATATGATATGAACATAATGAAATGTGAATGATATAAT
1 TTAATGATTATTGTATATGTTATAAGATATATGA-ATGAACATAATGAAATGTGAATGATATAAT
*
2441834 ATGATAATGATAGAGTATAAGATAATTATATGCATGTGTGGATTTGTTATATGAATGGATATATT
65 ATGATAATGATAGAGTATAAGATAATTATATGCATGTGTGGATTTGTTATATGAATGGATAT-GT
2441899 TGGGTATGAGGTGATAGCAGT
129 TGGGTATGAGGTGATAGCAGT
2441920 TTAATGATTATTGTATATGTTATAAGATATATG-ATGAACATAATAGAAATGTGAATGATAATAA
1 TTAATGATTATTGTATATGTTATAAGATATATGAATGAACATAAT-GAAATGTGAATGAT-ATAA
2441984 TATGATAATGATAGAGTATAAGATAATTATATGCATGTGTGGATTTGTTATATGAATGGATATGT
64 TATGATAATGATAGAGTATAAGATAATTATATGCATGTGTGGATTTGTTATATGAATGGATATGT
2442049 TGGGTATGAGGTGATAGCAGT
129 TGGGTATGAGGTGATAGCAGT
2442070 AATTGTTCAT
Statistics
Matches: 147, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
149 11 0.07
150 36 0.24
151 100 0.68
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (149 bp):
TTAATGATTATTGTATATGTTATAAGATATATGAATGAACATAATGAAATGTGAATGATATAATA
TGATAATGATAGAGTATAAGATAATTATATGCATGTGTGGATTTGTTATATGAATGGATATGTTG
GGTATGAGGTGATAGCAGT
Found at i:2445388 original size:181 final size:183
Alignment explanation
Indices: 2445083--2445450 Score: 695
Period size: 181 Copynumber: 2.0 Consensus size: 183
2445073 AAGCTATGTG
2445083 ATTACATGTATATGTGAAAGAAGCTATGAGCTTATATCACATGTGAAATGATAAAGTGAAAATGC
1 ATTACATGTATATGTGAAAGAAGCTATGAGCTTATATCACATGTGAAATGATAAAGTGAAAATGC
2445148 CCATGTTATATGATACGAGAGCTATAGGTATAGTCAGCATGCCAAGAGTCGATGGTCTACGCGGT
66 CCATGTTATATGATACGAGAGCTATAGGTATAGTCAGCATGCCAAGAGTCGATGGTCTACGCGGT
2445213 CCTTCGGGATATACAGTGATCCTTCGGGATATTT-TAGGTCCTTCAAGACAAA
131 CCTTCGGGATATACAGTGATCCTTCGGGATATTTATAGGTCCTTCAAGACAAA
2445265 ATTACATGTATATGTGAAAGAAGCTATGAGCTTATATCACATGTGAAATGAT-AAGTGAAAATGC
1 ATTACATGTATATGTGAAAGAAGCTATGAGCTTATATCACATGTGAAATGATAAAGTGAAAATGC
* *
2445329 TCATGTTATATGATACGAGAGCTATAGGTATAGTCGGCATGCCAAGAGTCGATGGTCTACGCGGT
66 CCATGTTATATGATACGAGAGCTATAGGTATAGTCAGCATGCCAAGAGTCGATGGTCTACGCGGT
2445394 CCTTCGGGATATACAGTGATCCTTCGGGATATTTCATAGGTCCTTCAAGACAAA
131 CCTTCGGGATATACAGTGATCCTTCGGGATATTT-ATAGGTCCTTCAAGACAAA
2445448 ATT
1 ATT
2445451 TCATAGCCCC
Statistics
Matches: 182, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
181 109 0.60
182 52 0.29
183 21 0.12
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (183 bp):
ATTACATGTATATGTGAAAGAAGCTATGAGCTTATATCACATGTGAAATGATAAAGTGAAAATGC
CCATGTTATATGATACGAGAGCTATAGGTATAGTCAGCATGCCAAGAGTCGATGGTCTACGCGGT
CCTTCGGGATATACAGTGATCCTTCGGGATATTTATAGGTCCTTCAAGACAAA
Found at i:2450680 original size:25 final size:25
Alignment explanation
Indices: 2450651--2450703 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
2450641 AGATAAATTC
2450651 GGAGAAAATTGAGTGAAATAGAAAA
1 GGAGAAAATTGAGTGAAATAGAAAA
2450676 GGAGAAAATTGAGTGAAATAGAAAA
1 GGAGAAAATTGAGTGAAATAGAAAA
2450701 GGA
1 GGA
2450704 TAAATGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.30, T:0.15
Consensus pattern (25 bp):
GGAGAAAATTGAGTGAAATAGAAAA
Found at i:2452050 original size:20 final size:20
Alignment explanation
Indices: 2452006--2452055 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2451996 TTTAATAAAT
*
2452006 AAAATTATTATTATATTATG
1 AAAATTATTATTAAATTATG
2452026 AAAATTATTATTAAACTTAT-
1 AAAATTATTATTAAA-TTATG
*
2452046 TAAATTATTA
1 AAAATTATTA
2452056 CAAACTTGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAATTATTATTAAATTATG
Found at i:2455528 original size:2 final size:2
Alignment explanation
Indices: 2455516--2455558 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2455506 AAAATGCATC
*
2455516 TA TA AA 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
2455558 T
1 T
2455559 GTTTCTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2460387 original size:25 final size:25
Alignment explanation
Indices: 2460353--2460406 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
2460343 CATGCTCATG
2460353 GTCAGCATCAATACTTGATATCCGA
1 GTCAGCATCAATACTTGATATCCGA
2460378 GTCAGCATCAATACTTGATATCCGA
1 GTCAGCATCAATACTTGATATCCGA
2460403 GTCA
1 GTCA
2460407 AATTTCTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (25 bp):
GTCAGCATCAATACTTGATATCCGA
Found at i:2461781 original size:20 final size:20
Alignment explanation
Indices: 2461753--2461790 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2461743 TGGCACTTGC
*
2461753 AACAAAATTAGGTAATAATT
1 AACAAAATTAGATAATAATT
*
2461773 AACATAATTAGATAATAA
1 AACAAAATTAGATAATAA
2461791 CACCTGAGGG
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:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (20 bp):
AACAAAATTAGATAATAATT
Found at i:2469360 original size:3 final size:3
Alignment explanation
Indices: 2469352--2469377 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2469342 TTTCGTCCCG
2469352 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2469378 TAAGATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2469949 original size:2 final size:2
Alignment explanation
Indices: 2469942--2469969 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2469932 TTTGCATACA
2469942 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
2469970 GCGAGTCTAA
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:2470882 original size:2 final size:2
Alignment explanation
Indices: 2470875--2470961 Score: 126
Period size: 2 Copynumber: 44.5 Consensus size: 2
2470865 TTTTGTTAGG
* *
2470875 AT AT AT AT AT AT AT AT AT AT AT TT A- AGT GT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
2470916 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2470958 -T AT A
1 AT AT A
2470962 GTATGTAGAA
Statistics
Matches: 77, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
1 3 0.04
2 74 0.96
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2474129 original size:18 final size:18
Alignment explanation
Indices: 2474108--2474143 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2474098 CAAATTTTTC
2474108 GCCTATAGTGGATTTCCT
1 GCCTATAGTGGATTTCCT
2474126 GCCTATAGTGGATTTCCT
1 GCCTATAGTGGATTTCCT
2474144 CAACAAATGC
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:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (18 bp):
GCCTATAGTGGATTTCCT
Found at i:2476014 original size:21 final size:21
Alignment explanation
Indices: 2475981--2476022 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2475971 ATCGTGGAAA
* *
2475981 AGCTTCAAATATTGGTGTTAC
1 AGCTCCAAATATTGGTATTAC
*
2476002 AGCTCCAACTATTGGTATTAC
1 AGCTCCAAATATTGGTATTAC
2476023 CTCTGAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (21 bp):
AGCTCCAAATATTGGTATTAC
Found at i:2486035 original size:41 final size:41
Alignment explanation
Indices: 2485980--2486091 Score: 134
Period size: 42 Copynumber: 2.7 Consensus size: 41
2485970 ATCCTACCCG
* * * *
2485980 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTA
1 AAGG-CTTACGGATGGCCCGAAGGACTTAGCATCATGCTCGA
* *
2486022 AAGGCTTACGGATGACCCGAAGGATTTAAGCATCATGCTCGA
1 AAGGCTTACGGATGGCCCGAAGGACTT-AGCATCATGCTCGA
* *
2486064 AAGACTTACTGATGGCCCGAAGGACTTA
1 AAGGCTTACGGATGGCCCGAAGGACTTA
2486092 CAAATCGTGA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 21 0.36
42 38 0.64
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (41 bp):
AAGGCTTACGGATGGCCCGAAGGACTTAGCATCATGCTCGA
Found at i:2486240 original size:21 final size:21
Alignment explanation
Indices: 2486216--2486283 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
2486206 TGGCTCGAAG
2486216 GACTTATCATCTTGCTCTAAA
1 GACTTATCATCTTGCTCTAAA
** **
2486237 GACTTA-CA-GATGAC-CCGAA
1 GACTTATCATCTTG-CTCTAAA
2486256 GAACTTATCATCTTGCTCTAAA
1 G-ACTTATCATCTTGCTCTAAA
2486278 GACTTA
1 GACTTA
2486284 CAGATAACCC
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 6 0.18
20 8 0.24
21 14 0.41
22 6 0.18
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (21 bp):
GACTTATCATCTTGCTCTAAA
Found at i:2486268 original size:41 final size:41
Alignment explanation
Indices: 2486211--2486343 Score: 182
Period size: 41 Copynumber: 3.3 Consensus size: 41
2486201 ATGGATGGCT
*
2486211 CGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACC
1 CGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATAACC
*
2486252 CGAAGAACTTATCATCTTGCTCTAAAGACTTACAGATAACC
1 CGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATAACC
* * * *
2486293 CGAAGGATTTAAGCATCATGCTCGAAAGACTTAC---TAACC
1 CGAAGGACTT-ATCATCTTGCTCTAAAGACTTACAGATAACC
2486332 CGAAGGACTTAT
1 CGAAGGACTTAT
2486344 AAATTGTGAA
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
38 1 0.01
39 14 0.17
41 47 0.57
42 20 0.24
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.26
Consensus pattern (41 bp):
CGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATAACC
Found at i:2486458 original size:251 final size:253
Alignment explanation
Indices: 2485991--2486551 Score: 826
Period size: 251 Copynumber: 2.2 Consensus size: 253
2485981 AGGTCTTATG
* * * *
2485991 GATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGCTTACGGATGACCCGAAGGATTTAAGCATC
1 GATGACCCGAAGGACTTATCATCATGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
* *
2486056 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTAAAAAGCGCATTC
66 ATGCTCGAAAGACTTACTGA-GACCCGAAGGACTTACAAATCGTGAAATTTTAAAAAGCACATTC
* *
2486121 TTTGTTTTCAAAATTTTCATCTTCTTAAACATCATTTTTCATTTTCAAATTAATGTGAAAACATC
