Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007967.1 Hibiscus syriacus cultivar Beakdansim tig00110402_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: 2476418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1595273 original size:2 final size:2
Alignment explanation
Indices: 1595266--1595301 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1595256 TAGTATCCGG
1595266 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
1595302 CATTCCCCAT
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1595657 original size:15 final size:15
Alignment explanation
Indices: 1595637--1595665 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1595627 ATGAGGTTGT
1595637 GGTTGAGAAGAACTA
1 GGTTGAGAAGAACTA
1595652 GGTTGAGAAGAACT
1 GGTTGAGAAGAACT
1595666 TTGAGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.34, T:0.21
Consensus pattern (15 bp):
GGTTGAGAAGAACTA
Found at i:1596654 original size:200 final size:199
Alignment explanation
Indices: 1595984--1596922 Score: 1202
Period size: 200 Copynumber: 4.7 Consensus size: 199
1595974 ATTTAGCAAT
* * * **
1595984 TGTCGATACTTTATGCT-GACATATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGGA
1 TGTCGATACATTATG-TAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTAAA
* * ** * * * *
1596048 AATTTACCTATCACATTATAATTACCGGTTTCGATGTTTTTGGGATTGACACTTTTTAAAAATGT
65 AAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGT
* * * * **
1596113 ATCGACACTTAATGGGTGTACCCTTTT-GGCATTGTTTCTGGACAAAAAGTATCGACACAAATTC
130 ATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATT-
*
1596177 CAGAAA-
194 TA-AAAG
* * * *
1596183 TGTCGATACATTTTCTAGACCTATTCTCGCATAAAACCGGTATATTTATACCGGTTACATTGAAA
1 TGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTAAAA
*
1596248 AATTACCTATTACATTATAATCATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGTA
66 AATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGTA
* * * * * *
1596313 TTGACACTTTATGCGTGCACCATATTTTAGGCATTCATTTTGGACAAAATGTATCAACACATACT
131 TCGACACTTTATGCGTGCACC--ATTTTGGGCATTCATTCTGGACAAAAAGTATCGACACA-AAT
*
1596378 TAAAAAG
193 TTAAAAG
* * *
1596385 TGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACAA
1 TGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTAAAA
* * * *
1596450 AATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGTGATCGATACTTTTAAAAAATGTA
66 AATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGTA
* ** * * *
1596515 TCAACACTTTATTTGTGCACCCTTTTGGGCATTCCTTCTGGACAAACAGTATCGACACAAATTCT
131 TCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATT-T
*
1596580 ATAAG
195 AAAAG
* *
1596585 TGTCGATACATTATGTAAACCTATTCTCTCATAAAACCGGTATAGTTATACCGGTTACATTAAAA
1 TGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTAAAA
*
1596650 AATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCAATACTTTTTATAAATGTA
66 AATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGTA
* ** * *
1596715 TCGACACTTTATGCGTTCACCATTTTGGAAAATTCATTCTGGACAAAAAGTATCGGCACTAATTT
131 TCGACACTTTATGCGTGCACCATTTTGG-GCATTCATTCTGGACAAAAAGTATCGACACAAATTT
1596780 CAAAAG
195 -AAAAG
* * * *
1596786 TGTCGATACATTATGTAGACATATTCT-TACTTAAAACCGGTATATTTATACCGGTTATATTACA
1 TGTCGATACATTATGTAGACCTATTCTCT-CATAAAACCGGTATATTTATACCGGTTACATTAAA
* * * *
1596850 AAATTACCTATGATATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACCTTTTATAAATGT
65 AAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGT
1596915 ATCGACAC
130 ATCGACAC
1596923 ATCTGCTTAC
Statistics
Matches: 644, Mismatches: 86, Indels: 18
0.86 0.11 0.02
Matches are distributed among these distances:
198 1 0.00
199 132 0.20
200 180 0.28
201 164 0.25
202 164 0.25
203 3 0.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (199 bp):
TGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTAAAA
AATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGTA
TCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTTA
AAAG
Found at i:1596705 original size:402 final size:398
Alignment explanation
Indices: 1595984--1596922 Score: 1326
Period size: 401 Copynumber: 2.3 Consensus size: 398
1595974 ATTTAGCAAT
* * * * **
1595984 TGTCGATACTTTATGCT-GACATATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGGA
1 TGTCGATACATTATG-TAGACATATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACA
* ** * *
1596048 AATTTACCTATCACATTATAATTACCGGTTTCGATGTTTTTGGGATTGACACTTTTTAAAAATGT
65 AAATTACCTATCACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATAC-TTTTAAAAATGT
* **
1596113 ATCGACACTTAATGGGTGTACCCTTTTGGCATTGTTTCTGGACAAAAAGTATCGACACAAATTCC
129 ATCGACACTTAATGGGTGCACCCTTTTGGCATTCCTTCTGGACAAAAAGTATCGACACAAATTCC
* * *
1596178 AGAAATGTCGATACATTTTCTAGACCTATTCTCGCATAAAACCGGTATATTTATACCGGTTACAT
194 AGAAATGTCGATACATTATCTAAACCTATTCTCGCATAAAACCGGTATAGTTATACCGGTTACAT
* *
1596243 TGAAAAATTACCTATTACATTATAATCATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAA
259 TAAAAAATTACCTATTACATTATAATCATGGGTTTCGATGTTTCTGGGATCAATACTTTTTATAA
* * * *
1596308 ATGTATTGACACTTTATGCGTGCACCATATTTTAGG-CATTCATTTTGGACAAAATGTATCAACA
324 ATGTATCGACACTTTATGCGTGCACC--ATTTT-GGAAATTCATTCTGGACAAAAAGTATCAACA
1596372 C-ATACTTAAAAAG
386 CTA-ACTTAAAAAG
*
1596385 TGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACAA
1 TGTCGATACATTATGTAGACATATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACAA
* * * *
1596450 AATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGTGATCGATACTTTTAAAAAATGTA
66 AATTACCTATCACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTTTT-AAAAATGTA
* * ** * *
1596515 TCAACACTTTATTTGTGCACCCTTTTGGGCATTCCTTCTGGACAAACAGTATCGACACAAATTCT
130 TCGACACTTAATGGGTGCACCCTTTT-GGCATTCCTTCTGGACAAAAAGTATCGACACAAATTCC
* * * *
1596580 ATAAGTGTCGATACATTATGTAAACCTATTCTCTCATAAAACCGGTATAGTTATACCGGTTACAT
194 AGAAATGTCGATACATTATCTAAACCTATTCTCGCATAAAACCGGTATAGTTATACCGGTTACAT
*
1596645 TAAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCAATACTTTTTATAA
259 TAAAAAATTACCTATTACATTATAATCATGGGTTTCGATGTTTCTGGGATCAATACTTTTTATAA
* **
1596710 ATGTATCGACACTTTATGCGTTCACCATTTTGGAAAATTCATTCTGGACAAAAAGTATCGGCACT
324 ATGTATCGACACTTTATGCGTGCACCATTTTGG-AAATTCATTCTGGACAAAAAGTATCAACACT
* *
1596775 AATTTCAAAAG
388 AACTTAAAAAG
* *
1596786 TGTCGATACATTATGTAGACATATTCTTACTTAAAACCGGTATATTTATACCGGTTATATTACAA
1 TGTCGATACATTATGTAGACATATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACAA
* * *
1596851 AATTACCTATGATATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACCTTTTATAAATGTA
66 AATTACCTATCACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATA-CTTTTAAAAATGTA
1596916 TCGACAC
130 TCGACAC
1596923 ATCTGCTTAC
Statistics
Matches: 477, Mismatches: 54, Indels: 14
0.88 0.10 0.03
Matches are distributed among these distances:
399 2 0.00
400 10 0.02
401 281 0.59
402 184 0.39
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (398 bp):
TGTCGATACATTATGTAGACATATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACAA
AATTACCTATCACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTTTTAAAAATGTAT
CGACACTTAATGGGTGCACCCTTTTGGCATTCCTTCTGGACAAAAAGTATCGACACAAATTCCAG
AAATGTCGATACATTATCTAAACCTATTCTCGCATAAAACCGGTATAGTTATACCGGTTACATTA
AAAAATTACCTATTACATTATAATCATGGGTTTCGATGTTTCTGGGATCAATACTTTTTATAAAT
GTATCGACACTTTATGCGTGCACCATTTTGGAAATTCATTCTGGACAAAAAGTATCAACACTAAC
TTAAAAAG
Found at i:1596965 original size:15 final size:15
Alignment explanation
Indices: 1596945--1596977 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1596935 ATTTTATGGA
1596945 AACTTTACGTTTGGG
1 AACTTTACGTTTGGG
1596960 AACTTTACGTTTGGG
1 AACTTTACGTTTGGG
1596975 AAC
1 AAC
1596978 CATACTGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (15 bp):
AACTTTACGTTTGGG
Found at i:1597311 original size:19 final size:19
Alignment explanation
Indices: 1597287--1597335 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1597277 TTACATTCAC
1597287 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1597306 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1597325 ATACAAAATTA
1 ATACAAAATTA
1597336 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1599135 original size:33 final size:33
Alignment explanation
Indices: 1599098--1599197 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
1599088 CCATCTTAAG
*
1599098 TTCACCCTTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
*
1599131 TTCACCCCTCAACACCTCAACTTCTTTCACCAA
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
*
1599164 TTCACCCCTCAACACCTCAATTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1599197 T
1 T
1599198 CCATCTATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.25, C:0.45, G:0.00, T:0.30
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAC
Found at i:1601962 original size:182 final size:181
Alignment explanation
Indices: 1601655--1602508 Score: 1216
Period size: 182 Copynumber: 4.7 Consensus size: 181
1601645 TACGCGTACT
* * * * *
1601655 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGT-TTTACCGGTTTTGTCATTTCGAGACC
1 TATTAAAGTATCGACACTTTCAATATAT-TGGTCGC-TCTATACCGGTTTTGTCCTTTAGAGACC
* * *
1601719 GATTTTATCATATTTTTACATGTTATATCGTTGTGGACCGATACATTGTTATAAAGTATCGACAC
64 GGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACAC
* * * *
1601784 TTTATAAGTGCTAAAACTGTTTCTCTTTTACATTCACAAAGTGTCGATACTTA
129 TTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * *
1601837 TATTAAAGTATTGACACTTTAAATACATCTGGTCGCTCTATATCGGTTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATAT-TGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* *
1601902 GTTTTGTCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTGTTATAAAGTATCGACACT
65 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
*
1601967 TTATGGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
130 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * *
1602019 TATTAAAGTATTGACACTTTCAATATATTCGATCGCTCTATACCGATTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATT-GGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
*
1602084 ATTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
65 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
1602149 TTATAGGCACTAAAACTGCTTCTCTTTTAAATT--CAAAGTGTTGATACTTA
130 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* *
1602199 TATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTACATCGGTTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATT-GGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* *
1602264 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCAACACT
65 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* ** *
1602329 TTATAGGCTCTAAAACTATTTTTCTTTTAAATTCACAAAGTGTCGATACTTA
130 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
** *
1602381 TATTAAAGTATCGACACTTTCAATATATATGGTACCGCT-T-TACCGGTTTTGTATTTTCGAGAC
1 TATTAAAGTATCGACACTTTCAATATAT-TGGT--CGCTCTATACCGGTTTTGTCCTTTAGAGAC
* * * * *
1602444 CTGCTTTGTCATATTTTTACATGTTATATTGATGTGGATCGATACAGTT-TTATAAAGTATTGAC
63 CGGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACA-TTGTTATAAAGTATCGAC
1602508 A
127 A
1602509 TAAACCGACA
Statistics
Matches: 609, Mismatches: 55, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
180 167 0.27
181 2 0.00
182 432 0.71
183 4 0.01
184 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (181 bp):
TATTAAAGTATCGACACTTTCAATATATTGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCGG
TTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTT
TATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:1602316 original size:362 final size:361
Alignment explanation
Indices: 1601655--1602508 Score: 1286
Period size: 362 Copynumber: 2.3 Consensus size: 361
1601645 TACGCGTACT
* * *
1601655 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATTC-G-ATCGCTTTACCGGTTTTGTCATTTCGAGACCG
* *
1601720 ATTTTATCATATTTTTACATGTTATATCGTTGTGGACCGATACATTGTTATAAAGTATCGACACT
64 ATTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
** * * *
1601785 TTATAAGTGCTAAAACTGTTTCTCTTTTACATTCACAAAGTGTCGATACTTATATTAAAGTATTG
129 TTATAAGCACTAAAACTGCTTCTCTTTTAAATT-ACAAAGTGTCGATACTTATATTAAAGTATCG
*
1601850 ACACTTTAAATACATCTGGTCGCTCTATATCGGTTTTGTCCTTTAGAGACCGGTTTTGTCATATT
193 ACACTTTAAATACATCTGGTCGCTCTACATCGGTTTTGTCCTTTAGAGACCGGTTTTGTCATATT
* * *
1601915 TTTACCTGTTATATCGTTTTGGATCGATACATTGTTATAAAGTATCGACACTTTATGGGCGCTAA
258 TTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCAACACTTTATAGGCGCTAA
*
1601980 AACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
323 AACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * *
1602019 TATTAAAGTATTGACACTTTCAATATATTCGATCGCTCTATACCGATTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATTCGATCGCT-T-TACCGGTTTTGTCATTTCGAGACCG
1602084 ATTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
64 ATTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
1602149 TTATAGGCACTAAAACTGCTTCTCTTTTAAATT-CAAAGTGTTGATACTTATATTAAAGTATCGA
129 TTATAAGCACTAAAACTGCTTCTCTTTTAAATTACAAAGTGTCGATACTTATATTAAAGTATCGA
* *
1602213 CACTTTCAATATAT-TCGGTCGCTCTACATCGGTTTTGTCCTTTAGAGACCGGTTTTGTCATATT
194 CACTTTAAATACATCT-GGTCGCTCTACATCGGTTTTGTCCTTTAGAGACCGGTTTTGTCATATT
*
1602277 TTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCAACACTTTATAGGCTCTAA
258 TTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCAACACTTTATAGGCGCTAA
* *
1602342 AACTATTTTTCTTTTAAATTCACAAAGTGTCGATACTTA
323 AACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* *
1602381 TATTAAAGTATCGACACTTTCAATATATATGGTACCGCTTTACCGGTTTTGT-ATTTTCGAGACC
1 TATTAAAGTATCGACACTTTCAATATAT-TCG-ATCGCTTTACCGGTTTTGTCA-TTTCGAGACC
* * * *
1602445 TG-CTTTGTCATATTTTTACATGTTATATTGATGTGGATCGATACAGTT-TTATAAAGTATTGAC
63 -GATTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACA-TTGTTATAAAGTATCGAC
1602508 A
126 A
1602509 TAAACCGACA
Statistics
Matches: 446, Mismatches: 36, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
361 1 0.00
362 291 0.65
363 8 0.02
364 146 0.33
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (361 bp):
TATTAAAGTATCGACACTTTCAATATATTCGATCGCTTTACCGGTTTTGTCATTTCGAGACCGAT
TTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTTT
ATAAGCACTAAAACTGCTTCTCTTTTAAATTACAAAGTGTCGATACTTATATTAAAGTATCGACA
CTTTAAATACATCTGGTCGCTCTACATCGGTTTTGTCCTTTAGAGACCGGTTTTGTCATATTTTT
ACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCAACACTTTATAGGCGCTAAAAC
TACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:1606017 original size:10 final size:10
Alignment explanation
Indices: 1606002--1606077 Score: 71
Period size: 10 Copynumber: 7.3 Consensus size: 10
1605992 TTTGGTGTTT
1606002 TAAGCTTATA
1 TAAGCTTATA
* *
1606012 TAAGCTTTCTT
1 TAAGC-TTATA
1606023 TAAGCTTATA
1 TAAGCTTATA
* *
1606033 TAAGCTTTCTT
1 TAAGC-TTATA
1606044 TAAGCTTATA
1 TAAGCTTATA
* *
1606054 TAAGCTTTCTT
1 TAAGC-TTATA
1606065 TAAGCTTATA
1 TAAGCTTATA
1606075 TAA
1 TAA
1606078 CACTCAAAGA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
10 27 0.53
11 24 0.47
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (10 bp):
TAAGCTTATA
Found at i:1606026 original size:21 final size:21
Alignment explanation
Indices: 1606000--1606077 Score: 156
Period size: 21 Copynumber: 3.7 Consensus size: 21
1605990 CTTTTGGTGT
1606000 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
1606021 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
1606042 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
1606063 TTTAAGCTTATATAA
1 TTTAAGCTTATATAA
1606078 CACTCAAAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (21 bp):
TTTAAGCTTATATAAGCTTTC
Found at i:1606028 original size:11 final size:11
Alignment explanation
Indices: 1606012--1606071 Score: 70
Period size: 11 Copynumber: 5.6 Consensus size: 11
1606002 TAAGCTTATA
1606012 TAAGCTTTCTT
1 TAAGCTTTCTT
* *
1606023 TAAGC-TTATA
1 TAAGCTTTCTT
1606033 TAAGCTTTCTT
1 TAAGCTTTCTT
* *
1606044 TAAGC-TTATA
1 TAAGCTTTCTT
1606054 TAAGCTTTCTT
1 TAAGCTTTCTT
1606065 TAAGCTT
1 TAAGCTT
1606072 ATATAACACT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 16 0.41
11 23 0.59
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (11 bp):
TAAGCTTTCTT
Found at i:1606587 original size:14 final size:14
Alignment explanation
Indices: 1606553--1606612 Score: 86
Period size: 14 Copynumber: 4.2 Consensus size: 14
1606543 GGCTACTTAG
1606553 AGAATATGAAGGAAGA
1 AGAA-ATGAA-GAAGA
1606569 AGAAATGAAGAAGA
1 AGAAATGAAGAAGA
*
1606583 GGAAATGAAGAAGA
1 AGAAATGAAGAAGA
1606597 AGAAATGAAG-AGA
1 AGAAATGAAGAAGA
1606610 AGA
1 AGA
1606613 GAAATATGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
13 6 0.14
14 27 0.64
15 5 0.12
16 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.32, T:0.08
Consensus pattern (14 bp):
AGAAATGAAGAAGA
Found at i:1608959 original size:20 final size:20
Alignment explanation
Indices: 1608915--1609182 Score: 224
Period size: 20 Copynumber: 13.2 Consensus size: 20
1608905 AATGACCAAC
**
1608915 AAAATCGCAACGCGAAATA-
1 AAAATCGCAACGCGATTTAG
1608934 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* **
1608954 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
**
1608974 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
**
1608994 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TTAG
* *
1609015 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
* **
1609036 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
1609057 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
*
1609078 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
*
1609098 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
*
1609118 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTTAG
*
1609138 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* *
1609158 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
1609178 AAAAT
1 AAAAT
1609183 GAGTAAATTC
Statistics
Matches: 206, Mismatches: 29, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
18 1 0.00
19 20 0.10
20 141 0.68
21 16 0.08
22 28 0.14
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1609149 original size:60 final size:60
Alignment explanation
Indices: 1608917--1609182 Score: 263
Period size: 60 Copynumber: 4.4 Consensus size: 60
1608907 TGACCAACAA
** * ****
1608917 AATCGCAACGCGAAATA-AAAATCGCAACGCGATTTAGAAAATCGCAACGTTGAAAAGAA-
1 AATCGCAACGCGATTTAGAAAATCGCAACGCGATTTAGAAAATCGCAACG-CGATTCCAAG
** ** * *
1608976 AATCGCAACG-G-TCAAAAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT-AAGAG
1 AATCGCAACGCGAT--TTAGAAAATCGCAACGCGAT-TTAGAA-AATCGCAACGCGATTCCA-AG
** *
1609038 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGAT-TTAGAA-AATCGCAACGCGATTTAGAAAATCGCAACGCGATTCCAAG
*
1609100 AATCGCAACGCGATTTAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTTAGAAAATCGCAACGCGATTTAGAAAATCGCAACGCGATTCCAAG
*
1609160 AATCGCAACGCGATTCAGAAAAT
1 AATCGCAACGCGATTTAGAAAAT
1609183 GAGTAAATTC
Statistics
Matches: 173, Mismatches: 23, Indels: 21
0.80 0.11 0.10
Matches are distributed among these distances:
58 1 0.01
59 12 0.07
60 78 0.45
61 11 0.06
62 49 0.28
63 7 0.04
64 15 0.09
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (60 bp):
AATCGCAACGCGATTTAGAAAATCGCAACGCGATTTAGAAAATCGCAACGCGATTCCAAG
Found at i:1609289 original size:6 final size:6
Alignment explanation
Indices: 1609278--1609364 Score: 174
Period size: 6 Copynumber: 14.5 Consensus size: 6
1609268 GACACGTATT
1609278 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1609326 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1609365 CGAGACGAGA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1609876 original size:6 final size:6
Alignment explanation
Indices: 1609865--1609939 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
1609855 TCTCGTCTCG
1609865 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1609913 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1609940 AATACGTGTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1610090 original size:40 final size:41
Alignment explanation
Indices: 1610035--1610242 Score: 223
Period size: 42 Copynumber: 5.1 Consensus size: 41
1610025 GAATTTACTC
1610035 ATTTTCTTAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGATATCGCGTTGCG
*
1610075 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-ATATCGCGTTGCG
* *
1610117 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-ATATCGCGTTGCG
* ** * *
1610159 ATTTTCTT--TTGACCGTTGCGATT-TT-CTTTTCAACGTTGCG
1 ATTTTCTTAATCG--CGTTGCGATTCTTGGATATC-GCGTTGCG
* * *
1610199 ATTTTCTAAATCGCGTTGCGATT-TT-TATTTCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGATATCGCGTTGCG
1610238 ATTTT
1 ATTTT
1610243 GTTGGTCATT
Statistics
Matches: 146, Mismatches: 15, Indels: 15
0.83 0.09 0.09
Matches are distributed among these distances:
39 15 0.10
40 60 0.41
41 3 0.02
42 68 0.47
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (41 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGATATCGCGTTGCG
Found at i:1610215 original size:20 final size:20
Alignment explanation
Indices: 1610035--1610242 Score: 147
Period size: 20 Copynumber: 10.2 Consensus size: 20
1610025 GAATTTACTC
*
1610035 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1610055 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
1610075 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1610095 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
1610117 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1610137 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
1610159 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
1610179 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
1610199 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1610219 ATTTT-TATTTCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
1610238 ATTTT
1 ATTTT
1610243 GTTGGTCATT
Statistics
Matches: 149, Mismatches: 28, Indels: 23
0.75 0.14 0.12
Matches are distributed among these distances:
18 2 0.01
19 19 0.13
20 86 0.58
21 15 0.10
22 27 0.18
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:1615032 original size:17 final size:17
Alignment explanation
Indices: 1615010--1615048 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1615000 TTCTTCCCCA
1615010 CTCTTCTATCTCATTTC
1 CTCTTCTATCTCATTTC
1615027 CTCTTCTATCTCATTTC
1 CTCTTCTATCTCATTTC
1615044 CTCTT
1 CTCTT
1615049 GAAGAACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.36, G:0.00, T:0.54
Consensus pattern (17 bp):
CTCTTCTATCTCATTTC
Found at i:1619573 original size:21 final size:21
Alignment explanation
Indices: 1619547--1619593 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1619537 GTCATGGATT
1619547 TGCTATGGAAACTATATTATG
1 TGCTATGGAAACTATATTATG
1619568 TGCTATGGAAACTATATTATG
1 TGCTATGGAAACTATATTATG
1619589 TGCTA
1 TGCTA
1619594 CGAATGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (21 bp):
TGCTATGGAAACTATATTATG
Found at i:1620010 original size:27 final size:27
Alignment explanation
Indices: 1619980--1620031 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
1619970 AAATAGTGAA
1619980 CAAAACAT-CATTTAA-ACATAAAAATAT
1 CAAAACATCCA-TTAACACA-AAAAATAT
*
1620007 CAAACCATCCATTAACACAAAAAAT
1 CAAAACATCCATTAACACAAAAAAT
1620032 CAACCAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (27 bp):
CAAAACATCCATTAACACAAAAAATAT
Found at i:1624642 original size:35 final size:35
Alignment explanation
Indices: 1624602--1624677 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
1624592 AAAAGATGTG
* * *
1624602 GCAAAAGTTTAA-TAAAATTGTAAAAGTATGCT-AA
1 GCAAAAGTTAAAGT-AAATTATAAAAGCATGCTGAA
1624636 TGCAAAAGTTAAAGTAAATTATAAAAGCATGCTGAA
1 -GCAAAAGTTAAAGTAAATTATAAAAGCATGCTGAA
1624672 GCAAAA
1 GCAAAA
1624678 ATAAATTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 33 0.92
36 3 0.08