130 TTCGTTTTCAAAAATTTCATCTTCTTAAACATCATTTTTCATTTTCAAATTAATGTGAAAACATC
** *
2486186 CTACCTGAAGGTTTAATGGATGG-CTCGAAGGACTTATCATCTTGCTCTAAAGACTTACA
195 CTACCCAAAGGTTTAATGGATGGTCT-GAAAGACTTATCATCTTGCTCTAAAGACTTACA
* * *
2486245 GATGACCCGAAGAACTTATCATCTTGCTCTAAAGACTTACAGATAACCCGAAGGATTTAAGCATC
1 GATGACCCGAAGGACTTATCATCATGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
* * * *
2486310 ATGCTCGAAAGACTTACT-A-ACCCGAAGGACTTATAAATTGTGAAATTTT-GAAATCACATTCT
66 ATGCTCGAAAGACTTACTGAGACCCGAAGGACTTACAAATCGTGAAATTTTAAAAAGCACATTCT
*
2486372 TCGTTTTTAAAAATTTCATCTTCTTAAAACATCATTTTTCATTTTCAAATTAATGTGAAAACATC
131 TCGTTTTCAAAAATTTCATCTTCTT-AAACATCATTTTTCATTTTCAAATTAATGTGAAAACATC
*
2486437 CTACCCAAAGGTCTT-ATGGATGGTCTGAAAGACTTATCATCTTGGTCTAAAGACTTACA
195 CTACCCAAAGGT-TTAATGGATGGTCTGAAAGACTTATCATCTTGCTCTAAAGACTTACA
* * * *
2486496 GATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGA
1 GATGACCCGAAGGACTT-ATCATCATGCTCTAAAGACTTACAGATGACCCGAAGGA
2486552 CTTACAAATC
Statistics
Matches: 277, Mismatches: 26, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
250 32 0.12
251 130 0.47
252 37 0.13
253 1 0.00
254 77 0.28
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (253 bp):
GATGACCCGAAGGACTTATCATCATGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
ATGCTCGAAAGACTTACTGAGACCCGAAGGACTTACAAATCGTGAAATTTTAAAAAGCACATTCT
TCGTTTTCAAAAATTTCATCTTCTTAAACATCATTTTTCATTTTCAAATTAATGTGAAAACATCC
TACCCAAAGGTTTAATGGATGGTCTGAAAGACTTATCATCTTGCTCTAAAGACTTACA
Found at i:2486563 original size:42 final size:42
Alignment explanation
Indices: 2486485--2486564 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
2486475 ATCTTGGTCT
* *
2486485 AAAGACTTACAGATGACCCGAAGGATTTAATCATCATGCTCG
1 AAAGACTTACAGATGACCCGAAGGACTTAATAATCATGCTCG
* *
2486527 AAAGACTTACTGATGGCCCGAAGGACTTACA-AATCATG
1 AAAGACTTACAGATGACCCGAAGGACTTA-ATAATCATG
2486565 AAATTTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.97
43 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (42 bp):
AAAGACTTACAGATGACCCGAAGGACTTAATAATCATGCTCG
Found at i:2486646 original size:464 final size:459
Alignment explanation
Indices: 2485785--2486764 Score: 1358
Period size: 464 Copynumber: 2.1 Consensus size: 459
2485775 AGGTCTTATG
* * * * *
2485785 GATGGCCCGAAGGACTTATCATCCA-ACTCTAAAGGCTTACGGATGACCCGAAGGATTTAAGCAC
1 GATGACCCGAAGAACTTATCAT-CATGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCAC
* * * *
2485849 CATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTACAAATCGTGAAATTTTGAACTCGCATTC
65 CATGCTCGAAAGACTTACTGA-GACCCGAAGGACTTACAAATCGTGAAATTTTGAAATCACATTC
* **
2485914 TTTGTTCAAAATTTCATCTTAAAACATCATTTTTCATTTTCAATTCTTGTGAAAACATCCTACCC
129 TTTGTTAAAAATTTCATCTTAAAACATCATTTTTCATTTTCAATTAATGTGAAAACATCCTACCC
* * * *
2485979 GAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGCTTACGGATGACCCGAAG
194 AAAGGTCTTATGGATGGCCCGAAAGACTTATCATCCTGCTCTAAAGACTTACAGATGACCCGAAG
*
2486044 GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTA
259 GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCATGAAATTTTA
* * * * *
2486109 AAAAGCGCATTCTTTGTTTTCAAAATTTTCATCTTCTTAAACATCATTTTTCATTTTCAAATTAA
324 AAAAGCACATTCTTTGTTTTCAAAAATTCCAGCTTCTTAAACATCATTTTTAATTTTCAAATTAA
* * * *
2486174 TGTGAAAACATCCTACCTGAAGGT-TTAATGGATGGCTCGAAGGACTTATCATCTTGCTCTAAAG
389 TGTGAAAACATCCTACCCGAAGGTCTT-ATGGATGGCCCGAAGGACTTATCATCCTACTCTAAAG
2486238 ACTTACA
453 ACTTACA
* * *
2486245 GATGACCCGAAGAACTTATCATCTTGCTCTAAAGACTTACAGATAACCCGAAGGATTTAAGCATC
1 GATGACCCGAAGAACTTATCATCATGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCACC
* *
2486310 ATGCTCGAAAGACTTACT-A-ACCCGAAGGACTTATAAATTGTGAAATTTTGAAATCACATTCTT
66 ATGCTCGAAAGACTTACTGAGACCCGAAGGACTTACAAATCGTGAAATTTTGAAATCACATTC-T
*
2486373 CGTTTTTAAAAATTTCATCTTCTTAAAACATCATTTTTCATTTTCAAATTAATGTGAAAACATCC
130 --TTGTTAAAAATTTCA---TCTTAAAACATCATTTTTCATTTTC-AATTAATGTGAAAACATCC
* * * *
2486438 TACCCAAAGGTCTTATGGATGGTCTGAAAGACTTATCATCTTGGTCTAAAGACTTACAGATGACC
189 TACCCAAAGGTCTTATGGATGGCCCGAAAGACTTATCATCCTGCTCTAAAGACTTACAGATGACC
*
2486503 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCATGAAA
254 CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCATGAAA
* * *
2486568 TTTTGAAAATCACATTCTTTGTTTTCAAAAATTCCAGCTTCTTAAAACCTCATTTTTAATTTT-A
319 TTTTAAAAAGCACATTCTTTGTTTTCAAAAATTCCAGCTTCTT-AAACATCATTTTTAATTTTCA
* *
2486632 AATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTC
383 AATTAATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTC
* * *
2486697 TAAAGGCTTCCG
448 TAAAGACTTACA
* * * * * *
2486709 GATGACCCAAAGAATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGA
1 GATGACCCGAAGAACTT-ATCATCATGCTCTAAAGACTTACAGATGACCCGAAGGA
2486765 CTTACAAATC
Statistics
Matches: 456, Mismatches: 53, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
457 36 0.08
458 1 0.00
459 2 0.00
460 86 0.19
463 25 0.05
464 255 0.56
465 51 0.11
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (459 bp):
GATGACCCGAAGAACTTATCATCATGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCACC
ATGCTCGAAAGACTTACTGAGACCCGAAGGACTTACAAATCGTGAAATTTTGAAATCACATTCTT
TGTTAAAAATTTCATCTTAAAACATCATTTTTCATTTTCAATTAATGTGAAAACATCCTACCCAA
AGGTCTTATGGATGGCCCGAAAGACTTATCATCCTGCTCTAAAGACTTACAGATGACCCGAAGGA
TTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCATGAAATTTTAAA
AAGCACATTCTTTGTTTTCAAAAATTCCAGCTTCTTAAACATCATTTTTAATTTTCAAATTAATG
TGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTCTAAAGACT
TACA
Found at i:2486688 original size:213 final size:213
Alignment explanation
Indices: 2486245--2486886 Score: 968
Period size: 213 Copynumber: 3.0 Consensus size: 213
2486235 AAGACTTACA
* * *
2486245 GATGACCCGAAGAACTTATCATCTTGCTCTAAAGACTTACAGATAACCCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
* * *
2486310 ATGCTCGAAAGACTTACT-A--ACCCGAAGGACTTATAAATTGTGAAATTTTG-AAATCACATTC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCACATTC
* * * * * *
2486371 TTCGTTTTTAAAAATTTCATCTTCTTAAAACATCATTTTTCATTTTCAAATTAATGTGAAAACAT
131 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTAATTTT-AAATTCATTTGAAAACAT
*
2486436 CCTACCCAAAGGTCTTATG
195 CCTACCCGAAGGTCTTATG
* * * * *
2486455 GATGGTCTGAAAGACTTATCATCTTGGTCTAAAGACTTACAGATGACCCGAAGGATTTAATCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
*
2486520 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCATGAAATTTTGAAAATCACATTC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCACATTC
* *
2486585 TTTGTTTTCAAAAATTCCAGCTTCTTAAAACCTCATTTTTAATTTTAAATTCATTTGAAAACATC
131 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTAATTTTAAATTCATTTGAAAACATC
2486650 CTACCCGAAGGTCTTATG
196 CTACCCGAAGGTCTTATG
* * * * * * *
2486668 GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTCCGGATGACCCAAAGAATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
*
2486733 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCACATTC
*
2486798 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTTAAATTCATTTGAAAACAT
131 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT-AATTTTAAATTCATTTGAAAACAT
2486863 CCTACCCGAAGGTCTTATG
195 CCTACCCGAAGGTCTTATG
2486882 GATGG
1 GATGG
2486887 TTTGCTTCAC
Statistics
Matches: 389, Mismatches: 38, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
210 75 0.19
211 1 0.00
213 215 0.55
214 98 0.25
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32
Consensus pattern (213 bp):
GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCACATTC
TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTAATTTTAAATTCATTTGAAAACATC
CTACCCGAAGGTCTTATG
Found at i:2489289 original size:2 final size:2
Alignment explanation
Indices: 2489282--2489317 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2489272 TTATTGTAAT
2489282 CA CA CA CA 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 CA CA CA CA
2489318 TATATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2489322 original size:2 final size:2
Alignment explanation
Indices: 2489317--2489412 Score: 155
Period size: 2 Copynumber: 50.0 Consensus size: 2
2489307 ACACACACAC
*
2489317 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2489358 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2489397 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2489413 TTGGGTATAC
Statistics
Matches: 88, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
1 4 0.05
2 84 0.95
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2493674 original size:20 final size:20
Alignment explanation
Indices: 2493649--2493694 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2493639 TTGAAGGTAG
2493649 TCTTCAATAAACTTGAAACT
1 TCTTCAATAAACTTGAAACT
*
2493669 TCTTCAATCAACTTGAAACT
1 TCTTCAATAAACTTGAAACT
2493689 TCTTCA
1 TCTTCA
2493695 TTCATCGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (20 bp):
TCTTCAATAAACTTGAAACT
Found at i:2497395 original size:30 final size:32
Alignment explanation
Indices: 2497361--2497425 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
2497351 GGAGCAGGGT
*
2497361 GCATGAGCTGTTGCTC-G-TGGGAACGGTGAA
1 GCATGAGCTGCTGCTCGGTTGGGAACGGTGAA
* *
2497391 GCATGAGTTGCTGCTCGGTTGGGAATGGTGAA
1 GCATGAGCTGCTGCTCGGTTGGGAACGGTGAA
2497423 GCA
1 GCA
2497426 CGGGTAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 14 0.47