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.25
Consensus pattern (35 bp):
GCAAAAGTTAAAGTAAATTATAAAAGCATGCTGAA
Found at i:1631343 original size:21 final size:22
Alignment explanation
Indices: 1631300--1631382 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 22
1631290 ATAATTTGCA
*
1631300 CCGAAGTACCACATA-TTTGTGT
1 CCGAAGGACCACATAGTTT-TGT
*
1631322 -CGAAGGACCACATAGGTTTGT
1 CCGAAGGACCACATAGTTTTGT
1631343 CCTGAAGGACCACATAGTTTTGT
1 CC-GAAGGACCACATAGTTTTGT
*
1631366 CACGATGGACCACATAG
1 C-CGAAGGACCACATAG
1631383 AACCCTCGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
21 16 0.30
22 3 0.06
23 33 0.62
24 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (22 bp):
CCGAAGGACCACATAGTTTTGT
Found at i:1632093 original size:20 final size:22
Alignment explanation
Indices: 1632068--1632122 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1632058 TTCATACTGC
1632068 ATAGTATCGATAC-TCT-TCCT
1 ATAGTATCGATACTTCTCTCCT
* *
1632088 ATAGTACCGATACTTCTCTTCT
1 ATAGTATCGATACTTCTCTCCT
*
1632110 ATGGTATCGATAC
1 ATAGTATCGATAC
1632123 CCACTTCGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 12 0.41
21 3 0.10
22 14 0.48
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (22 bp):
ATAGTATCGATACTTCTCTCCT
Found at i:1634908 original size:18 final size:18
Alignment explanation
Indices: 1634870--1634924 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
1634860 GATTCTAATA
1634870 ATACTCATGGGAGTA-CTG
1 ATACTCATGGGAGTATC-G
1634888 ATACTCATGGGAGTATCG
1 ATACTCATGGGAGTATCG
*
1634906 ATACTGA--GGAGTATCG
1 ATACTCATGGGAGTATCG
1634922 ATA
1 ATA
1634925 TCAAGGGTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 12 0.34
18 22 0.63
19 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (18 bp):
ATACTCATGGGAGTATCG
Found at i:1637922 original size:2 final size:2
Alignment explanation
Indices: 1637915--1637951 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1637905 CGTGCTACAA
1637915 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1637952 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1637956 original size:2 final size:2
Alignment explanation
Indices: 1637951--1638004 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1637941 ATATATATAT
1637951 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1637993 AG AG AG AG AG AG
1 AG AG AG AG AG AG
1638005 CAATTTAACC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1639356 original size:17 final size:17
Alignment explanation
Indices: 1639334--1639366 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1639324 TTTTATGAGA
*
1639334 TGAAAATATTATTATTG
1 TGAAAATATAATTATTG
1639351 TGAAAATATAATTATT
1 TGAAAATATAATTATT
1639367 TAAAATAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (17 bp):
TGAAAATATAATTATTG
Found at i:1639469 original size:17 final size:17
Alignment explanation
Indices: 1639447--1639479 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1639437 CGAAATCATA
1639447 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
1639464 ATATTATATTTTATAT
1 ATATTATATTTTATAT
1639480 AAACAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:1645841 original size:11 final size:11
Alignment explanation
Indices: 1645827--1645864 Score: 76
Period size: 11 Copynumber: 3.5 Consensus size: 11
1645817 TGAAAGAAAT
1645827 GGAAATGAGAA
1 GGAAATGAGAA
1645838 GGAAATGAGAA
1 GGAAATGAGAA
1645849 GGAAATGAGAA
1 GGAAATGAGAA
1645860 GGAAA
1 GGAAA
1645865 ATGAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.37, T:0.08
Consensus pattern (11 bp):
GGAAATGAGAA
Found at i:1646140 original size:21 final size:21
Alignment explanation
Indices: 1646094--1646140 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1646084 ACAAGGAGAA
1646094 GAATTAGAAATTTCATAAAGG
1 GAATTAGAAATTTCATAAAGG
*
1646115 AAATTATG-AATTTC-TAATAGG
1 GAATTA-GAAATTTCATAA-AGG
1646136 GAATT
1 GAATT
1646141 GGGGATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.14
21 18 0.82
22 1 0.05
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (21 bp):
GAATTAGAAATTTCATAAAGG
Found at i:1650716 original size:19 final size:19
Alignment explanation
Indices: 1650692--1650735 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1650682 CCCCTAGTAT
1650692 CGATACTACACTTCAATAC
1 CGATACTACACTTCAATAC
*
1650711 CGATACTACACTTCAGTAC
1 CGATACTACACTTCAATAC
1650730 CGATAC
1 CGATAC
1650736 CTCATGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.34, C:0.32, G:0.09, T:0.25
Consensus pattern (19 bp):
CGATACTACACTTCAATAC
Found at i:1652566 original size:23 final size:22
Alignment explanation
Indices: 1652519--1652584 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
1652509 AGGGTTCATA
*
1652519 GGTCCTTCGGGACA-T-ACAGT
1 GGTCCTTCGGGACATTCATAGT
1652539 GGTCCTTCGGGACATTTCATAGT
1 GGTCCTTCGGGACA-TTCATAGT
*
1652562 GGTCCTTTGGGACAAATTCATAG
1 GGTCCTTCGGGAC--ATTCATAG
1652585 ACCCTAGTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 14 0.36
22 1 0.03
23 16 0.41
24 7 0.18
25 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCATAGT
Found at i:1663311 original size:21 final size:23
Alignment explanation
Indices: 1663267--1663314 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1663257 AGCATGTACT
*
1663267 TATGTCATTTCCCTTGTAATCACA
1 TATGTCATTT-CCTTCTAATCACA
1663291 TATGTCATTT-CTTCT-ATCACA
1 TATGTCATTTCCTTCTAATCACA
1663312 TAT
1 TAT
1663315 CACATGTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 4 0.17
24 10 0.43
ACGTcount: A:0.25, C:0.23, G:0.06, T:0.46
Consensus pattern (23 bp):
TATGTCATTTCCTTCTAATCACA
Found at i:1663921 original size:20 final size:22
Alignment explanation
Indices: 1663850--1663923 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 22
1663840 CGATGTTTTC
*
1663850 TGGTATCGATACC-CT-CATTA
1 TGGTATCGATACCTCTACACTA
*
1663870 TGGTATCGATA-CTACTATACTA
1 TGGTATCGATACCT-CTACACTA
*
1663892 TGGTACCGATACCTCTACA-T-
1 TGGTATCGATACCTCTACACTA
1663912 TGGTATCGATAC
1 TGGTATCGATAC
1663924 TCCCTAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
19 1 0.02
20 22 0.49
21 3 0.07
22 17 0.38
23 2 0.04
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (22 bp):
TGGTATCGATACCTCTACACTA
Found at i:1669652 original size:81 final size:82
Alignment explanation
Indices: 1669557--1669717 Score: 261
Period size: 81 Copynumber: 2.0 Consensus size: 82
1669547 CACCATAAAT
*
1669557 TTTTTTCTCATTAAAAAATAATGGGACAATCACCTATTTACGCCTTTAAATTTTAATTTATATTG
1 TTTTTTATCATTAAAAAATAATGGGACAATCACCTATTTACGCCTTTAAATTTTAATTTATATTG
1669622 ATTTTG-TCCCCTCAAA
66 ATTTTGCTCCCCTCAAA
* * * *
1669638 TTTTTTATCATTAAAAAATAATGGGACAATTACCTATTTAGGTCTTTAAATTTTAATTTATTTTG
1 TTTTTTATCATTAAAAAATAATGGGACAATCACCTATTTACGCCTTTAAATTTTAATTTATATTG
*
1669703 ATTTTGCTCTCCTCA
66 ATTTTGCTCCCCTCA
1669718 TTTTCTGTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 66 0.90
82 7 0.10
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (82 bp):
TTTTTTATCATTAAAAAATAATGGGACAATCACCTATTTACGCCTTTAAATTTTAATTTATATTG
ATTTTGCTCCCCTCAAA
Found at i:1675359 original size:7 final size:7
Alignment explanation
Indices: 1675347--1675377 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1675337 TTTTTCTTTA
1675347 TGAACAG
1 TGAACAG
*
1675354 TGAACAT
1 TGAACAG
1675361 TGAACAG
1 TGAACAG
1675368 TGAACAG
1 TGAACAG
1675375 TGA
1 TGA
1675378 GGGTATCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (7 bp):
TGAACAG
Found at i:1675942 original size:45 final size:45
Alignment explanation
Indices: 1675876--1676102 Score: 328
Period size: 45 Copynumber: 5.0 Consensus size: 45
1675866 ATAAAATTTC
* ** *
1675876 TTACCAATATACTTGTCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATACACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
** *
1675921 TTACCAGCACACTTACCATTTATTTCATAAGCTCGTAAGCTTATT
1 TTACCAATACACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
* *
1675966 TTACCAATACGCTTACCATTTATTCCATAAGCTAGTAAGCTTATT
1 TTACCAATACACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
* *
1676011 TTACCAATACACTTACCATTTATTCCATAAGATAGTAAGCTTATT
1 TTACCAATACACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
* * *
1676056 TTACCAATACACTTGCCATTTATTCTATAAGCTCGTAAACTTATT
1 TTACCAATACACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1676101 TT
1 TT
1676103 CATGCTTACC
Statistics
Matches: 163, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 163 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (45 bp):
TTACCAATACACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
Found at i:1677294 original size:39 final size:39
Alignment explanation
Indices: 1677251--1677371 Score: 92
Period size: 39 Copynumber: 3.2 Consensus size: 39
1677241 TTAGACAACT
1677251 CACACTACCTTTAAAGAATCAGTATTTTGTATTGATATA
1 CACACTACCTTTAAAGAATCAGTATTTTGTATTGATATA
* * * * * *
1677290 CACACTGGA-ATTT--A-ATTCTGT-TTATTCTGTTGA-AAA
1 CACACT--ACCTTTAAAGAATCAGTATT-TTGTATTGATATA
* *
1677326 CTAGACTCCCTTTAAAGAATCAGTATTTTGTATTGATATA
1 C-ACACTACCTTTAAAGAATCAGTATTTTGTATTGATATA
1677366 CACACT
1 CACACT
1677372 GGAATTTAAT
Statistics
Matches: 57, Mismatches: 15, Indels: 20
0.62 0.16 0.22
Matches are distributed among these distances:
36 8 0.14
37 16 0.28
38 2 0.04
39 22 0.39
40 8 0.14
41 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (39 bp):
CACACTACCTTTAAAGAATCAGTATTTTGTATTGATATA
Found at i:1677389 original size:76 final size:76
Alignment explanation
Indices: 1677258--1677409 Score: 288
Period size: 76 Copynumber: 2.0 Consensus size: 76
1677248 ACTCACACTA
1677258 CCTTTAAAGAATCAGTATTTTGTATTGATATACACACTGGAATTTAATTCTGTTTATTCTGTTGA
1 CCTTTAAAGAATCAGTATTTTGTATTGATATACACACTGGAATTTAATTCTGTTTATTCTGTTGA
1677323 AAACTAGACTC
66 AAACTAGACTC
1677334 CCTTTAAAGAATCAGTATTTTGTATTGATATACACACTGGAATTTAATT-TCGTTTATTCTGTTG
1 CCTTTAAAGAATCAGTATTTTGTATTGATATACACACTGGAATTTAATTCT-GTTTATTCTGTTG
1677398 AAAACTAGACTC
65 AAAACTAGACTC
1677410 GAATATGAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
75 1 0.01
76 74 0.99
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (76 bp):
CCTTTAAAGAATCAGTATTTTGTATTGATATACACACTGGAATTTAATTCTGTTTATTCTGTTGA
AAACTAGACTC
Found at i:1682509 original size:3 final size:3
Alignment explanation
Indices: 1682497--1682535 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1682487 TGTATTTTTG
1682497 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1682536 CAATGATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1689144 original size:16 final size:17
Alignment explanation
Indices: 1689104--1689144 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1689094 ACGAAATAGC
1689104 ATTTAAAATAATCTAAA
1 ATTTAAAATAATCTAAA
**
1689121 A-TCCAAATAAT-TAAA
1 ATTTAAAATAATCTAAA
1689136 ATTTAAAAT
1 ATTTAAAAT
1689145 TGATCGAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 3
0.73 0.15 0.12
Matches are distributed among these distances:
15 5 0.26
16 13 0.68
17 1 0.05
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTTAAAATAATCTAAA
Found at i:1690877 original size:30 final size:28
Alignment explanation
Indices: 1690841--1690904 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
1690831 GTAAATTTCG
*
1690841 AAAGTTTAGTGGTCAAAATATAAATTTATA
1 AAAGTTTAG-GGCCAAAATAT-AATTTATA
* * *
1690871 AAAGTTTAGGGCCAAAGTGTAATTTTTA
1 AAAGTTTAGGGCCAAAATATAATTTATA
1690899 AAAGTT
1 AAAGTT
1690905 ATATATTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 13 0.43
29 8 0.27
30 9 0.30
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (28 bp):
AAAGTTTAGGGCCAAAATATAATTTATA
Found at i:1691639 original size:23 final size:23
Alignment explanation
Indices: 1691613--1691657 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1691603 CACCACAGCT
*
1691613 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1691636 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1691658 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1692327 original size:19 final size:20
Alignment explanation
Indices: 1692290--1692327 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1692280 TTTTTTTATA
*
1692290 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1692310 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1692328 TCTAGCATTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1692905 original size:19 final size:19
Alignment explanation
Indices: 1692856--1692897 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1692846 CACGTTTAGA
1692856 AGAAGAGAAG-AGTGAAGAAG
1 AGAAGA-AAGAAG-GAAGAAG
*
1692876 ATAAGAAAGAAGGAAGAAG
1 AGAAGAAAGAAGGAAGAAG
1692895 AGA
1 AGA
1692898 TGAGAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.05
Consensus pattern (19 bp):
AGAAGAAAGAAGGAAGAAG
Found at i:1694752 original size:5 final size:5
Alignment explanation
Indices: 1694744--1694771 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1694734 TTTTGTATCG
1694744 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
1694772 AGTATATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:1695681 original size:29 final size:29
Alignment explanation
Indices: 1695637--1695702 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
1695627 TCTATTTTCG
*
1695637 TCTCCTAAAATCTTATAAGTTCAAGTTCC
1 TCTCCTAAAATCTTATAAATTCAAGTTCC
* * *
1695666 TCTCCTTAAATTTTATAAATTCAAGTTCA
1 TCTCCTAAAATCTTATAAATTCAAGTTCC
*
1695695 TCCCCTAA
1 TCTCCTAA
1695703 CATAAAATCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (29 bp):
TCTCCTAAAATCTTATAAATTCAAGTTCC
Found at i:1696290 original size:31 final size:31
Alignment explanation
Indices: 1696252--1696318 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1696242 ATGGTTTTAA
* * *
1696252 AAAAATTGAAAGTTTTGGTACTAAAATGGAC
1 AAAAATTGAAAGTTTAGATACTAAAATGAAC
*
1696283 AAAAATTGATAGTTTAGATACTAAAATGAAC
1 AAAAATTGAAAGTTTAGATACTAAAATGAAC
1696314 AAAAA
1 AAAAA
1696319 ATAATCGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (31 bp):
AAAAATTGAAAGTTTAGATACTAAAATGAAC
Found at i:1699050 original size:21 final size:22
Alignment explanation
Indices: 1699024--1699077 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1699014 ATGATGGGTG
1699024 GTATCGATACTCTTAT-CTAGA
1 GTATCGATACTCTTATACTAGA
* *
1699045 GTATCGATACTCTTGTACTAGG
1 GTATCGATACTCTTATACTAGA
*
1699067 GTATTGATACT
1 GTATCGATACT
1699078 ACCCTGAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (22 bp):
GTATCGATACTCTTATACTAGA
Found at i:1699215 original size:14 final size:14
Alignment explanation
Indices: 1699196--1699223 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1699186 GAGTACCGAT
1699196 ACCAAAATAGGCTA
1 ACCAAAATAGGCTA
1699210 ACCAAAATAGGCTA
1 ACCAAAATAGGCTA
1699224 CTGAAATTTG
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:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (14 bp):
ACCAAAATAGGCTA
Found at i:1705557 original size:19 final size:20
Alignment explanation
Indices: 1705524--1705561 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1705514 TAGTTTTTTA
*
1705524 ATTTTTAGAATTATATATAT
1 ATTTTTAGAAATATATATAT
1705544 ATTTTTA-AAATATATATA
1 ATTTTTAGAAATATATATA
1705562 GAACATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTTTTAGAAATATATATAT
Found at i:1705809 original size:39 final size:39
Alignment explanation
Indices: 1705766--1705879 Score: 153
Period size: 39 Copynumber: 2.9 Consensus size: 39
1705756 TATTTTAAAA
1705766 AATAATTTAGAATGTTAATGTGAAATAATTTAAGAAATT
1 AATAATTTAGAATGTTAATGTGAAATAATTTAAGAAATT
1705805 AATAATTTAGAATGTT-ATGGTAGAAA-AATTTAAGAAATT
1 AATAATTTAGAATGTTAAT-GT-GAAATAATTTAAGAAATT
** *
1705844 AGGAATTTAGAATGTTAGA-GTGAAATAATTTGAGAA
1 AATAATTTAGAATGTTA-ATGTGAAATAATTTAAGAA
1705880 TTATAAATAA
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
38 6 0.09
39 56 0.84
40 4 0.06
41 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (39 bp):
AATAATTTAGAATGTTAATGTGAAATAATTTAAGAAATT
Found at i:1705909 original size:2 final size:2
Alignment explanation
Indices: 1705902--1705926 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1705892 TTTTAATAAA
1705902 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1705927 ATAAATCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1708671 original size:15 final size:15
Alignment explanation
Indices: 1708651--1708680 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1708641 CATTGAGTCC
1708651 TTTATAATTTAAATT
1 TTTATAATTTAAATT
1708666 TTTATAATTTAAATT
1 TTTATAATTTAAATT
1708681 AATAGTGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTATAATTTAAATT
Found at i:1708765 original size:16 final size:16
Alignment explanation
Indices: 1708744--1708774 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1708734 ACAAAAACAA
*
1708744 TCAAAATCTAATACAG
1 TCAAAATCCAATACAG
1708760 TCAAAATCCAATACA
1 TCAAAATCCAATACA
1708775 AACAATGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.23, G:0.03, T:0.23
Consensus pattern (16 bp):
TCAAAATCCAATACAG
Found at i:1708983 original size:3 final size:3
Alignment explanation
Indices: 1708975--1709018 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1708965 TTGTAATCAT
1708975 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1709019 TTTACATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1709252 original size:29 final size:29
Alignment explanation
Indices: 1709204--1709259 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
1709194 TTTGAGAATA
1709204 ACATTACTGGAATGTAACATTA-TGTGAT
1 ACATTACTGGAATGTAACATTAGTGTGAT
*
1709232 ACATTACTGGGAATGTTACATTAGTGTG
1 ACATTACT-GGAATGTAACATTAGTGTG
1709260 TTTGGTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 8 0.32
29 13 0.52
30 4 0.16
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (29 bp):
ACATTACTGGAATGTAACATTAGTGTGAT
Found at i:1709588 original size:30 final size:32
Alignment explanation
Indices: 1709538--1709598 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
1709528 CATGTTTTAT
*
1709538 TTTAATTATAAATAATATT-AATTTTACATTA
1 TTTAATTAAAAATAATATTAAATTTTACATTA
*
1709569 TTTATTTAAAAAT-ATATTAAAATTTTACAT
1 TTTAATTAAAAATAATATT-AAATTTTACAT
1709599 CAACATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.19
31 11 0.42
32 10 0.38
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTAATTAAAAATAATATTAAATTTTACATTA
Found at i:1714366 original size:21 final size:23
Alignment explanation
Indices: 1714340--1714391 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1714330 GGTCATTGGT
*
1714340 ATAATTTACCTTT-TA-TTTTAA
1 ATAATTTACCTTTAAATTTTTAA
*
1714361 ATAATTTATCTTTAAATTTTTAA
1 ATAATTTACCTTTAAATTTTTAA
1714384 ATAATTTA
1 ATAATTTA
1714392 TAATTACACG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 12 0.44
22 1 0.04
23 14 0.52
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (23 bp):
ATAATTTACCTTTAAATTTTTAA
Found at i:1715625 original size:17 final size:17
Alignment explanation
Indices: 1715603--1715646 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
1715593 ACTATAAGAT
*
1715603 AATGTCATGCCATCATA
1 AATGTCACGCCATCATA
1715620 AATGTCACGCCATCATA
1 AATGTCACGCCATCATA
1715637 AATGTCACGC
1 AATGTCACGC
1715647 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (17 bp):
AATGTCACGCCATCATA
Found at i:1715904 original size:2 final size:2
Alignment explanation
Indices: 1715897--1715987 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
1715887 TCAAGTAATA
1715897 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
1715939 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
1715981 AT AT AT A
1 AT AT AT A
1715988 CGTTACAATA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1718084 original size:16 final size:16
Alignment explanation
Indices: 1718065--1718100 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1718055 GTTGTTTATG
*
1718065 TGATATTTAATTATAT
1 TGATAGTTAATTATAT
1718081 TGATAGTTAATTATAT
1 TGATAGTTAATTATAT
1718097 TGAT
1 TGAT
1718101 GTGATAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (16 bp):
TGATAGTTAATTATAT
Found at i:1718273 original size:14 final size:14
Alignment explanation
Indices: 1718254--1718283 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1718244 GTCTATTTTT
*
1718254 TTTAAATTATCTTA
1 TTTAAAATATCTTA
1718268 TTTAAAATATCTTA
1 TTTAAAATATCTTA
1718282 TT
1 TT
1718284 AGACAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAAAATATCTTA
Found at i:1721576 original size:3 final size:3
Alignment explanation
Indices: 1721562--1721642 Score: 155
Period size: 3 Copynumber: 27.3 Consensus size: 3
1721552 TGTAATTATT
1721562 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1721609 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1721643 TGTCCGTGCG
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 75 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1721941 original size:60 final size:60
Alignment explanation
Indices: 1721877--1721991 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
1721867 ATAGCCCCCA
** * *
1721877 ACTATAAGACATTTTTTTATTTAGTCCC-CTAACTATTAAAAGTTACAAAATGATCCTCTG
1 ACTATAAGACATTACTTTATTGAGTCCCTC-AACTAATAAAAGTTACAAAATGATCCTCTG
* * * * *
1721937 ACTATAGGACGTTACTTTCTTGAGTCCTTCGACTAATAAAAGTTACAAAATGATC
1 ACTATAAGACATTACTTTATTGAGTCCCTCAACTAATAAAAGTTACAAAATGATC
1721992 ACCTGACCAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
60 44 0.98
61 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (60 bp):
ACTATAAGACATTACTTTATTGAGTCCCTCAACTAATAAAAGTTACAAAATGATCCTCTG
Found at i:1725526 original size:51 final size:51
Alignment explanation
Indices: 1725410--1725664 Score: 289
Period size: 51 Copynumber: 4.8 Consensus size: 51
1725400 CAAATGACGG
*
1725410 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG----ATCTTCAACAAACGT
* *
1725465 GTCCGCTCCCTATTACTTCAGAGAGTATAGGACTCGATCTTCAACAAATGT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAACAAACGT
* * ** * * *
1725516 TTCTGCTCCCTATTTGTTCA-AGGAGTATAGAACTCGAACAATCTT-AATAAAACAT
1 GTCCGCTCCCTATTCCTTCAGA-GAGTATAGGACTCG----ATCTTCAA-CAAACGT
* * *
1725571 GTTCGCTCTCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAACAAACAT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAACAAACGT
1725622 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCA
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCA
1725665 TAAAATGAGT
Statistics
Matches: 171, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
50 1 0.01
51 95 0.56
52 2 0.01
54 2 0.01
55 70 0.41
56 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (51 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAACAAACGT
Found at i:1725584 original size:106 final size:106
Alignment explanation
Indices: 1725410--1725658 Score: 358
Period size: 106 Copynumber: 2.3 Consensus size: 106
1725400 CAAATGACGG
* *
1725410 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCCGCTCCC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAACATGTCCGCTCCC
**
1725475 TATTACTTCAGAGAGTATAGGACTCGATCTTCAACAAATGT
66 TATTACTTCAGAGAGTATAGGACTCGATCTTCAACAAACAT
* * ** *
1725516 TTCTGCTCCCTATTTGTTCA-AGGAGTATAGAACTCGAACAATCTT-AATAAAACATGTTCGCTC
1 GTCCGCTCCCTATTCCTTCAGA-GAGTATAGAACTCGAACAATCTTCAA-AAAACATGTCCGCTC
* *
1725579 TCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAACAAACAT
64 CCTATTACTTCAGAGAGTATAGGACTCGATCTTCAACAAACAT
*
1725622 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGA
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGA
1725659 TCTTCATAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
105 3 0.02
106 120 0.97
107 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (106 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAACATGTCCGCTCCC
TATTACTTCAGAGAGTATAGGACTCGATCTTCAACAAACAT
Found at i:1725719 original size:37 final size:37
Alignment explanation
Indices: 1725675--1725784 Score: 148
Period size: 37 Copynumber: 3.0 Consensus size: 37