31 1 0.03
32 15 0.50
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (32 bp):
GCATGAGCTGCTGCTCGGTTGGGAACGGTGAA
Found at i:2498091 original size:16 final size:15
Alignment explanation
Indices: 2498052--2498091 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
2498042 TATTTTGTCT
2498052 GAAAAAAATGAAAAA
1 GAAAAAAATGAAAAA
*
2498067 GATTAAAAATGAAAAA
1 GA-AAAAAATGAAAAA
2498083 GAAAGAAAA
1 GAAA-AAAA
2498092 AAGGAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (15 bp):
GAAAAAAATGAAAAA
Found at i:2498098 original size:12 final size:11
Alignment explanation
Indices: 2498078--2498119 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
2498068 ATTAAAAATG
2498078 AAAAAGAAAGA
1 AAAAAGAAAGA
2498089 AAAAAGGAAAGA
1 AAAAA-GAAAGA
* *
2498101 AAAATG-AGGA
1 AAAAAGAAAGA
2498111 AAAAAGAAA
1 AAAAAGAAA
2498120 AATAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 8 0.32
11 7 0.28
12 10 0.40
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:2499673 original size:110 final size:111
Alignment explanation
Indices: 2499363--2499742 Score: 602
Period size: 111 Copynumber: 3.4 Consensus size: 111
2499353 GTGACAGCGG
* * *
2499363 AATGGATCAACTCCTCTAGATCTAATATTCCCTTAGAAGAAGTGGAACATATCACCATATTCCAA
1 AATGGATCAACTCCTCCATATCTGATATTCCCTTAGAAGAAGTGGAACATATCACCATATTCCAA
*
2499428 GATTTGATATTCCCTGAGTAACAGCGGAACAAGTCTACCCCGATTC
66 GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTC
* * * *
2499474 AATGGATTAATTCCTCCATATCTGATATTCCCTTTGAAGAAGTGGAACATATCACTATATTCCAA
1 AATGGATCAACTCCTCCATATCTGATATTCCCTTAGAAGAAGTGGAACATATCACCATATTCCAA
2499539 GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTC
66 GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTC
* *
2499585 AATGGATCAACTCCTCCAAATCTGATATT-CCTTAGAAGAAGTGGAACATATCACCCTATTCCAA
1 AATGGATCAACTCCTCCATATCTGATATTCCCTTAGAAGAAGTGGAACATATCACCATATTCCAA
* *
2499649 GATTTGATATTCTCTGAGTGACAGCGGAACAAGTCTACCCCAATTC
66 GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTC
* *
2499695 AATGTATCAACTCC-CTCATATCTGATATTCCCTTTAGAAGAAGCGGAA
1 AATGGATCAACTCCTC-CATATCTGATATTCCC-TTAGAAGAAGTGGAA
2499743 TAGATCCCTC
Statistics
Matches: 247, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
109 1 0.00
110 101 0.41
111 131 0.53
112 14 0.06
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (111 bp):
AATGGATCAACTCCTCCATATCTGATATTCCCTTAGAAGAAGTGGAACATATCACCATATTCCAA
GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTC
Found at i:2499924 original size:3 final size:3
Alignment explanation
Indices: 2499916--2499967 Score: 86
Period size: 3 Copynumber: 16.7 Consensus size: 3
2499906 TTTCGTCCCG
2499916 TTA TTA TTAA GTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2499963 TTA TT
1 TTA TT
2499968 TAAGATTACT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 43 0.91
4 2 0.04
5 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2501458 original size:2 final size:2
Alignment explanation
Indices: 2501451--2501515 Score: 68
Period size: 2 Copynumber: 34.5 Consensus size: 2
2501441 TTTTGTAAGG
* *
2501451 AT AT AT AT AT AT AT AT AT -T AT AT -T AT TT A- AGT GT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
2501490 AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2501516 GTATGTAGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
1 5 0.09
2 48 0.91
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2501607 original size:2 final size:2
Alignment explanation
Indices: 2501594--2501662 Score: 76
Period size: 2 Copynumber: 37.0 Consensus size: 2
2501584 GCGTAACACT
* * *
2501594 TA TA TG TA TA TA TA T- TA TT TA T- TA -A T- TA CA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2501631 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
2501663 ATTATGCATA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
1 5 0.09
2 51 0.91
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2501793 original size:2 final size:2
Alignment explanation
Indices: 2501788--2501817 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2501778 TTTTTTTTAT
2501788 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
2501818 ATTATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2512196 original size:21 final size:21
Alignment explanation
Indices: 2512172--2512232 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
2512162 AAGACTATTT
2512172 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
2512193 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
* **
2512214 TCATTCTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
2512233 ATAAAGTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:2514095 original size:21 final size:21
Alignment explanation
Indices: 2514069--2514119 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
2514059 GAGAGCGTAT
2514069 GGTGCATCGATGCATAGCCAA
1 GGTGCATCGATGCATAGCCAA
2514090 GGTGCATCGATGCATAGCCAA
1 GGTGCATCGATGCATAGCCAA
2514111 GGTGCATCG
1 GGTGCATCG
2514120 GTACACTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.20
Consensus pattern (21 bp):
GGTGCATCGATGCATAGCCAA
Found at i:2514258 original size:65 final size:63
Alignment explanation
Indices: 2514185--2514339 Score: 161
Period size: 65 Copynumber: 2.4 Consensus size: 63
2514175 TACACTAGGA
* * * *
2514185 TGCATCGGTACACT-AATTACATTCGATGTTTCAA-ACATGCTATGAGTGCATCGATGCATGGTC
1 TGCATCGGTACA-TAAAATACATTCGATGTTTAAATAAAT-CCA-GAGTGCATCGATGCATGG-C
2514248 TG
62 TG
* * *
2514250 TGCATCGGTGCATAAAATGCATTCGATGTTTAAATTAAATCCAGAGTGCGTCGATGCATGGCTG
1 TGCATCGGTACATAAAATACATTCGATGTTTAAA-TAAATCCAGAGTGCATCGATGCATGGCTG
* * *
2514314 TGCATCGATGCATAAAATGCATTCGA
1 TGCATCGGTACATAAAATACATTCGA
2514340 AATGGGGTGT
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 29 0.37
65 45 0.57
66 2 0.03
67 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (63 bp):
TGCATCGGTACATAAAATACATTCGATGTTTAAATAAATCCAGAGTGCATCGATGCATGGCTG
Found at i:2516307 original size:188 final size:188
Alignment explanation
Indices: 2515990--2516367 Score: 747
Period size: 188 Copynumber: 2.0 Consensus size: 188
2515980 GTTTCGTATG
2515990 ATGGAATTTCAAATTTTTAAATAATATTTAGAATGTAAAGTTTAAAATTTTAAAAAATAAATTAA
1 ATGGAATTTCAAATTTTTAAATAATATTTAGAATGTAAAGTTTAAAATTTTAAAAAATAAATTAA
2516055 GTTAAAACAATTGTTTTATGATAATGTTTTAGGTAAACTATATATTTAGTCATCTAATTATCATT
66 GTTAAAACAATTGTTTTATGATAATGTTTTAGGTAAACTATATATTTAGTCATCTAATTATCATT
2516120 ATATTTTCGTTTTAGTCACCTAATTATTTTTTTAAATCATCATTAATGTTAAGTTTTA
131 ATATTTTCGTTTTAGTCACCTAATTATTTTTTTAAATCATCATTAATGTTAAGTTTTA
2516178 ATGGAATTTCAAATTTTTAAATAATATTTAGAATGTAAAGTTTAAAATTTTAAAAAATAAATTAA
1 ATGGAATTTCAAATTTTTAAATAATATTTAGAATGTAAAGTTTAAAATTTTAAAAAATAAATTAA
2516243 GTTAAAACAATTGTTTTATGATAATGTTTTAGGTAAACTATATATTTAGTCATCTAATTATCATT
66 GTTAAAACAATTGTTTTATGATAATGTTTTAGGTAAACTATATATTTAGTCATCTAATTATCATT
*
2516308 ATATTTTCGTTTTAGTCACCTAATTATTTTTTTAAATCATCATTAATGTTACGTTTTA
131 ATATTTTCGTTTTAGTCACCTAATTATTTTTTTAAATCATCATTAATGTTAAGTTTTA
2516366 AT
1 AT
2516368 TTTATTTTAA
Statistics
Matches: 189, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
188 189 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (188 bp):
ATGGAATTTCAAATTTTTAAATAATATTTAGAATGTAAAGTTTAAAATTTTAAAAAATAAATTAA
GTTAAAACAATTGTTTTATGATAATGTTTTAGGTAAACTATATATTTAGTCATCTAATTATCATT
ATATTTTCGTTTTAGTCACCTAATTATTTTTTTAAATCATCATTAATGTTAAGTTTTA
Found at i:2518733 original size:2 final size:2
Alignment explanation
Indices: 2518722--2518751 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2518712 AATATGTTTT
2518722 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2518752 TGTTGAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2519994 original size:14 final size:14
Alignment explanation
Indices: 2519975--2520002 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2519965 TTAATGAAGT
2519975 TATTCATCCAATCC
1 TATTCATCCAATCC
2519989 TATTCATCCAATCC
1 TATTCATCCAATCC
2520003 AATGATCTTG
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:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (14 bp):
TATTCATCCAATCC
Found at i:2523156 original size:58 final size:58
Alignment explanation
Indices: 2523041--2523183 Score: 137
Period size: 58 Copynumber: 2.4 Consensus size: 58
2523031 ATTTTAGAGT
* * * *
2523041 AAAATATAC-AAATGATCTTCTAATTATAAAGTGTTATTTTATTGAATCTTCAACTATTA
1 AAAAT-TACAAAATGATC-TCTAATTACAAAATATTATTTTATTAAATCTTCAACTATTA
* ** * **
2523100 AAAGTTATTAAATGATCTCTAATTACAAAATATTGTTTTATTAAATC-TCTGGCTATTA
1 AAAATTACAAAATGATCTCTAATTACAAAATATTATTTTATTAAATCTTC-AACTATTA
*
2523158 AAAATTACAAAATGATCACTCAATTA
1 AAAATTACAAAATGATCTCT-AATTA
2523184 TTATTTTGTA
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
57 2 0.03
58 49 0.72
59 17 0.25
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (58 bp):
AAAATTACAAAATGATCTCTAATTACAAAATATTATTTTATTAAATCTTCAACTATTA
Found at i:2532959 original size:14 final size:14
Alignment explanation
Indices: 2532940--2532968 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2532930 AATATGGTGT
2532940 AATTATTCATATGG
1 AATTATTCATATGG
2532954 AATTATTCATATGG
1 AATTATTCATATGG
2532968 A
1 A
2532969 TGGTTGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (14 bp):
AATTATTCATATGG
Found at i:2533052 original size:22 final size:22