1725665 TAAAATGAGT
*
1725675 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTAAA
* **
1725712 TTTCTTCACTACTCTTCTATGAAGGCTTAAGTTTAAA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTAAA
* * * *
1725749 TTGCTTCACTGCTCTTTCGTGAAGGATTAAGATTAA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTAA
1725785 CTTGTTTCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTAAA
Found at i:1727080 original size:8 final size:8
Alignment explanation
Indices: 1727067--1727215 Score: 86
Period size: 8 Copynumber: 18.6 Consensus size: 8
1727057 CCTTTTATTT
1727067 ATTTTTTC
1 ATTTTTTC
*
1727075 ATTTTTTT
1 ATTTTTTC
*
1727083 TTCTTTTTC
1 AT-TTTTTC
1727092 ATTTTTCTC
1 ATTTTT-TC
*
1727101 -TTTCTTC
1 ATTTTTTC
*
1727108 -TTTCTTC
1 ATTTTTTC
1727115 -TTTTTTC
1 ATTTTTTC
1727122 ATTATTATT-
1 ATT-TT-TTC
1727131 ATTATTTT-
1 ATT-TTTTC
1727139 -TTCCTTTTC
1 ATT--TTTTC
1727148 ATTTTTTC
1 ATTTTTTC
1727156 ATCATTTTTC
1 AT--TTTTTC
1727166 ATTTTTTC
1 ATTTTTTC
1727174 -TCATTTTTC
1 AT--TTTTTC
1727183 ---TTTTC
1 ATTTTTTC
1727188 ATTTTTTC
1 ATTTTTTC
1727196 ATTTTTTC
1 ATTTTTTC
1727204 ATTTTTT-
1 ATTTTTTC
1727211 ATTTT
1 ATTTT
1727216 CAGGCGAAAT
Statistics
Matches: 119, Mismatches: 7, Indels: 31
0.76 0.04 0.20
Matches are distributed among these distances:
5 5 0.04
7 23 0.19
8 57 0.48
9 22 0.18
10 12 0.10
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTTC
Found at i:1727089 original size:10 final size:11
Alignment explanation
Indices: 1727059--1727194 Score: 52
Period size: 11 Copynumber: 12.1 Consensus size: 11
1727049 TGAACCCTCC
1727059 TTTT-ATTTATT
1 TTTTCATTT-TT
1727070 TTTTCATTTTT
1 TTTTCATTTTT
*
1727081 TTTTCTTTTTCAT
1 TTTTCATTTT--T
1727094 TTTTC-TCTTTCT
1 TTTTCAT-TTT-T
*
1727106 TCTTTC-TTCTT
1 T-TTTCATTTTT
*
1727117 TTTTCA-TTAT
1 TTTTCATTTTT
*
1727127 TATT-ATTATTT
1 TTTTCATT-TTT
* *
1727138 TTTCCTTTTCATT
1 TTTTCATTT--TT
**
1727151 TTTTCA-TCAT
1 TTTTCATTTTT
1727161 TTTTCA-TTTT
1 TTTTCATTTTT
*
1727171 TTCTCATTTTT
1 TTTTCATTTTT
1727182 CTTTTCATTTTT
1 -TTTTCATTTTT
1727194 T
1 T
1727195 CATTTTTTCA
Statistics
Matches: 94, Mismatches: 18, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
9 1 0.01
10 24 0.26
11 27 0.29
12 22 0.23
13 20 0.21
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCATTTTT
Found at i:1727210 original size:10 final size:10
Alignment explanation
Indices: 1727149--1727210 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
1727139 TTCCTTTTCA
*
1727149 TTTTTTCATC
1 TTTTTTCATT
*
1727159 ATTTTTCATT
1 TTTTTTCATT
*
1727169 TTTTCTCATTT
1 TTTTTTCA-TT
1727180 TTCTTTTCA--
1 TT-TTTTCATT
1727189 TTTTTTCA--
1 TTTTTTCATT
1727197 TTTTTTCATT
1 TTTTTTCATT
1727207 TTTT
1 TTTT
1727211 ATTTTCAGGC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 14 0.33
9 2 0.05
10 18 0.42
11 4 0.09
12 5 0.12
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:1727215 original size:22 final size:23
Alignment explanation
Indices: 1727157--1727215 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 23
1727147 CATTTTTTCA
1727157 TCATTTTTCATTTTTTCTCATTTT
1 TCATTTTTCA-TTTTTCTCATTTT
1727181 TC--TTTTCATTTTT-TCATTTTT
1 TCATTTTTCATTTTTCTCA-TTTT
*
1727202 TCATTTTTTATTTT
1 TCATTTTTCATTTT
1727216 CAGGCGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.10
21 11 0.35
22 6 0.19
23 9 0.29
24 2 0.06
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.75
Consensus pattern (23 bp):
TCATTTTTCATTTTTCTCATTTT
Found at i:1738734 original size:27 final size:27
Alignment explanation
Indices: 1738695--1738748 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1738685 AAATCAGAAA
*
1738695 TAAATCAGTGACCTAAACATAAAATAC
1 TAAATCAGCGACCTAAACATAAAATAC
*
1738722 TAAATCAGCGACCTAAATATAAAATAC
1 TAAATCAGCGACCTAAACATAAAATAC
1738749 GTATAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (27 bp):
TAAATCAGCGACCTAAACATAAAATAC
Found at i:1743785 original size:13 final size:14
Alignment explanation
Indices: 1743768--1743816 Score: 64
Period size: 13 Copynumber: 3.4 Consensus size: 14
1743758 GAATTATTTA
1743768 AATTTTATATTTTT
1 AATTTTATATTTTT
*
1743782 ATTTTTA-ATTTTT
1 AATTTTATATTTTT
1743795 AATTTTATATATTCTT
1 AATTTTATAT-TT-TT
1743811 AATTTT
1 AATTTT
1743817 TCTAGTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 12 0.40
14 8 0.27
15 2 0.07
16 8 0.27
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (14 bp):
AATTTTATATTTTT
Found at i:1743805 original size:29 final size:30
Alignment explanation
Indices: 1743752--1743817 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
1743742 ACGTAAAAAA
*
1743752 TATTTTGAATTATTTAAATTTTATATT-TT
1 TATTTTTAATTATTTAAATTTTATATTCTT
*
1743781 TATTTTTAATT-TTTAATTTTATATATTCTT
1 TATTTTTAATTATTTAAATTT-TATATTCTT
*
1743811 AATTTTT
1 TATTTTT
1743818 CTAGTTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 8 0.25
29 16 0.50
30 8 0.25
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (30 bp):
TATTTTTAATTATTTAAATTTTATATTCTT
Found at i:1781121 original size:22 final size:22
Alignment explanation
Indices: 1781064--1781114 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1781054 AATATTTTCA
1781064 ATTAATTTAGTTAATTCAATCG
1 ATTAATTTAGTTAATTCAATCG
* **
1781086 ATTAATTTATTTAATTTGATCG
1 ATTAATTTAGTTAATTCAATCG
1781108 ATTAATT
1 ATTAATT
1781115 CGGTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (22 bp):
ATTAATTTAGTTAATTCAATCG
Found at i:1782249 original size:164 final size:165
Alignment explanation
Indices: 1782056--1782384 Score: 651
Period size: 164 Copynumber: 2.0 Consensus size: 165
1782046 ATTGACATGG
1782056 TTTATTAAGGGGTCAGAGTTTAGGATTTATATTTCATTGATTATGATTTAAGATTTAGCTTTTAA
1 TTTATTAAGGGGTCAGAGTTTAGGATTTATATTTCATTGATTATGATTTAAGATTTAGCTTTTAA
1782121 GGCTTAGGAATAACAATATTTAAACAATGTTTAAGAAAATAAATATTCCACAGGTAGTATTGTAT
66 GGCTTAGGAATAACAATATTTAAACAATGTTTAAGAAAATAAATATTCCACAGGTAGTATTGTAT
1782186 CAAATACCCA-CTTACGTGAAATGTAAAGATATTT
131 CAAATACCCACCTTACGTGAAATGTAAAGATATTT
1782220 TTTATTAAGGGGTCAGAGTTTAGGATTTATATTTCATTGATTATGATTTAAGATTTAGCTTTTAA
1 TTTATTAAGGGGTCAGAGTTTAGGATTTATATTTCATTGATTATGATTTAAGATTTAGCTTTTAA
1782285 GGCTTAGGAATAACAATATTTAAACAATGTTTAAGAAAATAAATATTCCACAGGTAGTATTGTAT
66 GGCTTAGGAATAACAATATTTAAACAATGTTTAAGAAAATAAATATTCCACAGGTAGTATTGTAT
1782350 CAAATACCCACCTTACGTGAAATGTAAAGATATTT
131 CAAATACCCACCTTACGTGAAATGTAAAGATATTT
1782385 ACTGGAAAAA
Statistics
Matches: 164, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
164 140 0.85
165 24 0.15
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (165 bp):
TTTATTAAGGGGTCAGAGTTTAGGATTTATATTTCATTGATTATGATTTAAGATTTAGCTTTTAA
GGCTTAGGAATAACAATATTTAAACAATGTTTAAGAAAATAAATATTCCACAGGTAGTATTGTAT
CAAATACCCACCTTACGTGAAATGTAAAGATATTT
Found at i:1782945 original size:30 final size:29
Alignment explanation
Indices: 1782890--1782966 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
1782880 GTGACTAAAA
* * *
1782890 TATAAATTTTGAATGTTTAGTGACCAAAG
1 TATAAATTTTAAAAGTTTAGGGACCAAAG
1782919 TATAAATTTGTAAAAGTTTAGGGACCAAAG
1 TATAAATTT-TAAAAGTTTAGGGACCAAAG
* *
1782949 TGTAATTTTTAAAAGTTT
1 TATAAATTTTAAAAGTTT
1782967 TATATTTTGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 18 0.43
30 24 0.57
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (29 bp):
TATAAATTTTAAAAGTTTAGGGACCAAAG
Found at i:1782955 original size:29 final size:30
Alignment explanation
Indices: 1782890--1782966 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
1782880 GTGACTAAAA
* * *
1782890 TATAAATTT-TGAATGTTTAGTGACCAAAG
1 TATAAATTTGTAAAAGTTTAGGGACCAAAG
1782919 TATAAATTTGTAAAAGTTTAGGGACCAAAG
1 TATAAATTTGTAAAAGTTTAGGGACCAAAG
* *
1782949 TGT-AATTTTTAAAAGTTT
1 TATAAATTTGTAAAAGTTT
1782967 TATATTTTGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 23 0.55
30 19 0.45
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (30 bp):
TATAAATTTGTAAAAGTTTAGGGACCAAAG
Found at i:1784081 original size:36 final size:35
Alignment explanation
Indices: 1784040--1784156 Score: 110
Period size: 36 Copynumber: 3.2 Consensus size: 35
1784030 CTAGAGACAG
*
1784040 TTTTTCTTATAAATAAATTTTGTCTCGCTTGAAACA
1 TTTTTCTTA-AAACAAATTTTGTCTCGCTTGAAACA
*
1784076 TTTTTCTCTAAAAACAAATTTTGTCTCGTTTGAGATA-A
1 TTTTTCT-T-AAAACAAATTTTGTCTCGCTTGA-A-ACA
* * * ** *
1784114 TTTCTCTCAAAACAAATTTTGTATTACTTGAGACA
1 TTTTTCTTAAAACAAATTTTGTCTCGCTTGAAACA
1784149 TTTTTCTT
1 TTTTTCTT
1784157 TTGAGATGCA
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
34 1 0.02
35 7 0.11
36 26 0.40
37 21 0.32
38 9 0.14
39 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.47
Consensus pattern (35 bp):
TTTTTCTTAAAACAAATTTTGTCTCGCTTGAAACA
Found at i:1784095 original size:37 final size:37
Alignment explanation
Indices: 1784027--1784155 Score: 136
Period size: 37 Copynumber: 3.5 Consensus size: 37
1784017 AAGTGTCGTA
* * *
1784027 TCGCTAGAGACAGTTTTTCT-TATAAATAAATTTTGTC
1 TCGCTTGAGACA-TTTTTCTCTAAAAACAAATTTTGTC
*
1784064 TCGCTTGAAACATTTTTCTCTAAAAACAAATTTTGTC
1 TCGCTTGAGACATTTTTCTCTAAAAACAAATTTTGTC
* * * * *
1784101 TCGTTTGAGATA-ATTTCTCTCAAAACAAATTTTGTA
1 TCGCTTGAGACATTTTTCTCTAAAAACAAATTTTGTC
**
1784137 TTACTTGAGACATTTTTCT
1 TCGCTTGAGACATTTTTCT
1784156 TTTGAGATGC
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
36 36 0.48
37 39 0.52
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (37 bp):
TCGCTTGAGACATTTTTCTCTAAAAACAAATTTTGTC
Found at i:1784246 original size:36 final size:36
Alignment explanation
Indices: 1784206--1784276 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
1784196 ATTGATATCA
** *
1784206 CTTGAGATTATTTCTCTAAAAACAAATTTTGTCTCG
1 CTTGAGACAATTTCTCTAAAAACAAATTTCGTCTCG
*
1784242 CTTGAGACAATTTCTCTCAAAACAAATTTCGTCTC
1 CTTGAGACAATTTCTCTAAAAACAAATTTCGTCTC
1784277 AGTTGAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (36 bp):
CTTGAGACAATTTCTCTAAAAACAAATTTCGTCTCG
Found at i:1784289 original size:138 final size:138
Alignment explanation
Indices: 1784078--1784520 Score: 637
Period size: 138 Copynumber: 3.2 Consensus size: 138
1784068 TTGAAACATT
* * * * *
1784078 TTTCTCTAAAAACAAATTTTGTCTCGTTTGAGATAATTTCTCTCAAAACAAATTTTGTATTACTT
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATTTTGTCTCAGTT
* * *
1784143 GAGACATTTTTCTTTTGAGATGCAAATTTCTAATTCTTTTCACCTGAAACAAAATTGATATCACT
66 GAGACATTTTTCCTTTGAGATGCAAATTTCGAATTCTTTTCACCTGAAACAAAATTGATCTCACT
1784208 TGAGATTA
131 TGAGATTA
*
1784216 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATTTCGTCTCAGTT
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATTTTGTCTCAGTT
* * * *
1784281 GAAACATTTTTCCTTTGAGATGCAAATTTCGAATTCGTTCCACCTGAAACTAAATTGATCTCACT
66 GAGACATTTTTCCTTTGAGATGCAAATTTCGAATTCTTTTCACCTGAAACAAAATTGATCTCACT
1784346 TGAGATTA
131 TGAGATTA
* *
1784354 TTTCTCTAGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTCAAAATAAATTTTGTCTC-GCT
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATTTTGTCTCAG-T
* *
1784418 TGAGACATTTTTCCTTTGAGATGCAAATTTCGAATTCGTTTT-ACTTGAAACAAAATTAATCTCA
65 TGAGACATTTTTCCTTTGAGATGCAAATTTCGAATTC-TTTTCACCTGAAACAAAATTGATCTCA
*
1784482 GTTGAGATT-
129 CTTGAGATTA
* * *
1784491 GTTCTC--AAAA-AAATTTCGTCTCACTTGAGA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGA
1784521 TAGTTTTTCT
Statistics
Matches: 276, Mismatches: 27, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
134 18 0.07
135 3 0.01
137 6 0.02
138 247 0.89
139 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (138 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATTTTGTCTCAGTT
GAGACATTTTTCCTTTGAGATGCAAATTTCGAATTCTTTTCACCTGAAACAAAATTGATCTCACT
TGAGATTA
Found at i:1784384 original size:36 final size:36
Alignment explanation
Indices: 1784339--1784424 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
1784329 ACTAAATTGA
* **
1784339 TCTCACTTGAGATTATTTCTCT-AGAAACAAATTTTG
1 TCTCGCTTGAGACAATTTCTCTCA-AAACAAATTTTG
*
1784375 TCTCGCTTGAGACAATTTCTCTCAAAATAAATTTTG