Alignment explanation
Indices: 2533024--2533070 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2533014 GATGTAATTG
*
2533024 TTCATATGAATAGATATAACTA
1 TTCATATGAAAAGATATAACTA
*
2533046 TTCATATGAAAAGATATAATTA
1 TTCATATGAAAAGATATAACTA
2533068 TTC
1 TTC
2533071 CAATAATCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (22 bp):
TTCATATGAAAAGATATAACTA
Found at i:2533757 original size:108 final size:108
Alignment explanation
Indices: 2533566--2533922 Score: 412
Period size: 108 Copynumber: 3.3 Consensus size: 108
2533556 TAAATGTTAG
* * * * *
2533566 AAAATAAGTAAATTACTTATTTTGTTATTAATATTATCAACATATTATAGAGCGTCTAAAATGTT
1 AAAATAGGTTAATTACTTATTTTGTTATTAATATTATCAACATATTAGAGAGCGCCTAAAATATT
*
2533631 ACCAAAGTTTAAGCTGATGGA-GCCTTAGAAATCTGACGATAAC
66 ACCAAAGTTTAAGCTGAT-GATGCCGTAGAAATCTGACGATAAC
* * *
2533674 AAAATAGGTTAATTACTTATATTGTTATTAATATTATCAACATATTAGATAGTGCCTAAAATATT
1 AAAATAGGTTAATTACTTATTTTGTTATTAATATTATCAACATATTAGAGAGCGCCTAAAATATT
** *
2533739 ATTAAAGTTTAAGTTGATGATGCCGTAGAAATCTGACGATAAC
66 ACCAAAGTTTAAGCTGATGATGCCGTAGAAATCTGACGATAAC
* * * * * *
2533782 AAAATAGGTTAATTACTTATTTTGTTATAAAGATTATCAACATATTAG-GCGCAACCTAATATGT
1 AAAATAGGTTAATTACTTATTTTGTTATTAATATTATCAACATATTAGAGAGC-GCCTAAAATAT
* * ** * ** * *
2533846 TGCCAAAGCTTAAGCTGATGGGGCCTTAGAAATCCCACGACAAT
65 TACCAAAGTTTAAGCTGATGATGCCGTAGAAATCTGACGATAAC
* * *
2533890 AAAATATGTTAAATACTTATTTTGTTATAAATA
1 AAAATAGGTTAATTACTTATTTTGTTATTAATA
2533923 AATATTATCG
Statistics
Matches: 211, Mismatches: 36, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
107 3 0.01
108 208 0.99
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (108 bp):
AAAATAGGTTAATTACTTATTTTGTTATTAATATTATCAACATATTAGAGAGCGCCTAAAATATT
ACCAAAGTTTAAGCTGATGATGCCGTAGAAATCTGACGATAAC
Found at i:2534230 original size:36 final size:36
Alignment explanation
Indices: 2534183--2534270 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
2534173 ATTATTGATT
* *
2534183 CTTAGTATAGATGTATAAAAATTATTCATATCGATA
1 CTTAGTGTAGATGTATAAAAATTATTAATATCGATA
*
2534219 CTTAGTGTAGATGTATGAAAATTATTAATATCGATA
1 CTTAGTGTAGATGTATAAAAATTATTAATATCGATA
*
2534255 CTTAGTGTATATGTAT
1 CTTAGTGTAGATGTAT
2534271 TGATACACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.41
Consensus pattern (36 bp):
CTTAGTGTAGATGTATAAAAATTATTAATATCGATA
Found at i:2534621 original size:76 final size:76
Alignment explanation
Indices: 2534494--2534655 Score: 227
Period size: 76 Copynumber: 2.1 Consensus size: 76
2534484 TTTCAAATGG
* *
2534494 TTATTTTAATGTTTACATTATTATTATACCTTTAAACAAACAGGTAACTAGTTTAACGTAATAGG
1 TTATTTTAACGTTTACATTAATATTATACCTTTAAACAAACAGGTAACTAGTTTAACGTAATAGG
* * * *
2534559 TTGCGCCTCTT
66 TAGCACATATT
* * *
2534570 TTATTTTACCGTTTACATTAATATTATACCTTTAAACATATC-GGTAGCTAGTTTAACGTAATAG
1 TTATTTTAACGTTTACATTAATATTATACCTTTAAACA-AACAGGTAACTAGTTTAACGTAATAG
2534634 GTAGCACATATT
65 GTAGCACATATT
2534646 TTATTTTAAC
1 TTATTTTAAC
2534656 ATATTAAGTT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
76 73 0.97
77 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (76 bp):
TTATTTTAACGTTTACATTAATATTATACCTTTAAACAAACAGGTAACTAGTTTAACGTAATAGG
TAGCACATATT
Found at i:2534694 original size:100 final size:100
Alignment explanation
Indices: 2534571--2535053 Score: 623
Period size: 100 Copynumber: 4.8 Consensus size: 100
2534561 GCGCCTCTTT
* * *
2534571 TATTTTACCGTTTACATTAATATTATACCTTTAAACATATCGGTAGCTAGTTTAACGTAATAGGT
1 TATTTTACCGCTTACATTAATATTATACCTTTAAACAAATCGGTAGCTAGTTTAACGTAATATGT
**
2534636 AGCACATATTTTATTTTAACATATTAAGTTGTAAA
66 AGCACATATTTTATTTTAACCGATTAAGTTGTAAA
* * *
2534671 TATTTTACAGTTTATATTAATATTATACCTTTAAACAAATCGGTTA-CTAGTTTAACGTAATATG
1 TATTTTACCGCTTACATTAATATTATACCTTTAAACAAATCGG-TAGCTAGTTTAACGTAATATG
* * * * *
2534735 TAACGCTTATTTTATTTTAACCTG-TTAAATTGTACA
65 TAGCACATATTTTATTTTAACC-GATTAAGTTGTAAA
* * * **
2534771 TATTTTACCGCTTACATTATTATTATACTTTTAAACAAACCAATAGCTAGTTTAACGTAATA-GA
1 TATTTTACCGCTTACATTAATATTATACCTTTAAACAAATCGGTAGCTAGTTTAACGTAATATG-
* * * * * *
2534835 TAACGCTTATCTTATTTTAACCGGTTAATTTGTAAA
65 TAGCACATATTTTATTTTAACCGATTAAGTTGTAAA
** *
2534871 TATTTTACCG-TTACATTGCTATTATACCTTTAAACAAATCGGTAGCTAGTTTAGCGTAATATGT
1 TATTTTACCGCTTACATTAATATTATACCTTTAAACAAATCGGTAGCTAGTTTAACGTAATATGT
*
2534935 AGCACCTATTTTATTTTAACCGATTAAGTTGTAAA
66 AGCACATATTTTATTTTAACCGATTAAGTTGTAAA
* * * *
2534970 TATTTTACCGCTTACATTATTATTATACCTTTAAATAAACCAGTAGCTAGTTTAACGTAATATGT
1 TATTTTACCGCTTACATTAATATTATACCTTTAAACAAATCGGTAGCTAGTTTAACGTAATATGT
2535035 AGCACATATTTTATTTTAA
66 AGCACATATTTTATTTTAA
2535054 ACTGTTGAAA
Statistics
Matches: 334, Mismatches: 42, Indels: 14
0.86 0.11 0.04
Matches are distributed among these distances:
99 88 0.26
100 244 0.73
101 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (100 bp):
TATTTTACCGCTTACATTAATATTATACCTTTAAACAAATCGGTAGCTAGTTTAACGTAATATGT
AGCACATATTTTATTTTAACCGATTAAGTTGTAAA
Found at i:2534980 original size:199 final size:200
Alignment explanation
Indices: 2534571--2535053 Score: 650
Period size: 199 Copynumber: 2.4 Consensus size: 200
2534561 GCGCCTCTTT
* * * * * *
2534571 TATTTTACCGTTTACATTAATATTATACCTTTAAACATATCGGTAGCTAGTTTAACGTAATAGGT
1 TATTTTACCGCTTACATTATTATTATACCTTTAAACAAACCAGTAGCTAGTTTAACGTAATAGAT
* * * *
2534636 AGCACATATTTTATTTTAACATATTAAGTTGTAAATATTTTACAGTTTATATTAATATTATACCT
66 AACACATATCTTATTTTAACAGATTAAGTTGTAAATATTTTACAGTTTACATTAATATTATACCT
* *
2534701 TTAAACAAATCGGTTACTAGTTTAACGTAATATGTAACGCTTATTTTATTTTAACCTGTTAAATT
131 TTAAACAAATCGGTTACTAGTTTAACGTAATATGTAACACCTATTTTATTTTAACCTGTTAAATT
*
2534766 GTACA
196 GTAAA
* *
2534771 TATTTTACCGCTTACATTATTATTATACTTTTAAACAAACCAATAGCTAGTTTAACGTAATAGAT
1 TATTTTACCGCTTACATTATTATTATACCTTTAAACAAACCAGTAGCTAGTTTAACGTAATAGAT
* * * * * * **
2534836 AACGCTTATCTTATTTTAACCGGTTAATTTGTAAATATTTTACCG-TTACATTGCTATTATACCT
66 AACACATATCTTATTTTAACAGATTAAGTTGTAAATATTTTACAGTTTACATTAATATTATACCT
* * *
2534900 TTAAACAAATCGG-TAGCTAGTTTAGCGTAATATGTAGCACCTATTTTATTTTAACC-GATTAAG
131 TTAAACAAATCGGTTA-CTAGTTTAACGTAATATGTAACACCTATTTTATTTTAACCTG-TTAAA
2534963 TTGTAAA
194 TTGTAAA
*
2534970 TATTTTACCGCTTACATTATTATTATACCTTTAAATAAACCAGTAGCTAGTTTAACGTAATATG-
1 TATTTTACCGCTTACATTATTATTATACCTTTAAACAAACCAGTAGCTAGTTTAACGTAATA-GA
* *
2535034 TAGCACATATTTTATTTTAA
65 TAACACATATCTTATTTTAA
2535054 ACTGTTGAAA
Statistics
Matches: 247, Mismatches: 33, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
198 3 0.01
199 150 0.61
200 94 0.38
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (200 bp):
TATTTTACCGCTTACATTATTATTATACCTTTAAACAAACCAGTAGCTAGTTTAACGTAATAGAT
AACACATATCTTATTTTAACAGATTAAGTTGTAAATATTTTACAGTTTACATTAATATTATACCT
TTAAACAAATCGGTTACTAGTTTAACGTAATATGTAACACCTATTTTATTTTAACCTGTTAAATT
GTAAA
Found at i:2535445 original size:65 final size:64
Alignment explanation
Indices: 2535341--2535500 Score: 173
Period size: 65 Copynumber: 2.5 Consensus size: 64
2535331 AATTAAATTG
* * *
2535341 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATGCACCAATGCAC-CGAGGATGTTATA
1 AACATCGAATGCAATTGATGCATCGATGCACCATA-CATGCACCAATGCACTC-AGGATATT-TA
2535404 AA
63 AA
* * * * **
2535406 AACATCGAATGCAATTGATGCATCGATGCACCAGT-CATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCAATTGATGCATCGATGCACCA-TACATGCACCAATGCACTCAGGATATTTAAA
*
2535470 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCAATTGATGCATCGATGCAC
2535501 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
64 32 0.39
65 46 0.56
66 3 0.04
67 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (64 bp):
AACATCGAATGCAATTGATGCATCGATGCACCATACATGCACCAATGCACTCAGGATATTTAAA
Found at i:2535500 original size:17 final size:19
Alignment explanation
Indices: 2535472--2535520 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2535462 TATTTTGAAA
2535472 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
2535490 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
2535509 CACCGATGCACT
1 CATCGATGCACT
2535521 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:2540435 original size:149 final size:149
Alignment explanation
Indices: 2540165--2540460 Score: 592
Period size: 149 Copynumber: 2.0 Consensus size: 149
2540155 CTTATTGTCG
2540165 GAAAAGTATCGATACTTTTAGAATAAGTATAAATATCGAAACTATGCAAATTTTGTTTCGAAATT
1 GAAAAGTATCGATACTTTTAGAATAAGTATAAATATCGAAACTATGCAAATTTTGTTTCGAAATT
2540230 AATAATATTGATACTTGGAGTATGTGTATCAATACTATGTCAGGAAAATTTTGTAACATAGGAAA
66 AATAATATTGATACTTGGAGTATGTGTATCAATACTATGTCAGGAAAATTTTGTAACATAGGAAA
2540295 CTGTCGTAAACATATCGTC
131 CTGTCGTAAACATATCGTC
2540314 GAAAAGTATCGATACTTTTAGAATAAGTATAAATATCGAAACTATGCAAATTTTGTTTCGAAATT
1 GAAAAGTATCGATACTTTTAGAATAAGTATAAATATCGAAACTATGCAAATTTTGTTTCGAAATT
2540379 AATAATATTGATACTTGGAGTATGTGTATCAATACTATGTCAGGAAAATTTTGTAACATAGGAAA
66 AATAATATTGATACTTGGAGTATGTGTATCAATACTATGTCAGGAAAATTTTGTAACATAGGAAA
2540444 CTGTCGTAAACATATCG
131 CTGTCGTAAACATATCG
2540461 ATACTTTAAT
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (149 bp):
GAAAAGTATCGATACTTTTAGAATAAGTATAAATATCGAAACTATGCAAATTTTGTTTCGAAATT
AATAATATTGATACTTGGAGTATGTGTATCAATACTATGTCAGGAAAATTTTGTAACATAGGAAA
CTGTCGTAAACATATCGTC
Found at i:2551857 original size:20 final size:19
Alignment explanation
Indices: 2551795--2551888 Score: 82
Period size: 20 Copynumber: 4.8 Consensus size: 19
2551785 TTAATCGATA
* *
2551795 TTGTCAAATTCCTACCAGTT
1 TTGTCAAATTGCAACC-GTT
* * *
2551815 TGGTTAAATTTCAACCG-T
1 TTGTCAAATTGCAACCGTT
*
2551833 TTGTCAAATTCGTAACCGTT
1 TTGTCAAATT-GCAACCGTT
2551853 TTGTCAAATTGCAACCGGTT
1 TTGTCAAATTGCAACC-GTT
* *
2551873 TTTTCAAATTTCAACC
1 TTGTCAAATTGCAACC
2551889 TGCTATATTG
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
18 9 0.15
19 11 0.18
20 40 0.67
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (19 bp):
TTGTCAAATTGCAACCGTT
Found at i:2551862 original size:38 final size:38
Alignment explanation
Indices: 2551795--2551869 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
2551785 TTAATCGATA
* *
2551795 TTGTCAAATTCCTACCAGTTTGGTTAAATTTCAACCGT
1 TTGTCAAATTCCTACCAGTTTGGTCAAATTGCAACCGT
* *
2551833 TTGTCAAATTCGTAACC-GTTTTGTCAAATTGCAACCG
1 TTGTCAAATTCCT-ACCAGTTTGGTCAAATTGCAACCG
2551870 GTTTTTTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 29 0.91
39 3 0.09
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (38 bp):
TTGTCAAATTCCTACCAGTTTGGTCAAATTGCAACCGT
Found at i:2565650 original size:34 final size:34
Alignment explanation
Indices: 2565607--2565731 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
2565597 TTCGTCCTAC
2565607 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
2565641 TAGGATTCAAACTCCTAAAGATATGATAGAATTTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA--TTT
2565677 CTAGGATTC--A-----AAAAATAGGATAGAATTT
1 -TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
2565705 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
2565732 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
28 3 0.04
29 1 0.01
30 13 0.18
34 39 0.53
35 1 0.01
36 3 0.04
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:2566110 original size:15 final size:15
Alignment explanation
Indices: 2566088--2566126 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2566078 ATTATATTGA
*
2566088 TATT-TTATTCATTT
1 TATTATTATTCATGT
*
2566102 TTTTATTATTCATGT
1 TATTATTATTCATGT
2566117 TATTATTATT
1 TATTATTATT
2566127 ATATGTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTATTATTCATGT
Found at i:2577211 original size:12 final size:11
Alignment explanation
Indices: 2577192--2577230 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 11
2577182 AAAAAAATCG
2577192 AAAAAAGAAAA
1 AAAAAAGAAAA
2577203 AAAACAAGAGAAA
1 AAAA-AAGA-AAA
2577216 AAAAAAGAACAA
1 AAAAAAGAA-AA
2577228 AAA
1 AAA
2577231 GGTGGGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.20
12 13 0.52
13 7 0.28
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:2578185 original size:98 final size:98
Alignment explanation
Indices: 2577963--2578224 Score: 283
Period size: 98 Copynumber: 2.6 Consensus size: 98
2577953 TCGTGCCACT
* * * **
2577963 CAAGAAAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAAC-AACAATTTCCCAGT
1 CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTT--C-G-
* * * * *
2578027 TTCAGGGCTAATTTCAACTTCACAGCGGAGGATATTGGACC
62 ----GAGCCAATCTCAACTTCACAACGAAGGATATTGGACC
* * *
2578068 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCGGAGC
1 CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTTCGGAGC
*
2578133 CAATCTCAACTTCACAACGAAGGATATTGGACT
66 CAATCTCAACTTCACAACGAAGGATATTGGACC
* * **
2578166 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT
1 CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTT
2578225 TCCGGTTCCA
Statistics
Matches: 135, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
98 83 0.61
103 1 0.01
104 1 0.01
105 42 0.31
106 8 0.06
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (98 bp):
CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTTCGGAGC
CAATCTCAACTTCACAACGAAGGATATTGGACC
Found at i:2578862 original size:34 final size:34
Alignment explanation
Indices: 2578819--2578943 Score: 111
Period size: 34 Copynumber: 3.8 Consensus size: 34
2578809 TTTCGTCTAC
2578819 TAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAAAATTT
* * *
2578853 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATA-AAATTT
*
2578888 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAAAATTT
* * *
2578917 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
2578944 CCACAAGCAC
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
27 6 0.08
29 5 0.07
30 10 0.14
34 36 0.51
35 6 0.08
37 8 0.11
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAAAATTT
Found at i:2579323 original size:14 final size:15
Alignment explanation
Indices: 2579300--2579336 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2579290 ATTATATGGA
2579300 TATT-TTATTCAT-T
1 TATTATTATTCATGT
*
2579313 TTTTATTATTCATGT
1 TATTATTATTCATGT
2579328 TATTATTAT
1 TATTATTAT
2579337 ATGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 3 0.15
14 8 0.40
15 9 0.45
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (15 bp):
TATTATTATTCATGT
Found at i:2579429 original size:28 final size:24
Alignment explanation
Indices: 2579374--2579438 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 24
2579364 TTTTCATTTG
* *
2579374 ATTTTTTTTACTATATTTTATTATT
1 ATTTTATTTA-TATATTTTATTAAT
2579399 ATTATTATTATATATATATTTATTTAAT
1 ATT-TTATT-TATATAT-TTTA-TTAAT
2579427 ATTTTATTTATA
1 ATTTTATTTATA
2579439 AGTCTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
25 3 0.09
26 13 0.38
27 11 0.32
28 7 0.21
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
ATTTTATTTATATATTTTATTAAT
Found at i:2579432 original size:12 final size:12
Alignment explanation
Indices: 2579386--2579436 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
2579376 TTTTTTTACT
2579386 ATATTTTA-TTA
1 ATATTTTATTTA
*
2579397 TTATTATTATTATA
1 ATATT-TTATT-TA
2579411 TATATATTTATTTA
1 -ATAT-TTTATTTA
2579425 ATATTTTATTTA
1 ATATTTTATTTA
2579437 TAAGTCTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
11 4 0.12
12 11 0.33
13 5 0.15
14 4 0.12
15 8 0.24
16 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTTTATTTA
Found at i:2579843 original size:2 final size:2
Alignment explanation
Indices: 2579836--2579879 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2579826 TAATACTTTG
*
2579836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2579878 AT
1 AT
2579880 TTCTTTTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2585117 original size:42 final size:42
Alignment explanation
Indices: 2585062--2585460 Score: 351
Period size: 42 Copynumber: 9.5 Consensus size: 42
2585052 ATACGGAGAG
*
2585062 CTCAGAGAAGAGGTGGCCACACTTAAAGCGGGAAACAAAGCA
1 CTCAGACAAGAGGTGGCCACACTTAAAGCGGGAAACAAAGCA
* * * * * ** *
2585104 TTAAGACACGAGGTGGCCACAATTGAAG-ATGATGAA-GAAGCA
1 CTCAGACAAGAGGTGGCCACACTTAAAGCGGGA--AACAAAGCA
*
2585146 CTCAGACAAGAGGTGGCCACACTTAAAGCGGGAAACAAGGCA
1 CTCAGACAAGAGGTGGCCACACTTAAAGCGGGAAACAAAGCA
* ** * ** *
2585188 CTCAGACAAGAGGTAGCCGA-ACTCGAAGCCGGAAACGGAGCT
1 CTCAGACAAGAGGTGGCC-ACACTTAAAGCGGGAAACAAAGCA
* * *
2585230 CTCAAACAAGAGGTGGCCACATTTGAAGC-GGAAGACATAA-CA
1 CTCAGACAAGAGGTGGCCACACTTAAAGCGGGAA-ACA-AAGCA
* *
2585272 CTCCGACAAGAGGTGGCCACACTAAAAGCGGGAAACAAAGCA
1 CTCAGACAAGAGGTGGCCACACTTAAAGCGGGAAACAAAGCA
* * * * ** *
2585314 CTCAGACAAGAGGTGGCCACAATTAAAGAGGTAGACGGAGAA
1 CTCAGACAAGAGGTGGCCACACTTAAAGCGGGAAACAAAGCA
* *
2585356 CTCAGACGAGAGGTGGTCACACTTAAAGCGGGAAACAAAGCA
1 CTCAGACAAGAGGTGGCCACACTTAAAGCGGGAAACAAAGCA
* ** ** * *
2585398 CTCAGACAAGAGGTGGACGTACTCGAAGCCGGG-AACGAAGCT
1 CTCAGACAAGAGGTGGCCACACTTAAAG-CGGGAAACAAAGCA
*
2585440 CTCAAACAAGAGGTGGCCACA
1 CTCAGACAAGAGGTGGCCACA
2585461 TTCGAAGCGC
Statistics
Matches: 278, Mismatches: 68, Indels: 22
0.76 0.18 0.06
Matches are distributed among these distances:
41 11 0.04
42 253 0.91
43 14 0.05
ACGTcount: A:0.38, C:0.22, G:0.29, T:0.11
Consensus pattern (42 bp):
CTCAGACAAGAGGTGGCCACACTTAAAGCGGGAAACAAAGCA
Found at i:2585239 original size:84 final size:83
Alignment explanation
Indices: 2585008--2585460 Score: 330
Period size: 84 Copynumber: 5.4 Consensus size: 83
2584998 GCTTGAGCAA
* * * * *
2585008 GAAATCAAGGCACTCAAACAAGAAGTGGCCACGA-TTGAAG-AGGAATACGGAG-AGCTCAGAGA
1 GAAA-CAA-GCACTCAGACAAGAGGTGGCCAC-ACTAGAAGCAGGAA-ACGAAGCA-CTCAGACA
2585070 AGAGGTGGCCACACTTAAAGCGG
61 AGAGGTGGCCACACTTAAAGCGG
* * * * * *
2585093 GAAACAAAGCATTAAGACACGAGGTGGCCACAATTGAAG-ATGATGAA-GAAGCACTCAGACAAG
1 GAAAC-AAGCACTCAGACAAGAGGTGGCCACACTAGAAGCAGGA--AACGAAGCACTCAGACAAG
2585156 AGGTGGCCACACTTAAAGCGG
63 AGGTGGCCACACTTAAAGCGG
* * * * * *
2585177 GAAACAAGGCACTCAGACAAGAGGTAGCCGA-ACTCGAAGCCGGAAACGGAGCTCTCAAACAAGA
1 GAAACAA-GCACTCAGACAAGAGGTGGCC-ACACTAGAAGCAGGAAACGAAGCACTCAGACAAGA
* *
2585241 GGTGGCCACATTTGAAGC-G
64 GGTGGCCACACTTAAAGCGG
* * * * *
2585260 GAAGACATAACACTCCGACAAGAGGTGGCCACACTAAAAGCGGGAAACAAAGCACTCAGACAAGA
1 GAA-ACA-AGCACTCAGACAAGAGGTGGCCACACTAGAAGCAGGAAACGAAGCACTCAGACAAGA
* *
2585325 GGTGGCCACAATTAAAGAGG
64 GGTGGCCACACTTAAAGCGG
* * * * * * * *
2585345 TAGACGGAGAACTCAGACGAGAGGTGGTCACACTTA-AAGCGGGAAACAAAGCACTCAGACAAGA
1 GAAAC-AAGCACTCAGACAAGAGGTGGCCACAC-TAGAAGCAGGAAACGAAGCACTCAGACAAGA
* ** **
2585409 GGTGGACGTACTCGAAGCCGG
64 GGTGGCCACACTTAAAG-CGG
* *
2585430 G-AACGAAGCTCTCAAACAAGAGGTGGCCACA
1 GAAAC-AAGCACTCAGACAAGAGGTGGCCACA
2585461 TTCGAAGCGC
Statistics
Matches: 295, Mismatches: 57, Indels: 33