1 TCTCGCTTGAGACAATTTCTCTCAAAACAAATTTTG
1784411 TCTCGCTTGAGACA
1 TCTCGCTTGAGACA
1784425 TTTTTCCTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 44 0.98
37 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
TCTCGCTTGAGACAATTTCTCTCAAAACAAATTTTG
Found at i:1784653 original size:63 final size:65
Alignment explanation
Indices: 1784575--1784701 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
1784565 AAATTGATAA
1784575 AACCTTTAAGATTGTTTCCCTTGAAACAA-A-TTT-TCTCTCTTGAGACAGTTTCTCTTGAAACA
1 AACCTTTAAGATTGTTTCCCTTGAAA-AACATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1784637 T
65 T
*
1784638 AACCTTTGAGATTGTTTCCCTTGAAAAACATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 AACCTTTAAGATTGTTTCCCTTGAAAAACATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1784702 AATTATCCCT
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
62 2 0.03
63 26 0.43
64 3 0.05
65 29 0.48
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (65 bp):
AACCTTTAAGATTGTTTCCCTTGAAAAACATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAT
Found at i:1784660 original size:29 final size:28
Alignment explanation
Indices: 1784574--1784663 Score: 81
Period size: 34 Copynumber: 3.0 Consensus size: 28
1784564 AAAATTGATA
*
1784574 AAACCTTTAAGATTGTTTCCCTTGAAAC
1 AAACCTTTGAGATTGTTTCCCTTGAAAC
** *
1784602 AAATTTTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 AAA----C-CT-TTGAGATTGTTTCCCTTGAAAC
1784636 ATAACCTTTGAGATTGTTTCCCTTGAAA
1 A-AACCTTTGAGATTGTTTCCCTTGAAA
1784664 AACATTTTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
28 3 0.06
29 18 0.38
30 2 0.04
31 1 0.02
32 1 0.02
33 2 0.04
34 19 0.40
35 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (28 bp):
AAACCTTTGAGATTGTTTCCCTTGAAAC
Found at i:1784782 original size:40 final size:42
Alignment explanation
Indices: 1784727--1784832 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 42
1784717 TGGTCAGTCA
* *
1784727 TCCTCATCACGTAGGAACCATGTCATCC-ACCGA-CCAGATT
1 TCCTCATCACGTAGGAACCATGTCATCCTACAGAGCCAGACT
* * * *
1784767 TCCTCATCACGTAGGAGCCGA-GTCATCCTTAGATAGCTAGACT
1 TCCTCATCACGTAGGAACC-ATGTCATCC-TACAGAGCCAGACT
1784810 TCCTCATCACGTAGGAACCATGT
1 TCCTCATCACGTAGGAACCATGT
1784833 TATCTCTATT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
40 25 0.46
41 1 0.02
42 3 0.06
43 25 0.46
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (42 bp):
TCCTCATCACGTAGGAACCATGTCATCCTACAGAGCCAGACT
Found at i:1784952 original size:138 final size:138
Alignment explanation
Indices: 1784704--1785177 Score: 608
Period size: 138 Copynumber: 3.4 Consensus size: 138
1784694 TTGAAACAAA
* * ** *
1784704 TTATCCCTAGAGATGGTCAGTCATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGATTTC
1 TTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGATCTC
* * *
1784769 CTCATCACGTAGGAGCCGAGTCATCCTTAGATAGCTAGACTTCCTCATCACGTAGGAACCATGTT
66 CTCATCACGTAGGAGCCGAGTCACCCTTAGATAGCCAGACTTCCTCATCACGTAGGAACCGTGTT
*
1784834 ATCTCTAT
131 ATCTCAAT
*
1784842 TTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCATGTCATCTACCGACCAGATCTC
1 TTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGATCTC
* * * *
1784907 CTCATCATGTAGGAGTCC-TGTCACCCGTAGATAGCCAGACTTCCTCATGACGTAGGAACCGTGT
66 CTCATCACGTAGGAG-CCGAGTCACCCTTAGATAGCCAGACTTCCTCATCACGTAGGAACCGTGT
*
1784971 TATCTCCAT
130 TATCTCAAT
* * * * * * **
1784980 TTATCCCTAAAGATGACTAGACGTCCTCATAACGTAGAAACTGTGTCATCCACCGACCAGATCTC
1 TTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGATCTC
* * * * * *
1785045 ATCATCACGTAGGAGCCGCGCCATCCTCCTTAGATTGCCAGACTTCCTCATCGCGTAGGAATCGT
66 CTCATCACGTAGGAGCCGAGTCA--C-CCTTAGATAGCCAGACTTCCTCATCACGTAGGAACCGT
1785110 GTTATCTCAAT
128 GTTATCTCAAT
* * **
1785121 TTATCCCTAAAGATGGCCAAACGTCCTCATCACGTTGGAATAATGTCATCCACCGAC
1 TTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCATGTCATCCACCGAC
1785178 GATTTGGTGA
Statistics
Matches: 289, Mismatches: 42, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
137 2 0.01
138 193 0.67
139 2 0.01
140 1 0.00
141 91 0.31
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (138 bp):
TTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGATCTC
CTCATCACGTAGGAGCCGAGTCACCCTTAGATAGCCAGACTTCCTCATCACGTAGGAACCGTGTT
ATCTCAAT
Found at i:1788528 original size:37 final size:37
Alignment explanation
Indices: 1788485--1788578 Score: 118
Period size: 37 Copynumber: 2.5 Consensus size: 37
1788475 CCTATTGCAT
* * *
1788485 TTGGTTTATGTATGT-AAGCATAGTGTACTGGTTTGGG
1 TTGGTTTGTGTATATGAA-CATAGTGTACTGGTTAGGG
* *
1788522 TTGGTTTGGGTATATGAACATAGTGTATTGGTTAGGG
1 TTGGTTTGTGTATATGAACATAGTGTACTGGTTAGGG
*
1788559 TTGGTTTGTGTATATAAACA
1 TTGGTTTGTGTATATGAACA
1788579 GTGTATTGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
37 47 0.96
38 2 0.04
ACGTcount: A:0.22, C:0.04, G:0.31, T:0.43
Consensus pattern (37 bp):
TTGGTTTGTGTATATGAACATAGTGTACTGGTTAGGG
Found at i:1788589 original size:35 final size:37
Alignment explanation
Indices: 1788506--1788589 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
1788496 ATGTAAGCAT
* * *
1788506 AGTGTACTGGTTTGGGTTGGTTTGGGTATATGAACAT
1 AGTGTATTGGTTAGGGTTGGTTTGGGTATATGAACAC
*
1788543 AGTGTATTGGTTAGGGTTGGTTTGTGTATAT-AA-AC
1 AGTGTATTGGTTAGGGTTGGTTTGGGTATATGAACAC
1788578 AGTGTATTGGTT
1 AGTGTATTGGTT
1788590 TGTGTATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 13 0.30
36 2 0.05
37 28 0.65
ACGTcount: A:0.20, C:0.04, G:0.33, T:0.43
Consensus pattern (37 bp):
AGTGTATTGGTTAGGGTTGGTTTGGGTATATGAACAC
Found at i:1788608 original size:27 final size:27
Alignment explanation
Indices: 1788559--1788740 Score: 157
Period size: 27 Copynumber: 7.4 Consensus size: 27
1788549 TTGGTTAGGG
1788559 TTGGTTTGTGTATATAAAC--AGTGTA
1 TTGGTTTGTGTATATAAACATAGTGTA
1788584 TTGGTTTGTGTATATAAACATAGTGTA
1 TTGGTTTGTGTATATAAACATAGTGTA
* * *
1788611 TTGGTTTGTGTATACAGACATACTGTA
1 TTGGTTTGTGTATATAAACATAGTGTA
*
1788638 TTGCTTTGTG----T----ATAGTGTA
1 TTGGTTTGTGTATATAAACATAGTGTA
* *
1788657 TAGGTTTGTGTATATAGACATAGTGTA
1 TTGGTTTGTGTATATAAACATAGTGTA
*
1788684 TTGCTTTGTG----T----ATAGTGTA
1 TTGGTTTGTGTATATAAACATAGTGTA
* *
1788703 TAGGTTTGTGTATATAAACGTAGTGTA
1 TTGGTTTGTGTATATAAACATAGTGTA
1788730 TTGGTTTGTGT
1 TTGGTTTGTGT
1788741 TTAGCTGGTG
Statistics
Matches: 125, Mismatches: 14, Indels: 34
0.72 0.08 0.20
Matches are distributed among these distances:
19 31 0.25
23 3 0.02
25 19 0.15
27 72 0.58
ACGTcount: A:0.24, C:0.05, G:0.25, T:0.46
Consensus pattern (27 bp):
TTGGTTTGTGTATATAAACATAGTGTA
Found at i:1788656 original size:46 final size:46
Alignment explanation
Indices: 1788603--1788740 Score: 222
Period size: 46 Copynumber: 3.0 Consensus size: 46
1788593 GTATATAAAC
* * *
1788603 ATAGTGTATTGGTTTGTGTATACAGACATACTGTATTGCTTTGTGT
1 ATAGTGTATAGGTTTGTGTATATAGACATAGTGTATTGCTTTGTGT
1788649 ATAGTGTATAGGTTTGTGTATATAGACATAGTGTATTGCTTTGTGT
1 ATAGTGTATAGGTTTGTGTATATAGACATAGTGTATTGCTTTGTGT
* * *
1788695 ATAGTGTATAGGTTTGTGTATATAAACGTAGTGTATTGGTTTGTGT
1 ATAGTGTATAGGTTTGTGTATATAGACATAGTGTATTGCTTTGTGT
1788741 TTAGCTGGTG
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (46 bp):
ATAGTGTATAGGTTTGTGTATATAGACATAGTGTATTGCTTTGTGT
Found at i:1788664 original size:19 final size:19
Alignment explanation
Indices: 1788642--1788716 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
1788632 ACTGTATTGC
1788642 TTTGTGTATAGTGTATAGG
1 TTTGTGTATAGTGTATAGG
* *
1788661 TTTGTGTATATAGACATAGTGTATTGC
1 TTTGTG--TAT----A--GTGTATAGG
1788688 TTTGTGTATAGTGTATAGG
1 TTTGTGTATAGTGTATAGG
1788707 TTTGTGTATA
1 TTTGTGTATA
1788717 TAAACGTAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
19 23 0.52
21 4 0.09
25 4 0.09
27 13 0.30
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.48
Consensus pattern (19 bp):
TTTGTGTATAGTGTATAGG
Found at i:1788727 original size:73 final size:74
Alignment explanation
Indices: 1788561--1788740 Score: 201
Period size: 73 Copynumber: 2.5 Consensus size: 74
1788551 GGTTAGGGTT
*
1788561 GGTTTGTGTATATAAAC-AGTGTATTGGTTTGTGTATATAAACATAGTGTATTGGTTTGTGTATA
1 GGTTTGTGTATATAAACTAGTGTATTGGTTTGTGTATATAAACATAGTGTATTGCTTTGTGTATA
1788625 CAGACATAC
66 CAGACATAC
* * ** * *
1788634 TGTATTGCT-T-TGTGTA-TAGTGTATAGGTTTGTGTATATAGACATAGTGTATTGCTTTGTGTA
1 GGT-TTG-TGTATATAAACTAGTGTATTGGTTTGTGTATATAAACATAGTGTATTGCTTTGTGTA
** *
1788696 TAGTG-TATA-
64 TACAGACATAC
1788705 GGTTTGTGTATATAAACGTAGTGTATTGGTTTGTGT
1 GGTTTGTGTATATAAAC-TAGTGTATTGGTTTGTGT
1788741 TTAGCTGGTG
Statistics
Matches: 85, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
69 1 0.01
70 4 0.05
71 5 0.06
72 3 0.04
73 67 0.79
74 4 0.05
75 1 0.01
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (74 bp):
GGTTTGTGTATATAAACTAGTGTATTGGTTTGTGTATATAAACATAGTGTATTGCTTTGTGTATA
CAGACATAC
Found at i:1790887 original size:22 final size:21
Alignment explanation
Indices: 1790854--1790897 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
1790844 AATTATGTAT
1790854 ATTTTAATTCTAAAGTCTAAA
1 ATTTTAATTCTAAAGTCTAAA
*
1790875 ATTTTAAATTCTAAATTCTAAA
1 ATTTT-AATTCTAAAGTCTAAA
1790897 A
1 A
1790898 CCCTTAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTTTAATTCTAAAGTCTAAA
Found at i:1791064 original size:12 final size:12
Alignment explanation
Indices: 1791047--1791076 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1791037 GATAACTTTC
1791047 TATTATTTGTGT
1 TATTATTTGTGT
1791059 TATTATTTGTGT
1 TATTATTTGTGT
1791071 TATTAT
1 TATTAT
1791077 AAAGTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (12 bp):
TATTATTTGTGT
Found at i:1796283 original size:35 final size:34
Alignment explanation
Indices: 1796209--1796293 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
1796199 AAACCATGCA
*
1796209 GGGGGAATCTGTACCCGGGGAATCGATACCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
*
1796243 GGGGGAATATGTTCCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATA-CCCCTG
1796278 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
1796294 CCTGGGGGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 26 0.55
35 21 0.45
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.20
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:1796301 original size:21 final size:21
Alignment explanation
Indices: 1796259--1796319 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1796249 ATATGTTCCC
1796259 GGGGAATC-GATACCCCCT-GG
1 GGGGAATCTG-TACCCCCTGGG
*
1796279 GGGGAATCTGTTCCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
1796300 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
1796320 ACAATCTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.15, C:0.30, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:1797459 original size:455 final size:455
Alignment explanation
Indices: 1796602--1797515 Score: 1738
Period size: 455 Copynumber: 2.0 Consensus size: 455
1796592 GTCAATTATT
*
1796602 ATTTTGAAGGAAAAGCTAGTTTTGGCTCCAATTGTTCAATCACTCAATTGAGATTTCCCTTTCAA
1 ATTTTAAAGGAAAAGCTAGTTTTGGCTCCAATTGTTCAATCACTCAATTGAGATTTCCCTTTCAA
* *
1796667 AAATTATGTATGATGTATCAGACATAAGGTTTGGAGCAGTTATTGGGCAGAAAATCGACAAAGAA
66 AAATTATGTATGATGTATCAGACACAAGGTTTGGAGCAATTATTGGGCAGAAAATCGACAAAGAA
*
1796732 CCTCATGAAATAGGTTACACATCAAGAACCTTACCTTCAACTCAACAAAATTACTCGACCACCGA
131 CCTCATGAAATAGGTTACACAACAAGAACCTTACCTTCAACTCAACAAAATTACTCGACCACCGA
*
1796797 AAAAGAATTATTTGTCATTGTCTTTGCCTTAGAAAAATTTAGATCTTATCTTCTCGACACTAAAA
196 AAAAGAATTATTTGTCATTGTCTTTGCCTTAGAAAAATTTAGATCATATCTTCTCGACACTAAAA
* *
1796862 TGATTTTTTTACTGATCATGCAACTTTGAAGTATTTGATGAGCAAAAAGGAGAAGAAGGCAAGAA
261 TGATTTTTTTACTGATCATGCAACTTTGAAGTATTTGATGAGAAAAAAGGAGAAGAAGCCAAGAA
1796927 TAATTTTTTGGATCTTTCTTTTGCAAGAATTTGATCTAGAAATTAAGAACAAGAAATGATGCAAA
326 TAATTTTTTGGATCTTTCTTTTGCAAGAATTTGATCTAGAAATTAAGAACAAGAAATGATGCAAA
1796992 AATTTTGTGGCCGATCACCTAAGTCAACTTCCACTCTCCACGTCTAATCCACAACTTCGAGAAGA
391 AATTTTGTGGCCGATCACCTAAGTCAACTTCCACTCTCCACGTCTAATCCACAACTTCGAGAAGA