0.77 0.15 0.09
Matches are distributed among these distances:
83 10 0.03
84 266 0.90
85 18 0.06
86 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.29, T:0.11
Consensus pattern (83 bp):
GAAACAAGCACTCAGACAAGAGGTGGCCACACTAGAAGCAGGAAACGAAGCACTCAGACAAGAGG
TGGCCACACTTAAAGCGG
Found at i:2585468 original size:42 final size:40
Alignment explanation
Indices: 2585017--2585462 Score: 265
Period size: 42 Copynumber: 10.7 Consensus size: 40
2585007 AGAAATCAAG
* * * * * *
2585017 GCACTCAAACAAGAAGTGGCCACGATTGAAGAGGAATACGGA
1 GCACTCAGACAAGAGGTGGCCAC-ATTAAAGCGGGA-ACGAA
* *
2585059 G-AGCTCAGAGAAGAGGTGGCCACACTTAAAGCGGGAAACAAA
1 GCA-CTCAGACAAGAGGTGGCCACA-TTAAAGCGGG-AACGAA
* * * * * *
2585101 GCATTAAGACACGAGGTGGCCACAATTGAAGATGATGAA-GAA
1 GCACTCAGACAAGAGGTGGCCAC-ATTAAAG-CG-GGAACGAA
2585143 GCACTCAGACAAGAGGTGGCCACACTTAAAGCGGGAAAC-AA
1 GCACTCAGACAAGAGGTGGCCACA-TTAAAGCGGG-AACGAA
* ** * *
2585184 GGCACTCAGACAAGAGGTAGCCGA-ACTCGAAGCCGGAAACGGA
1 -GCACTCAGACAAGAGGTGGCC-ACA-TTAAAG-CGGGAACGAA
* * * *
2585227 GCTCTCAAACAAGAGGTGGCCACATTTGAAGCGGAAGAC-ATA
1 GCACTCAGACAAGAGGTGGCCACA-TTAAAGCGGGA-ACGA-A
* * * *
2585269 ACACTCCGACAAGAGGTGGCCACACTAAAAGCGGGAAACAAA
1 GCACTCAGACAAGAGGTGGCCACA-TTAAAGCGGG-AACGAA
* * *
2585311 GCACTCAGACAAGAGGTGGCCACAATTAAAGAGGTAGACGGA
1 GCACTCAGACAAGAGGTGGCCAC-ATTAAAGCGGGA-ACGAA
* * * *
2585353 GAACTCAGACGAGAGGTGGTCACACTTAAAGCGGGAAACAAA
1 GCACTCAGACAAGAGGTGGCCACA-TTAAAGCGGG-AACGAA
* **
2585395 GCACTCAGACAAGAGGTGGACGTAC-TCGAAGCCGGGAACGAA
1 GCACTCAGACAAGAGGTGG-C-CACATTAAAG-CGGGAACGAA
* *
2585437 GCTCTCAAACAAGAGGTGGCCACATT
1 GCACTCAGACAAGAGGTGGCCACATT
2585463 CGAAGCGCAG
Statistics
Matches: 311, Mismatches: 66, Indels: 55
0.72 0.15 0.13
Matches are distributed among these distances:
40 3 0.01
41 18 0.06
42 268 0.86
43 19 0.06
44 3 0.01
ACGTcount: A:0.38, C:0.22, G:0.29, T:0.12
Consensus pattern (40 bp):
GCACTCAGACAAGAGGTGGCCACATTAAAGCGGGAACGAA
Found at i:2585867 original size:117 final size:115
Alignment explanation
Indices: 2585661--2586076 Score: 482
Period size: 117 Copynumber: 3.6 Consensus size: 115
2585651 AGGAAGAGTT
* * * *
2585661 GTTAAGGGA-GAGAGTAATGAATTTGGAATCCAAGTTGAG-GGAGGAAGGAGAAGAGAAGTCGAA
1 GTTAAGGGAGGA-AGTGATGAATTTGGAAGCCAAGTTGAGTGAAGGAA-GAGAAGAGAAGTTGAA
* * * *
2585724 AGCCATGAGTGAAGTTAACGAAAAGATGAGATACATGCAAAGGGAAAATGACAA
64 AGCCATGAGTGAAGTTGA-GAAAAGATGAGAGAAATGCAAAAGGAAAATGA-AA
2585778 GTTAAGGGAGGAAGTGATGAATTTGGAAGCCAAGTTGAGT-AAGGAAGCAGAAGAGAAGTTGAAA
1 GTTAAGGGAGGAAGTGATGAATTTGGAAGCCAAGTTGAGTGAAGGAAG-AGAAGAGAAGTTGAAA
* ** * * *
2585842 TCCATGAGTGAAGTTGAGAAAAAGATGAGAGAGTTACGAACGGAAAATGTAAA
65 GCCATGAGTGAAGTTGAG-AAAAGATGAGAGAAATGCAAAAGGAAAATG-AAA
* * *
2585895 GTTAACGGTGGAAGTGATGAATTTGGAAACCAAGTTGAGTGAA-GAATGAGAAGAGAAGTTGAAA
1 GTTAAGGGAGGAAGTGATGAATTTGGAAGCCAAGTTGAGTGAAGGAA-GAGAAGAGAAGTTGAAA
** * *
2585959 GCCATGAGTGAAGTTGAGGGTAAGATGAGAGAAATGCAAAACGAAAATGGTAA
65 GCCATGAGTGAAGTTGA-GAAAAGATGAGAGAAATGCAAAAGGAAAAT-GAAA
* * *
2586012 GTTAAGGAAGGAAGTGATGAATTTGGAAGCAAAGTTGAGTGAAAG-AGAAGAAGAGAAGTTGAAA
1 GTTAAGGGAGGAAGTGATGAATTTGGAAGCCAAGTTGAGTGAAGGAAG-AGAAGAGAAGTTGAAA
2586076 G
65 G
2586077 TGTTGAAAGA
Statistics
Matches: 258, Mismatches: 30, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
116 3 0.01
117 246 0.95
118 9 0.03
ACGTcount: A:0.43, C:0.06, G:0.33, T:0.18
Consensus pattern (115 bp):
GTTAAGGGAGGAAGTGATGAATTTGGAAGCCAAGTTGAGTGAAGGAAGAGAAGAGAAGTTGAAAG
CCATGAGTGAAGTTGAGAAAAGATGAGAGAAATGCAAAAGGAAAATGAAA
Found at i:2592411 original size:31 final size:31
Alignment explanation
Indices: 2592376--2592435 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2592366 AACTTAAAAG
* * **
2592376 AGTTTTGCAATACTGAGGTTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
2592407 AGTTTTACAATACTAAAATTTAAATAATT
1 AGTTTTACAATACTAAAATTTAAATAATT
2592436 CATACAACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:2592950 original size:21 final size:18
Alignment explanation
Indices: 2592908--2592954 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 18
2592898 AAATAATTAA
2592908 AATAA-ATATAAAATTTT
1 AATAATATATAAAATTTT
2592925 AATAATATATAAAATGATTT
1 AATAATATATAAAAT--TTT
2592945 ATATAATATA
1 A-ATAATATA
2592955 AAATTAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.19
18 9 0.35
20 4 0.15
21 8 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AATAATATATAAAATTTT
Found at i:2593016 original size:63 final size:63
Alignment explanation
Indices: 2592948--2593088 Score: 250
Period size: 62 Copynumber: 2.3 Consensus size: 63
2592938 ATGATTTATA
2592948 TAATA-TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAT
1 TAATATTAAAATTAAATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAT
*
2593011 TAATATTACAATT-AATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAT
1 TAATATTAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAT
2593073 TAATATTAAAATTAAA
1 TAATATTAAAATTAAA
2593089 ATTAAAATTA
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
62 41 0.55
63 27 0.36
64 6 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (63 bp):
TAATATTAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAT
Found at i:2593023 original size:12 final size:12
Alignment explanation
Indices: 2592948--2593122 Score: 112
Period size: 12 Copynumber: 14.2 Consensus size: 12
2592938 ATGATTTATA
2592948 TAATA-TAAAAT
1 TAATATTAAAAT
*
2592959 TAAATATCTATAAT
1 T-AATAT-TAAAAT
2592973 ATAATATTAAAAAAT
1 -TAATATT--AAAAT
*
2592988 TAATATT-TAAT
1 TAATATTAAAAT
*
2592999 TTAT-TTAAAAAT
1 TAATATT-AAAAT
*
2593011 TAATATTACAAT
1 TAATATTAAAAT
*
2593023 TAATATCTATAAT
1 TAATAT-TAAAAT
2593036 ATAATATTAAAAAT
1 -TAATATT-AAAAT
*
2593050 TAATATT-TAAT
1 TAATATTAAAAT
*
2593061 TTAT-TTAAAAAT
1 TAATATT-AAAAT
2593073 TAATATTAAAAT
1 TAATATTAAAAT
*
2593085 TAAAATTAAAAT
1 TAATATTAAAAT
* *
2593097 TAA-AATCAAAT
1 TAATATTAAAAT
2593108 ATAATA-TAAAAT
1 -TAATATTAAAAT
2593120 TAA
1 TAA
2593123 ATATAAAACC
Statistics
Matches: 130, Mismatches: 17, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
10 4 0.03
11 22 0.17
12 53 0.41
13 19 0.15
14 27 0.21
15 5 0.04
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATATTAAAAT
Found at i:2593023 original size:24 final size:23
Alignment explanation
Indices: 2592977--2593023 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2592967 TATAATATAA
*
2592977 TATTAAAAAATTAATATTTAATT
1 TATTAAAAAATTAATATTCAATT
*
2593000 TATTTAAAAATTAATATTACAATT
1 TATTAAAAAATTAATATT-CAATT
2593024 AATATCTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTAAAAAATTAATATTCAATT
Found at i:2593086 original size:6 final size:6
Alignment explanation
Indices: 2593068--2593123 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
2593058 AATTTATTTA
* * *
2593068 AAAATT AATATT AAAATT AAAATT AAAATT AAAA-T CAAA-T ATAATAT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT-T
2593115 AAAATT AAA
1 AAAATT AAA
2593124 TATAAAACCT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
5 7 0.17
6 30 0.71
7 5 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:2593125 original size:12 final size:12
Alignment explanation
Indices: 2593068--2593130 Score: 62
Period size: 12 Copynumber: 5.3 Consensus size: 12
2593058 AATTTATTTA
2593068 AAAATT-AATATT
1 AAAATTAAATA-T
2593080 AAAATTAAA-ATT
1 AAAATTAAATA-T
2593092 AAAATTAAA-AT
1 AAAATTAAATAT
*
2593103 CAAA-TATAATAT
1 AAAATTA-AATAT
2593115 AAAATTAAATAT
1 AAAATTAAATAT
2593127 AAAA
1 AAAA
2593131 CCTCTTTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
10 2 0.04
11 6 0.13
12 33 0.73
13 4 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:2595687 original size:19 final size:20
Alignment explanation
Indices: 2595663--2595701 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2595653 TTTGAAGAAT
*
2595663 TAATTT-AGAATGATAGTAA
1 TAATTTAAGAATGAAAGTAA
2595682 TAATTTAAGAATGAAAGTAA
1 TAATTTAAGAATGAAAGTAA
2595702 AATATCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (20 bp):
TAATTTAAGAATGAAAGTAA
Found at i:2606519 original size:17 final size:17
Alignment explanation
Indices: 2606499--2606532 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2606489 ATCAAATAAT
*
2606499 AAATATTAATATGATTA
1 AAATAATAATATGATTA
*
2606516 AAATAATAATATTATTA
1 AAATAATAATATGATTA
2606533 TTAATAACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AAATAATAATATGATTA
Found at i:2606544 original size:24 final size:24
Alignment explanation
Indices: 2606485--2606545 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
2606475 TTTTTATAAA
*
2606485 ATTAATCAAATAATAAATATTAAT
1 ATTAATAAAATAATAAATATTAAT
* * *
2606509 ATGATTAAAATAAT-AATATTATT
1 ATTAATAAAATAATAAATATTAAT
2606532 ATTAATAACAATAA
1 ATTAATAA-AATAA
2606546 AATTGCAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 14 0.47
24 16 0.53
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTAATAAAATAATAAATATTAAT
Found at i:2607875 original size:3 final size:3
Alignment explanation
Indices: 2607861--2607952 Score: 98
Period size: 3 Copynumber: 31.0 Consensus size: 3
2607851 GTTGTATCTG
* * *
2607861 TAA TAA -AA TAA TAA TAA TAA TAG TAA TAA TAA TAA AAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
2607908 TAA TAA TAG TAG TAA TAA AAA TAA AAA TAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
2607953 AAAACCAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
2 3 0.04
3 70 0.95
4 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:2608431 original size:73 final size:73
Alignment explanation
Indices: 2608350--2608510 Score: 250
Period size: 73 Copynumber: 2.2 Consensus size: 73
2608340 TTCAGATGAG
* * * * *
2608350 TTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCAAAAAGTTGA
1 TTCTCATTATGAACTCGCACTGGAAAAGTTGATCCATCGAATGATAAATTCAAGCAAAAAGTTGA
2608415 ACAAGTTC
66 ACAAGTTC
* * *
2608423 TTCTCATTATGAACTCGCACTGGCAATGTTGATCCATCGAATGATAAATTCAAGCGAAAAGTTGA
1 TTCTCATTATGAACTCGCACTGGAAAAGTTGATCCATCGAATGATAAATTCAAGCAAAAAGTTGA
2608488 ACAAGTTC
66 ACAAGTTC
2608496 TTCTCATTATGAACT
1 TTCTCATTATGAACT
2608511 TCTTCTTCCT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 80 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (73 bp):
TTCTCATTATGAACTCGCACTGGAAAAGTTGATCCATCGAATGATAAATTCAAGCAAAAAGTTGA
ACAAGTTC
Found at i:2608530 original size:24 final size:23
Alignment explanation
Indices: 2608495--2608539 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2608485 TGAACAAGTT
2608495 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
2608519 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
2608540 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:2608563 original size:113 final size:113
Alignment explanation
Indices: 2608418--2608888 Score: 849
Period size: 113 Copynumber: 4.2 Consensus size: 113
2608408 AAGTTGAACA
*
2608418 AGTTCTTCTCATTATGAACTCG-CACTGGCAATGTTGATCCATCGAATGATAAATTCAAGCGAAA
1 AGTTCTTCTCATTATGAACTCGAC-CTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAA
*
2608482 AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATG
65 AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
2608531 AGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
*
2608596 GTTGAACAAGTTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
2608644 AGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
2608709 GTTGAACAAGTTCTTCTCATTATGAAC-T-TTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* **
2608755 AGTTCTTCTCATTATGAACTCGACCTGGTAATACTGATCCATCGAATGATGAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
2608820 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
2608868 AGTTCTTCTCATTATGAACTC
1 AGTTCTTCTCATTATGAACTC
2608889 TTCCAGAAAT
Statistics
Matches: 348, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
111 108 0.31
112 2 0.01
113 237 0.68
114 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:2608829 original size:224 final size:226
Alignment explanation
Indices: 2608418--2608888 Score: 849
Period size: 224 Copynumber: 2.1 Consensus size: 226
2608408 AAGTTGAACA
2608418 AGTTCTTCTCATTATGAACTCGCACTGGCAATGTTGATCCATCGAATGATAAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGCACTGGCAATGTTGATCCATCGAATGATAAATTCAAGCGAAAA
*
2608483 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGA
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
**
2608548 ACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCT
131 ACTCGACCTGGCAATACTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCT
2608613 AATTATGAACTTCTTCTTCCTTCTTCAGATG
196 AATTATGAACTTCTTCTTCCTTCTTCAGATG
* *
2608644 AGTTCTTCTCATTATGAACTCG-ACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAA
1 AGTTCTTCTCATTATGAACTCGCA-CTGGCAATGTTGATCCATCGAATGATAAATTCAAGCGAAA
2608708 AGTTGAACAAGTTCTTCTCATTATGAAC-T-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
65 AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
*
2608771 AACTCGACCTGGTAATACTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTC
130 AACTCGACCTGGCAATACTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTC
*
2608836 TCATTATGAACTTCTTCTTCCTTCTTCAGATG
195 TAATTATGAACTTCTTCTTCCTTCTTCAGATG
2608868 AGTTCTTCTCATTATGAACTC
1 AGTTCTTCTCATTATGAACTC
2608889 TTCCAGAAAT
Statistics
Matches: 237, Mismatches: 7, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
224 147 0.62
225 2 0.01
226 88 0.37
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (226 bp):
AGTTCTTCTCATTATGAACTCGCACTGGCAATGTTGATCCATCGAATGATAAATTCAAGCGAAAA
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTCGACCTGGCAATACTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCT
AATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:2609344 original size:22 final size:22
Alignment explanation
Indices: 2609319--2609373 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
2609309 GATAAAGCTT
*
2609319 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
2609341 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2609363 TCATCTTTGAA
1 TCATCTTTGAA
2609374 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2609822 original size:54 final size:54
Alignment explanation
Indices: 2609740--2609895 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 54
2609730 AGAATAGCAG
* *
2609740 GTTCGTAAAACATTTGA-AAGCGCATTCATCATTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAA-CACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
2609794 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * * *
2609848 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTATGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
2609896 CAAGATTTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 91 0.98
55 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:2612159 original size:114 final size:113
Alignment explanation
Indices: 2611960--2612184 Score: 360
Period size: 114 Copynumber: 2.0 Consensus size: 113
2611950 ACGATCATAC
* * * * **
2611960 AATTCATCTTTCAATTCTAATGATTGGTTCTGGGGTTCCTACCGAACCTATCAGATAACTCAAAG
1 AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACAGATCAGATAACTCAAAG
*
2612025 AACACTTCTAGAAGATGTTATGGGGTCTCCTTATTTCTACTATGAGCA
66 AACACTTCCAGAAGATGTTATGGGGTCTCCTTATTTCTACTATGAGCA
*
2612073 AATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAA-CAGATCAGATAACTCAAA
*
2612138 GAACACTTCCAGAAGATGTTATTGGGTCTCCTTATTTCTACTATGAG
65 GAACACTTCCAGAAGATGTTATGGGGTCTCCTTATTTCTACTATGAG
2612185 AACGTGGCAC
Statistics
Matches: 102, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
113 41 0.40
114 61 0.60
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (113 bp):
AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGTTATGGGGTCTCCTTATTTCTACTATGAGCA
Found at i:2618716 original size:30 final size:30
Alignment explanation
Indices: 2618661--2618717 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2618651 AAATTAATCA
** *
2618661 AATAATAAATATTAATATGATTAAAATAAT
1 AATAATAAATATTAATAACAATAAAATAAT
*
2618691 AATAATAATTATTAATAACAATAAAAT
1 AATAATAAATATTAATAACAATAAAAT
2618718 TGCAATGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (30 bp):
AATAATAAATATTAATAACAATAAAATAAT
Found at i:2620058 original size:6 final size:6
Alignment explanation
Indices: 2620032--2620108 Score: 75
Period size: 6 Copynumber: 13.0 Consensus size: 6
2620022 GTCGTATCTG
* * * * *
2620032 TAATAA -AATTA TAATAT TAATAA TAATAT TAATAT TAATAA TAAAAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
* * *
2620079 TAATAA TAGTAA TAAAAA TAAAAA TAATAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA
2620109 ATATAAAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
5 4 0.07
6 54 0.93
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (6 bp):
TAATAA
Found at i:2620122 original size:6 final size:6
Alignment explanation
Indices: 2620071--2620123 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
2620061 TAATATTAAT
* **
2620071 AATAAA AATAAT AATAGT AATAAA AATAAA AATAATAA ATATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AAT-A-AA A-ATAAA AATAAA
2620122 AA
1 AA
2620124 AACCAAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 30 0.75
7 4 0.10
8 4 0.10
9 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (6 bp):
AATAAA
Found at i:2620131 original size:21 final size:21
Alignment explanation
Indices: 2620062--2620138 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 21
2620052 TAATAATATT
* *
2620062 AATATTAATAATAAAAATAATA
1 AATA-TAAAAATAAAAATAACA
*
2620084 ATAGTAATAAAAATAAAAATAATA
1 A-A-T-ATAAAAATAAAAATAACA
2620108 AATATAAAAATAAAAA-AACCA
1 AATATAAAAATAAAAATAA-CA
*
2620129 AATGTAAAAA
1 AATATAAAAA
2620139 ACTAGTGTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.04
21 23 0.48
22 2 0.04
23 2 0.04
24 18 0.38
25 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (21 bp):
AATATAAAAATAAAAATAACA
Found at i:2622133 original size:18 final size:19
Alignment explanation
Indices: 2622112--2622147 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2622102 ATCACAACGT
*
2622112 TTTATTT-TGGATAAAAAA
1 TTTATTTGTAGATAAAAAA
2622130 TTTATTTGTAGATAAAAA
1 TTTATTTGTAGATAAAAA
2622148 CTGTTAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (19 bp):
TTTATTTGTAGATAAAAAA
Found at i:2628939 original size:19 final size:19
Alignment explanation
Indices: 2628911--2628949 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2628901 TATAATCCAA
2628911 AATTTAATAT-ATTTATTTT
1 AATTTAATATAATTT-TTTT
*
2628930 AATTTGATATAATTTTTTT
1 AATTTAATATAATTTTTTT
2628949 A
1 A
2628950 TAAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