1797057 ATTTTAAAGGAAAAGCTAGTTTTGGCTCCAATTGTTCAATCACTCAATTGAGATTTCCCTTTCAA
1 ATTTTAAAGGAAAAGCTAGTTTTGGCTCCAATTGTTCAATCACTCAATTGAGATTTCCCTTTCAA
1797122 AAATTATGTATGATGTATCAGACACAAGGTTTGGAGCAATTATTGGGCAGAAAATCGACAAAGAA
66 AAATTATGTATGATGTATCAGACACAAGGTTTGGAGCAATTATTGGGCAGAAAATCGACAAAGAA
1797187 CCTCATGAAATAGGTTACACAACAAGAACCTTACCTTCAACTCAACAAAATTACTCGACCACCGA
131 CCTCATGAAATAGGTTACACAACAAGAACCTTACCTTCAACTCAACAAAATTACTCGACCACCGA
1797252 AAAAGAATTATTTGTCATTGTCTTTGCCTTAGAAAAATTTAGATCATATCTTCTCGACACTAAAA
196 AAAAGAATTATTTGTCATTGTCTTTGCCTTAGAAAAATTTAGATCATATCTTCTCGACACTAAAA
1797317 TGATTTTTTTACTGATCATGCAACTTTGAAGTATTTGATGAGAAAAAAGGAGAAGAAGCCAAGAA
261 TGATTTTTTTACTGATCATGCAACTTTGAAGTATTTGATGAGAAAAAAGGAGAAGAAGCCAAGAA
* * *
1797382 TAATTTTTTGGATTTTTCTTTTGCAAGAATTTGATCTGGAAATTAAGGACAAGAAATGATGCAAA
326 TAATTTTTTGGATCTTTCTTTTGCAAGAATTTGATCTAGAAATTAAGAACAAGAAATGATGCAAA
1797447 AATTTTGTGGCCGATCACCTAAGTCAACTTCCACTCTCCACGTCTAATCCACAACTTCGAGAAGA
391 AATTTTGTGGCCGATCACCTAAGTCAACTTCCACTCTCCACGTCTAATCCACAACTTCGAGAAGA
1797512 ATTT
1 ATTT
1797516 CCATAAAAAA
Statistics
Matches: 449, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
455 449 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (455 bp):
ATTTTAAAGGAAAAGCTAGTTTTGGCTCCAATTGTTCAATCACTCAATTGAGATTTCCCTTTCAA
AAATTATGTATGATGTATCAGACACAAGGTTTGGAGCAATTATTGGGCAGAAAATCGACAAAGAA
CCTCATGAAATAGGTTACACAACAAGAACCTTACCTTCAACTCAACAAAATTACTCGACCACCGA
AAAAGAATTATTTGTCATTGTCTTTGCCTTAGAAAAATTTAGATCATATCTTCTCGACACTAAAA
TGATTTTTTTACTGATCATGCAACTTTGAAGTATTTGATGAGAAAAAAGGAGAAGAAGCCAAGAA
TAATTTTTTGGATCTTTCTTTTGCAAGAATTTGATCTAGAAATTAAGAACAAGAAATGATGCAAA
AATTTTGTGGCCGATCACCTAAGTCAACTTCCACTCTCCACGTCTAATCCACAACTTCGAGAAGA
Found at i:1800067 original size:24 final size:23
Alignment explanation
Indices: 1800040--1800126 Score: 65
Period size: 24 Copynumber: 3.8 Consensus size: 23
1800030 TATCCCCATC
1800040 AGTGCTAAGACACTTCAGTGTAT
1 AGTGCTAAGACACTTCAGTGTAT
* * *
1800063 GAGTGTTAAGGA-ACTTTAGTATAT
1 -AGTGCTAA-GACACTTCAGTGTAT
*
1800087 CAGTGCTAA-AGCACTT--GCGTAT
1 -AGTGCTAAGA-CACTTCAGTGTAT
*
1800109 AGTGCTAAGAGACTTCAG
1 AGTGCTAAGACACTTCAG
1800127 ATACTAGTCG
Statistics
Matches: 49, Mismatches: 8, Indels: 13
0.70 0.11 0.19
Matches are distributed among these distances:
21 12 0.24
22 6 0.12
23 1 0.02
24 28 0.57
25 2 0.04
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (23 bp):
AGTGCTAAGACACTTCAGTGTAT
Found at i:1801627 original size:17 final size:18
Alignment explanation
Indices: 1801596--1801634 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
1801586 ATTTACAAAC
1801596 TTCTATATTACTTATCGG
1 TTCTATATTACTTATCGG
*
1801614 TTCTA-ATTATTTATCGG
1 TTCTATATTACTTATCGG
1801631 TTCT
1 TTCT
1801635 TGCCAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.54
Consensus pattern (18 bp):
TTCTATATTACTTATCGG
Found at i:1801886 original size:31 final size:31
Alignment explanation
Indices: 1801851--1801914 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1801841 TGTTACATAC
1801851 TCAAGTCATTAAGATGCATAATGTATATTGA
1 TCAAGTCATTAAGATGCATAATGTATATTGA
1801882 TCAAGTCATTAAGATGCATAATGTATATTGA
1 TCAAGTCATTAAGATGCATAATGTATATTGA
1801913 TC
1 TC
1801915 GAGTTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (31 bp):
TCAAGTCATTAAGATGCATAATGTATATTGA
Found at i:1807452 original size:809 final size:809
Alignment explanation
Indices: 1805895--1807512 Score: 3236
Period size: 809 Copynumber: 2.0 Consensus size: 809
1805885 TTCGACAGTT
1805895 GGCGAACAGAAGACTGGCTTATGCGGGACAGCATTGCCTCCTTCAGAAACTGAAATGTGGTCGTG
1 GGCGAACAGAAGACTGGCTTATGCGGGACAGCATTGCCTCCTTCAGAAACTGAAATGTGGTCGTG
1805960 CGGTTCTGTCCCAAAACCGAAGGAAAACCAAGATAACGCTCCAAGTCTGTAGCCTCCACAACCCC
66 CGGTTCTGTCCCAAAACCGAAGGAAAACCAAGATAACGCTCCAAGTCTGTAGCCTCCACAACCCC
1806025 CAAAACACATGACAAAAAATCACGGCAGGAAGTGTAGGTGTTTGTACTGAAAAATATCTTGGACT
131 CAAAACACATGACAAAAAATCACGGCAGGAAGTGTAGGTGTTTGTACTGAAAAATATCTTGGACT
1806090 CGTTGCCCAGAACACTCTTCAAATCTCTCAATAAGAGTTCGCACGGTGACCACTTCAGCGTGATT
196 CGTTGCCCAGAACACTCTTCAAATCTCTCAATAAGAGTTCGCACGGTGACCACTTCAGCGTGATT
1806155 AGCCCTGCTGAATATGAGGCAATTGTCGGCAAACAAAAGGTGATGAAAAGACGGACCTCCCCGAG
261 AGCCCTGCTGAATATGAGGCAATTGTCGGCAAACAAAAGGTGATGAAAAGACGGACCTCCCCGAG
1806220 TTAGGCGAATACTCAGAAATTGACCGCTTGCATGAGACTGGCGAAGTAGAGAAGATAGCCCCTCC
326 TTAGGCGAATACTCAGAAATTGACCGCTTGCATGAGACTGGCGAAGTAGAGAAGATAGCCCCTCC
1806285 ATACAGAATAAAAATAAATAAGGAGATAGTGGATCGCCTTAGAGCAGACCAAAACGAGGGTGTAT
391 ATACAGAATAAAAATAAATAAGGAGATAGTGGATCGCCTTAGAGCAGACCAAAACGAGGGTGTAT
1806350 AACCTTGGAGAGTGACGATTCACCCTATATCGTACAGACTGCACGCATGACATCAACAAAGCCAC
456 AACCTTGGAGAGTGACGATTCACCCTATATCGTACAGACTGCACGCATGACATCAACAAAGCCAC
1806415 CCATAGAATGTGAAACCCAAACCGGAGCAGGACTTGCTCAATAAAGCACCAACCTACACGGTCAT
521 CCATAGAATGTGAAACCCAAACCGGAGCAGGACTTGCTCAATAAAGCACCAACCTACACGGTCAT
1806480 AAGCTTTACTCGTATCAAGCTTAAGAGCAAAGAGTCCTTGACGACCCGAGCAACGGTGCCTATAA
586 AAGCTTTACTCGTATCAAGCTTAAGAGCAAAGAGTCCTTGACGACCCGAGCAACGGTGCCTATAA
1806545 GTATGCAAAGTTTCAGCGGCAAGAAGAGCATTATCTGTAATTAATCTCCACGGAATAAAAGCACT
651 GTATGCAAAGTTTCAGCGGCAAGAAGAGCATTATCTGTAATTAATCTCCACGGAATAAAAGCACT
1806610 CTAGCTATCATCAATACAACAACCCAACAAATGCTTAAACCGATTGACAATCACCCAAGAAAAAA
716 CTAGCTATCATCAATACAACAACCCAACAAATGCTTAAACCGATTGACAATCACCCAAGAAAAAA
1806675 AATCTTGTACACCACATTACAAAGGCTAA
781 AATCTTGTACACCACATTACAAAGGCTAA
1806704 GGCGAACAGAAGACTGGCTTATGCGGGACAGCATTGCCTCCTTCAGAAACTGAAATGTGGTCGTG
1 GGCGAACAGAAGACTGGCTTATGCGGGACAGCATTGCCTCCTTCAGAAACTGAAATGTGGTCGTG
1806769 CGGTTCTGTCCCAAAACCGAAGGAAAACCAAGATAACGCTCCAAGTCTGTAGCCTCCACAACCCC
66 CGGTTCTGTCCCAAAACCGAAGGAAAACCAAGATAACGCTCCAAGTCTGTAGCCTCCACAACCCC
1806834 CAAAACACATGACAAAAAATCACGGCAGGAAGTGTAGGTGTTTGTACTGAAAAATATCTTGGACT
131 CAAAACACATGACAAAAAATCACGGCAGGAAGTGTAGGTGTTTGTACTGAAAAATATCTTGGACT
1806899 CGTTGCCCAGAACACTCTTCAAATCTCTCAATAAGAGTTCGCACGGTGACCACTTCAGCGTGATT
196 CGTTGCCCAGAACACTCTTCAAATCTCTCAATAAGAGTTCGCACGGTGACCACTTCAGCGTGATT
1806964 AGCCCTGCTGAATATGAGGCAATTGTCGGCAAACAAAAGGTGATGAAAAGACGGACCTCCCCGAG
261 AGCCCTGCTGAATATGAGGCAATTGTCGGCAAACAAAAGGTGATGAAAAGACGGACCTCCCCGAG
1807029 TTAGGCGAATACTCAGAAATTGACCGCTTGCATGAGACTGGCGAAGTAGAGAAGATAGCCCCTCC
326 TTAGGCGAATACTCAGAAATTGACCGCTTGCATGAGACTGGCGAAGTAGAGAAGATAGCCCCTCC
1807094 ATACAGAATAAAAATAAATAAGGAGATAGTGGATCGCCTTAGAGCAGACCAAAACGAGGGTGTAT
391 ATACAGAATAAAAATAAATAAGGAGATAGTGGATCGCCTTAGAGCAGACCAAAACGAGGGTGTAT
1807159 AACCTTGGAGAGTGACGATTCACCCTATATCGTACAGACTGCACGCATGACATCAACAAAGCCAC
456 AACCTTGGAGAGTGACGATTCACCCTATATCGTACAGACTGCACGCATGACATCAACAAAGCCAC
1807224 CCATAGAATGTGAAACCCAAACCGGAGCAGGACTTGCTCAATAAAGCACCAACCTACACGGTCAT
521 CCATAGAATGTGAAACCCAAACCGGAGCAGGACTTGCTCAATAAAGCACCAACCTACACGGTCAT
1807289 AAGCTTTACTCGTATCAAGCTTAAGAGCAAAGAGTCCTTGACGACCCGAGCAACGGTGCCTATAA
586 AAGCTTTACTCGTATCAAGCTTAAGAGCAAAGAGTCCTTGACGACCCGAGCAACGGTGCCTATAA
1807354 GTATGCAAAGTTTCAGCGGCAAGAAGAGCATTATCTGTAATTAATCTCCACGGAATAAAAGCACT
651 GTATGCAAAGTTTCAGCGGCAAGAAGAGCATTATCTGTAATTAATCTCCACGGAATAAAAGCACT
1807419 CTAGCTATCATCAATACAACAACCCAACAAATGCTTAAACCGATTGACAATCACCCAAGAAAAAA
716 CTAGCTATCATCAATACAACAACCCAACAAATGCTTAAACCGATTGACAATCACCCAAGAAAAAA
1807484 AATCTTGTACACCACATTACAAAGGCTAA
781 AATCTTGTACACCACATTACAAAGGCTAA
1807513 TCGGCCGATA
Statistics
Matches: 809, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
809 809 1.00
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (809 bp):
GGCGAACAGAAGACTGGCTTATGCGGGACAGCATTGCCTCCTTCAGAAACTGAAATGTGGTCGTG
CGGTTCTGTCCCAAAACCGAAGGAAAACCAAGATAACGCTCCAAGTCTGTAGCCTCCACAACCCC
CAAAACACATGACAAAAAATCACGGCAGGAAGTGTAGGTGTTTGTACTGAAAAATATCTTGGACT
CGTTGCCCAGAACACTCTTCAAATCTCTCAATAAGAGTTCGCACGGTGACCACTTCAGCGTGATT
AGCCCTGCTGAATATGAGGCAATTGTCGGCAAACAAAAGGTGATGAAAAGACGGACCTCCCCGAG
TTAGGCGAATACTCAGAAATTGACCGCTTGCATGAGACTGGCGAAGTAGAGAAGATAGCCCCTCC
ATACAGAATAAAAATAAATAAGGAGATAGTGGATCGCCTTAGAGCAGACCAAAACGAGGGTGTAT
AACCTTGGAGAGTGACGATTCACCCTATATCGTACAGACTGCACGCATGACATCAACAAAGCCAC
CCATAGAATGTGAAACCCAAACCGGAGCAGGACTTGCTCAATAAAGCACCAACCTACACGGTCAT
AAGCTTTACTCGTATCAAGCTTAAGAGCAAAGAGTCCTTGACGACCCGAGCAACGGTGCCTATAA
GTATGCAAAGTTTCAGCGGCAAGAAGAGCATTATCTGTAATTAATCTCCACGGAATAAAAGCACT
CTAGCTATCATCAATACAACAACCCAACAAATGCTTAAACCGATTGACAATCACCCAAGAAAAAA
AATCTTGTACACCACATTACAAAGGCTAA
Found at i:1811147 original size:16 final size:16
Alignment explanation
Indices: 1811120--1811151 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1811110 ACAAAACAAT
1811120 ACTTTCACAAAGTAAA
1 ACTTTCACAAAGTAAA
1811136 ACTTTCACAAAGTAAA
1 ACTTTCACAAAGTAAA
1811152 GTTGTTATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (16 bp):
ACTTTCACAAAGTAAA
Found at i:1811986 original size:84 final size:83
Alignment explanation
Indices: 1811857--1812019 Score: 299
Period size: 84 Copynumber: 2.0 Consensus size: 83
1811847 CCCCATAATA
*
1811857 ATAAAACTGAGATGTCACTTTAAAATGTCTACCATGTGCCAAGAATGAAGAAAAAATCTTCTTTT
1 ATAAAACTGAGATGTCACTTCAAAATGTCTACCATGTGCCAAGAATGAAG-AAAAATCTTCTTTT
1811922 AGTAGCACAGTTGACGATT
65 AGTAGCACAGTTGACGATT
*
1811941 ATAATACTGAGATGTCACTTCAAAATGTCTACCATGTGCCAAGAATGAAGAAAAATCTTCTTTTA
1 ATAAAACTGAGATGTCACTTCAAAATGTCTACCATGTGCCAAGAATGAAGAAAAATCTTCTTTTA
1812006 GTAGCACAGTTGAC
66 GTAGCACAGTTGAC
1812020 ATCGTCGGGC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 29 0.38
84 48 0.62
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (83 bp):
ATAAAACTGAGATGTCACTTCAAAATGTCTACCATGTGCCAAGAATGAAGAAAAATCTTCTTTTA
GTAGCACAGTTGACGATT
Found at i:1815308 original size:15 final size:16
Alignment explanation
Indices: 1815276--1815308 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1815266 ATTGTTAGAG
*
1815276 TTTAACTCGAATTTGA
1 TTTAACTCGAAATTGA
1815292 TTTAACTC-AAATTGA
1 TTTAACTCGAAATTGA
1815307 TT
1 TT
1815309 GTAGAAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (16 bp):
TTTAACTCGAAATTGA
Found at i:1816801 original size:12 final size:11
Alignment explanation
Indices: 1816784--1816836 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
1816774 ACAAAAACAT
1816784 TTTATTATGTTA
1 TTTATTAT-TTA
1816796 TTTATTA-TTA
1 TTTATTATTTA
1816806 -TTATTA-TTA
1 TTTATTATTTA
1816815 TTATATT-TTTA
1 TT-TATTATTTA
1816826 TTTTATTATTT
1 -TTTATTATTT
1816837 TTACAGGCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 9 0.25
10 4 0.11
11 11 0.31
12 12 0.33
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:1816803 original size:3 final size:3
Alignment explanation
Indices: 1816797--1816835 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1816787 ATTATGTTAT
*
1816797 TTA TTA TTA TTA TTA TTA TTA -TA TTT TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1816836 TTTACAGGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:1816809 original size:9 final size:9
Alignment explanation
Indices: 1816797--1816835 Score: 55
Period size: 8 Copynumber: 4.6 Consensus size: 9
1816787 ATTATGTTAT
1816797 TTATTATTA
1 TTATTATTA
1816806 TTATTATTA
1 TTATTATTA
*
1816815 TTA-TATTT
1 TTATTATTA
1816823 TTATT-TTA
1 TTATTATTA
1816831 TTATT
1 TTATT
1816836 TTTACAGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 14 0.52
9 13 0.48
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTATTATTA
Found at i:1817334 original size:34 final size:37
Alignment explanation
Indices: 1817272--1817357 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 37
1817262 CTAATTTTAA
1817272 TATTTTTTATTTCTTTTTACATTGTTTTA-TATATATT
1 TATTTTTTATTTCTTTTTACATTGTTTTATTA-ATATT
1817309 TATTTTTTCA-TT-TTTTT-CATT-TTTTATTAATATT
1 TATTTTTT-ATTTCTTTTTACATTGTTTTATTAATATT
*
1817343 T-TTTATTA-TTCTTTT
1 TATTTTTTATTTCTTTT
1817358 CTCATGTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
32 3 0.07
33 9 0.20
34 11 0.24
35 6 0.13
36 5 0.11
37 10 0.22
38 1 0.02
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (37 bp):
TATTTTTTATTTCTTTTTACATTGTTTTATTAATATT
Found at i:1820528 original size:26 final size:26