AATTTAATATAATTTTTTT
Found at i:2629223 original size:31 final size:31
Alignment explanation
Indices: 2629178--2629256 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
2629168 TAATATACTT
*
2629178 GTCACTAATATTATCGATTTGTAACAAAATA
1 GTCACTAACATTATCGATTTGTAACAAAATA
* * *
2629209 TTCACTAACGTTATCGTTTTGTAACAAAATA
1 GTCACTAACATTATCGATTTGTAACAAAATA
2629240 GTCACTCCAACATTATC
1 GTCACT--AACATTATC
2629257 TCCGTTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
31 32 0.80
33 8 0.20
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (31 bp):
GTCACTAACATTATCGATTTGTAACAAAATA
Found at i:2632126 original size:3 final size:3
Alignment explanation
Indices: 2632097--2632173 Score: 109
Period size: 3 Copynumber: 24.7 Consensus size: 3
2632087 TTGGGTTTTG
* *
2632097 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TAA TAA TTAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA -TAA
2632145 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2632174 TAAATAACAT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
3 58 0.87
4 9 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2632585 original size:113 final size:113
Alignment explanation
Indices: 2632403--2633073 Score: 1055
Period size: 113 Copynumber: 6.0 Consensus size: 113
2632393 TAGAGTCATT
* ** * *
2632403 CAAAAGGTTGAATAAGCTCTTCTTATTATGAA---CTTATT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
**** * * * * * *
2632464 TTATGAACTTTCTCTGTAAAGGTTGATCCATTAAGTGATGAATTTGAA
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* * *
2632512 CAAAAGGTTAAACAAGTTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
2632577 TTATGAACTTGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
*
2632625 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
2632690 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATAGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
*
2632738 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
2632803 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* *
2632851 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
2632916 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
*
2632964 CAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
2633029 TTATGAACTTGAACTGGAAAAGCTGATCCATTGAA-TGATGGATTT
66 TTATGAACTCGAACTGGAAAAGCTGATCCA-TCAAGTGATGGATTT
2633074 AAATCTTTGC
Statistics
Matches: 527, Mismatches: 30, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
109 27 0.05
112 5 0.01
113 492 0.93
114 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
Found at i:2633908 original size:94 final size:92
Alignment explanation
Indices: 2633748--2633935 Score: 295
Period size: 94 Copynumber: 2.0 Consensus size: 92
2633738 CGATCATGCA
* * * *
2633748 ATTCATCTTTTAATTCCAATGATTGGTTCTCTGGTTCCTACCGAACCAGATCAGATAACTCAAAG
1 ATTCATCTTTCAAATCCAATGATTGGTTCTCTGGTTCATACCAAACCAGATCAGATAACTCAAAG
2633813 AACACTTCCAGAAGATGCTATGAGCAC
66 AACACTTCCAGAAGATGCTATGAGCAC
* * *
2633840 ATTCATCTTTCAAATCCAATGATTGGTTTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAA
1 ATTCATCTTTCAAATCCAATGATTGGTTCTCT--GGTTCATACCAAACCAGATCAGATAACTCAA
2633905 AGAACACTTCCAGAAGATGCTATGAGCAC
64 AGAACACTTCCAGAAGATGCTATGAGCAC
2633934 AT
1 AT
2633936 GGCATTTGTT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 28 0.32
94 59 0.68
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (92 bp):
ATTCATCTTTCAAATCCAATGATTGGTTCTCTGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATGAGCAC
Found at i:2635096 original size:12 final size:12
Alignment explanation
Indices: 2635072--2635171 Score: 79
Period size: 12 Copynumber: 8.6 Consensus size: 12
2635062 TCTTGACCCC
2635072 CCTTTTTCTTTTT
1 CCTTTTTC-TTTT
2635085 CCTTTTTCTTTT
1 CCTTTTTCTTTT
*
2635097 -CTCTTT-TTTT
1 CCTTTTTCTTTT
2635107 -CTTTCTT-TTTT
1 CCTTT-TTCTTTT
2635118 CTCTTTTTC--TT
1 C-CTTTTTCTTTT
*
2635129 CTTTTTTCTTTT
1 CCTTTTTCTTTT
*
2635141 CTTTTTTCTTTT
1 CCTTTTTCTTTT
*
2635153 -CTTTCTTTTTTT
1 CCTTT-TTCTTTT
2635165 CCTTTTT
1 CCTTTTT
2635172 TCTTCAAGCA
Statistics
Matches: 74, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
10 13 0.18
11 17 0.23
12 28 0.38
13 16 0.22
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
CCTTTTTCTTTT
Found at i:2635110 original size:28 final size:27
Alignment explanation
Indices: 2635074--2635171 Score: 94
Period size: 28 Copynumber: 3.4 Consensus size: 27
2635064 TTGACCCCCC
2635074 TTTTTCTTTTTCCTTTTTCTTTTCTCTT
1 TTTTTCTTTTT-CTTTTTCTTTTCTCTT
2635102 TTTTTCTTTCTT-TTTTCTCTTTT-TCTT
1 TTTTTCTTT-TTCTTTT-TCTTTTCTCTT
2635129 CTTTTT-TCTTTTCTTTTTTCTTTTCTTTCTT
1 -TTTTTCT-TTTTC-TTTTTCTTTTC--TCTT
2635160 TTTTTCCTTTTT
1 TTTTT-CTTTTT
2635172 TCTTCAAGCA
Statistics
Matches: 59, Mismatches: 0, Indels: 19
0.76 0.00 0.24
Matches are distributed among these distances:
27 11 0.19
28 28 0.47
29 6 0.10
30 5 0.08
31 8 0.14
32 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTTCTTTTTCTTTTTCTTTTCTCTT
Found at i:2635131 original size:37 final size:36
Alignment explanation
Indices: 2635087--2635175 Score: 119
Period size: 37 Copynumber: 2.4 Consensus size: 36
2635077 TTCTTTTTCC
*
2635087 TTTTTCTTTTCTCTTTT-TTTCTTTCTTTT-TTCTCTT
1 TTTTTCTTTTTTCTTTTCTTT-TTTCTTTTCTT-TCTT
2635123 TTTCTTCTTTTTTCTTTTCTTTTTTCTTTTCTTTCTT
1 TTT-TTCTTTTTTCTTTTCTTTTTTCTTTTCTTTCTT
2635160 TTTTTCCTTTTTTCTT
1 TTTTT-CTTTTTTCTT
2635176 CAAGCATAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
36 5 0.10
37 38 0.79
38 5 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (36 bp):
TTTTTCTTTTTTCTTTTCTTTTTTCTTTTCTTTCTT
Found at i:2635134 original size:30 final size:30
Alignment explanation
Indices: 2635074--2635170 Score: 107
Period size: 29 Copynumber: 3.3 Consensus size: 30
2635064 TTGACCCCCC
*
2635074 TTTTTCTTTTTCCTTTTTC--TTTTC-TCTT
1 TTTTTC-TTTTCTTTTTTCTTTTTTCTTCTT
2635102 TTTTTC-TTTCTTTTTTCTCTTTTTCTTC-T
1 TTTTTCTTTTCTTTTTTCT-TTTTTCTTCTT
*
2635131 TTTTTCTTTTCTTTTTTCTTTTCT-TTCTT
1 TTTTTCTTTTCTTTTTTCTTTTTTCTTCTT
2635160 TTTTTCCTTTT
1 TTTTT-CTTTT
2635171 TTCTTCAAGC
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
26 10 0.17
28 9 0.15
29 22 0.37
30 19 0.32
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (30 bp):
TTTTTCTTTTCTTTTTTCTTTTTTCTTCTT
Found at i:2642510 original size:15 final size:15
Alignment explanation
Indices: 2642487--2642518 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2642477 TGAAATGAAT
2642487 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2642502 AATGTATGTATGCAA
1 AATGAATGTATGCAA
2642517 AA
1 AA
2642519 AGGAATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2646915 original size:16 final size:16
Alignment explanation
Indices: 2646889--2646926 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
2646879 TATAAAGGAC
2646889 TAAAATAAAGAA-AAT
1 TAAAATAAAGAACAAT
2646904 TAAAATTAAAGAACGAAT
1 TAAAA-TAAAGAAC-AAT
2646922 TAAAA
1 TAAAA
2646927 GGATTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
18 8 0.40
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (16 bp):
TAAAATAAAGAACAAT
Found at i:2647711 original size:3 final size:3
Alignment explanation
Indices: 2647703--2647729 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2647693 ACCATTTGTT
2647703 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
2647730 TAAATAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2647861 original size:17 final size:18
Alignment explanation
Indices: 2647839--2647878 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2647829 CCCATTTCAA
2647839 ATTTTAAAT-TTGTATAT
1 ATTTTAAATATTGTATAT
* *
2647856 ATTTTAAATATTTTTTAT
1 ATTTTAAATATTGTATAT
2647874 ATTTT
1 ATTTT
2647879 TTTTATTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
ATTTTAAATATTGTATAT
Found at i:2656368 original size:21 final size:21
Alignment explanation
Indices: 2656344--2656383 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2656334 AGAATGGGGA
*
2656344 GAATCGGTACCCCTTCATAGG
1 GAATCGATACCCCTTCATAGG
2656365 GAATCGATACCCCTTCATA
1 GAATCGATACCCCTTCATA
2656384 ATATTCAAAT
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:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (21 bp):
GAATCGATACCCCTTCATAGG
Found at i:2656554 original size:19 final size:19
Alignment explanation
Indices: 2656495--2656568 Score: 70
Period size: 19 Copynumber: 4.1 Consensus size: 19
2656485 AAACCATGCA
*
2656495 GGGGGAATATGTA-CCCCT
1 GGGGGAATCTGTACCCCCT
*
2656513 GGGGGAAATCTGT--TCCC-
1 GGGGG-AATCTGTACCCCCT
2656530 -GGGGAATC-GATACCCCCT
1 GGGGGAATCTG-TACCCCCT
2656548 GGGGGAATCTGTACCCCCT
1 GGGGGAATCTGTACCCCCT
2656567 GG
1 GG
2656569 ACAATCTGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.02
15 5 0.11
16 4 0.09
17 3 0.07
18 8 0.17
19 24 0.52
20 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.34, T:0.20
Consensus pattern (19 bp):
GGGGGAATCTGTACCCCCT
Found at i:2657995 original size:19 final size:20
Alignment explanation
Indices: 2657952--2657999 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2657942 CTCTAAATCT
*
2657952 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
2657972 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
2657991 TTTTCAAAA
1 TTTTCAAAA
2658000 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Done.