Alignment explanation
Indices: 1820498--1820585 Score: 167
Period size: 26 Copynumber: 3.4 Consensus size: 26
1820488 TGAAAATTTG
*
1820498 TAAAAGAGTTGTAACTCTGAAACCAT
1 TAAAAGAGCTGTAACTCTGAAACCAT
1820524 TAAAAGAGCTGTAACTCTGAAACCAT
1 TAAAAGAGCTGTAACTCTGAAACCAT
1820550 TAAAAGAGCTGTAACTCTGAAACCAT
1 TAAAAGAGCTGTAACTCTGAAACCAT
1820576 TAAAAGAGCT
1 TAAAAGAGCT
1820586 ATTGATTCAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (26 bp):
TAAAAGAGCTGTAACTCTGAAACCAT
Found at i:1821123 original size:110 final size:110
Alignment explanation
Indices: 1820978--1821614 Score: 878
Period size: 110 Copynumber: 5.9 Consensus size: 110
1820968 GATGGTGGTT
* * *
1820978 GCTCAACTTCACAGCGAAGGGGCGATTGACAGTCAATAAACAACTTTTCAGTTTCATTCAAAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTC
* *
1821043 AATTTCAACTTCATAGCGAAGGATATTGAACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
1821088 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAAAAAACAACTTTTCAGTTTCATTCAGAGTT
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTC
*
1821153 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1821198 ACTCAACTTCACAGCGAAGGGGCGGCTGATTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTC
* *
1821263 AATTTCAATTTCACAGTGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
** * * ** * *
1821308 GCTCAACTTCACATTGAAAGGGAGACTGGTTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTC
* *** *
1821373 AATTTGAACTTCACAATAAAGTATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
1821418 GCTTAACTTCACAGCGAA--GG-TACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTC
*
1821480 AATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
1821525 GCTCAACTTCACAACAAAGGGGCGGA-TGGA-TGTCAACAAACAACTTTCCAG--T--TTCAAAG
1 GCTCAACTTCACAGCGAAGGGGC-GACT-GACTGTCAACAAACAACTTTTCAGTTTCATTCAAAG
*
1821584 TCAATTTCAACTTCACGGCGAAGGATATTGG
64 TCAATTTCAACTTCACAGCGAAGGATATTGG
1821615 CTTCGAAACA
Statistics
Matches: 472, Mismatches: 50, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
106 36 0.08
107 91 0.19
108 3 0.01
109 2 0.00
110 337 0.71
111 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:1821997 original size:84 final size:84
Alignment explanation
Indices: 1821732--1822504 Score: 621
Period size: 84 Copynumber: 9.3 Consensus size: 84
1821722 AAGGGAATCG
* * *
1821732 TGCCCACCAAAGGCCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACT
1 TGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* *
1821797 TAAGTCAATAAGGGTTATC
66 TAAGTCGAGAAGGGTTATC
* * * * * * ** * *
1821816 TGCCAACCGAAGACCCTC-ACATTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAA
1 TGCCAACCAAAGACCTTCGA-GTTTGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAA
* * *
1821880 CTCAAGGCTAGAAGGGTTATC
64 CTTAAGTCGAGAAGGGTTATC
*** * * *
1821901 T-ATGACCAAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAAC
1 TGCCAACC-AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
* *
1821965 TTAAGTTGATAAGGGTTATC
65 TTAAGTCGAGAAGGGTTATC
* * * *
1821985 TGCCAACCAAAGACCTTCGAGTTTGATTACGCTTAGCTTCAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
*
1822050 TAAGTCGAGAAGGGCTATC
66 TAAGTCGAGAAGGGTTATC
* * * * * * *
1822069 TG----CCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCGTTTACAGCATAAC
1 TGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAAC
* * *
1822130 TCAAGGCTAGAAGGGTTATC
65 TTAAGTCGAGAAGGGTTATC
** ** * * *
1822150 TG-TGACCAAAAGACCTTTAAGTTTGACTACGCTCAGCTCTAAGGCATATCATTTGCAACATAAC
1 TGCCAACC-AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
1822214 TTAAGTCGAGAAGGGTTATC
65 TTAAGTCGAGAAGGGTTATC
* * * * *
1822234 TGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGACACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* * *
1822299 TAAGTCGATAAAGGCTATC
66 TAAGTCGAGAAGGGTTATC
* * * * * * *
1822318 TG----CCAAAGACCCTAGA-TTTCGATTACACTCAACTTCGAGGGCACATCATTT--ATGTCAT
1 TGCCAACCAAAGACCTTCGAGTTT-GACTACGCTCAGC-TCCAAGGCACATCATTTGCA-G-CAT
* * *
1822376 AACTCAAGGCTAGAAGGGTTATC
62 AACTTAAGTCGAGAAGGGTTATC
* * * * * * * *
1822399 TGTCAA-CAAAGACCTTTGAGTTCGATTCCACTTAGCTCAAAGGCACCATCATTTGCAGCATAAC
1 TGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAAC
* * * *
1822463 TCAAGGCAAGAAGGGCTATC
65 TTAAGTCGAGAAGGGTTATC
1822483 T----ACCAAAGACCTTCGAGTTTGA
1 TGCCAACCAAAGACCTTCGAGTTTGA
1822505 TTCCATTAAG
Statistics
Matches: 552, Mismatches: 113, Indels: 51
0.77 0.16 0.07
Matches are distributed among these distances:
79 3 0.01
80 53 0.10
81 91 0.16
83 8 0.01
84 299 0.54
85 96 0.17
86 2 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (84 bp):
TGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
TAAGTCGAGAAGGGTTATC
Found at i:1822180 original size:249 final size:248
Alignment explanation
Indices: 1821732--1822504 Score: 1038
Period size: 249 Copynumber: 3.1 Consensus size: 248
1821722 AAGGGAATCG
* * * * *
1821732 TGCCCACCAAAGGCCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACT
1 TGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCT
* * * * *
1821797 TAAGTCAATAAGGGTTATCTGCCAACCGAAGACCCTCACATTCGATTACACTCAGCTTTGAGGGC
66 TAAGTCGATAAGGGCTATCTGCC-A---AAGACCCTC-GATTTGATTACACTCAGCTTCGAGGGC
* *
1821862 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACCTTCAAGTTCGA
126 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTAAGTTCGA
* * *
1821927 CTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTTGATAAGGGTTATC
191 CTACGCTCAGCTCAAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* *
1821985 TGCCAACCAAAGACCTTCGAGTTTGATTACGCTTAGCTTCAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCT
*
1822050 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACAT
66 TAAGTCGATAAGGGCTATCTGCCAAAGACCCTCGA-TTTGATTACACTCAGCTTCGAGGGCACAT
* *
1822115 CGTTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTAAGTTTGACTAC
130 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTAAGTTCGACTAC
* *
1822180 GCTCAGCTCTAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATC
195 GCTCAGCTCAAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* * *
1822234 TGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCTAAGACACATCATTTGCAGCATAGC
1 TGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTTC-AAGGCACATCATTTGCAGCATAGC
* * *
1822298 TTAAGTCGATAAAGGCTATCTGCCAAAGACCCTAGATTTCGATTACACTCAACTTCGAGGGCACA
65 TTAAGTCGATAAGGGCTATCTGCCAAAGACCCTCGATTT-GATTACACTCAGCTTCGAGGGCACA
* * * * *
1822363 TCATTTA-TGTCATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTTGAGTTCGATT
129 TCATTTACAG-CATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTAAGTTCGACT
* * * * * * * *
1822426 CCACTTAGCTCAAAGGCACCATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATC
193 ACGCTCAGCTCAAAGGCA-TATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
1822483 T----ACCAAAGACCTTCGAGTTTGA
1 TGCCAACCAAAGACCTTCGAGTTTGA
1822505 TTCCATTAAG
Statistics
Matches: 467, Mismatches: 48, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
245 20 0.04
248 38 0.08
249 330 0.71
252 1 0.00
253 78 0.17
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (248 bp):
TGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCT
TAAGTCGATAAGGGCTATCTGCCAAAGACCCTCGATTTGATTACACTCAGCTTCGAGGGCACATC
ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTAAGTTCGACTACG
CTCAGCTCAAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
Found at i:1822411 original size:333 final size:329
Alignment explanation
Indices: 1821738--1822488 Score: 787
Period size: 333 Copynumber: 2.3 Consensus size: 329
1821728 ATCGTGCCCA
* * * * * *
1821738 CCAAAGGCCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTC
1 CCAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGC
* * * * *
1821803 AATAAGGGTTATCTGCCAACCGAAGACCCTCACATTCGATTACACTCAGCTTTGAGGGCACATCA
66 AAGAAGGGTTATCTGCCAACCAAAGACCCTCACATTCGACTACACTCAGCTCTGAAGGCACATCA
* * ** *
1821868 TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACCTTCAAGTTCGACTACGC
131 TTTACAACATAACTCAAGGCGAGAAGGGTTATCTACAACCAAAAGACCTTCAAGTTCGACTACAC
* * * * *
1821933 TCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTTGATAAGGGTTATCTGCCAACCAAAGA
196 TCAGCTCCAAGACACATCATTTGCAGCATAACTTAAGTCGATAAAGGCTATCTG---ACCAAAGA
* * * * * * * *
1821998 CCTTCGAGTTTGATTACGCTTAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
258 CCCTAGAGTTTGATTACACTCAACTTCAAGGCACATCATTT-CAGCATAACTCAAGGCGAGAAGG
1822063 GCTATCTG
322 GCTATCTG
* * * *
1822071 CCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCGTTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTTGATTACACTCAGC-TCAAAGGCACATCATTTACAGCATAACTCAAGG
* ** * * * * *
1822136 CTAGAAGGGTTATCTG-TGACCAAAAGACCTTTA-AGTTTGACTACGCTCAGCTCT-AAGGCATA
65 CAAGAAGGGTTATCTGCCAACC-AAAGACCCTCACA-TTCGACTACACTCAGCTCTGAAGGCACA
* * * * *
1822198 TCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACT
128 TCATTTACAACATAACTCAAGGCGAGAAGGGTTATCT-ACAACCAAAAGACCTTCAAGTTCGACT
* *
1822262 ACACTCAGCTCTAAGACACATCATTTGCAGCATAGCTTAAGTCGATAAAGGCTATCTG-CCAAAG
192 ACACTCAGCTCCAAGACACATCATTTGCAGCATAACTTAAGTCGATAAAGGCTATCTGACCAAAG
* *
1822326 ACCCTAGA-TTTCGATTACACTCAACTTCGAGGGCACATCATTT-ATGTCATAACTCAAGGCTAG
257 ACCCTAGAGTTT-GATTACACTCAACTTC-AAGGCACATCATTTCA-G-CATAACTCAAGGCGAG
*
1822389 AAGGGTTATCTG
318 AAGGGCTATCTG
* * * * *
1822401 TCAACAAAGACCTTTGAGTTCGATTCCACTTAGCTCAAAGGCACCATCATTTGCAGCATAACTCA
1 -C--CAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCA-CATCATTTACAGCATAACTCA
* *
1822466 AGGCAAGAAGGGCTATCTACCAA
62 AGGCAAGAAGGGTTATCTGCCAA
1822489 AGACCTTCGA
Statistics
Matches: 341, Mismatches: 64, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
328 4 0.01
329 26 0.08
330 36 0.11
331 1 0.00
332 7 0.02
333 198 0.58
334 69 0.20
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (329 bp):
CCAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGC
AAGAAGGGTTATCTGCCAACCAAAGACCCTCACATTCGACTACACTCAGCTCTGAAGGCACATCA
TTTACAACATAACTCAAGGCGAGAAGGGTTATCTACAACCAAAAGACCTTCAAGTTCGACTACAC
TCAGCTCCAAGACACATCATTTGCAGCATAACTTAAGTCGATAAAGGCTATCTGACCAAAGACCC
TAGAGTTTGATTACACTCAACTTCAAGGCACATCATTTCAGCATAACTCAAGGCGAGAAGGGCTA
TCTG
Found at i:1822884 original size:25 final size:23
Alignment explanation
Indices: 1822856--1822909 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
1822846 ATTGTATTAC
1822856 ATTATTTATT-TATTTATTTATTATT
1 ATTATTTATTATA-TT-TTTATT-TT
1822881 ATTA-TTATTATATTTTTATTTT
1 ATTATTTATTATATTTTTATTTT
1822903 ATTATTT
1 ATTATTT
1822910 TTACAGGCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 6 0.22
23 8 0.30
24 7 0.26
25 6 0.22
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (23 bp):
ATTATTTATTATATTTTTATTTT
Found at i:1823381 original size:34 final size:33
Alignment explanation
Indices: 1823343--1823407 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
1823333 CCTAATTTTA
*
1823343 ATATTTTTTTATTTC-TTTTTACATTGTTTTATAT
1 ATATTTATTT-TTTCATTTTTACATT-TTTTATAT
*
1823377 ATATTTATTTTTTCATTTTTTCATTTTTTAT
1 ATATTTATTTTTTCATTTTTACATTTTTTAT
1823408 TAATATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (33 bp):
ATATTTATTTTTTCATTTTTACATTTTTTATAT
Found at i:1823406 original size:64 final size:66
Alignment explanation
Indices: 1823278--1823400 Score: 146
Period size: 65 Copynumber: 1.9 Consensus size: 66
1823268 ACTTTTGACT
* * *
1823278 TATTCTTTTTATTTCATTTTTTATTTATTTACTTTATATATATTTTTCATTTTCTCCTAATTTTA
1 TATTCTTTTTATTTCATTTTTCATTTATTTACTATATATATATTTTTCATTTTCTCATAATTTTA
1823343 A
66 A
* *
1823344 TATT-TTTTTATTTC-TTTTTACATTGT-TTTA-TATATATTTATTTTTTCATTTTTTCAT
1 TATTCTTTTTATTTCATTTTT-CATT-TATTTACTATATATATA-TTTTTCATTTTCTCAT
1823401 TTTTTATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
64 13 0.27
65 31 0.63
66 5 0.10
ACGTcount: A:0.21, C:0.09, G:0.01, T:0.69
Consensus pattern (66 bp):
TATTCTTTTTATTTCATTTTTCATTTATTTACTATATATATATTTTTCATTTTCTCATAATTTTA
A
Done.