Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008360.1 Hibiscus syriacus cultivar Beakdansim tig00111099_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: 1563863
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1450759 original size:40 final size:40
Alignment explanation
Indices: 1450706--1450896 Score: 238
Period size: 40 Copynumber: 4.7 Consensus size: 40
1450696 TTTAGAAGAA
* * *
1450706 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * *
1450746 AATCGCAATGCGATTGAGAGATTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGA-TT-G-AGAG
* *
1450789 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* *
1450829 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * *
1450869 AATCGCAACGCGATTTAGAAAATCGCAA
1 AATCGCAATGCGATTGAGAGAATCGCAA
1450897 CGTTAAAAAG
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 94 0.72
41 3 0.02
42 1 0.01
43 32 0.25
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
Found at i:1450794 original size:83 final size:83
Alignment explanation
Indices: 1450684--1450896 Score: 288
Period size: 83 Copynumber: 2.6 Consensus size: 83
1450674 AGCTTCCAAG
* * * *
1450684 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAAT
1450749 CGCAATGCGATTGAGAGA
66 CGCAATGCGATTGAGAGA
*
1450767 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAAT
* *
1450832 CGCAATGCGATTTATAGA
66 CGCAATGCGATTGAGAGA
* * * * * *
1450850 ATCGCAATGCGA-TT-G-AGAGAATCGCAACGCGATTTAGAAAATCGCAA
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAA
1450897 CGTTAAAAAG
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
80 27 0.23
81 1 0.01
82 2 0.02
83 86 0.74
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (83 bp):
TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAAT
CGCAATGCGATTGAGAGA
Found at i:1454084 original size:34 final size:34
Alignment explanation
Indices: 1454036--1454112 Score: 136
Period size: 34 Copynumber: 2.2 Consensus size: 34
1454026 AATGAGAGAT
*
1454036 TAAAAGTAACAAGTTCTTGAGAGAAAGCTAAGGAC
1 TAAAAG-ATCAAGTTCTTGAGAGAAAGCTAAGGAC
1454071 TAAAAGATCAAGTTCTTGAGAGAAAGCTAAGGAC
1 TAAAAGATCAAGTTCTTGAGAGAAAGCTAAGGAC
1454105 TAAAAGAT
1 TAAAAGAT
1454113 GGAGAAAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 35 0.85
35 6 0.15
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.21
Consensus pattern (34 bp):
TAAAAGATCAAGTTCTTGAGAGAAAGCTAAGGAC
Found at i:1466085 original size:2 final size:2
Alignment explanation
Indices: 1466080--1466112 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1466070 TTTATCAGAT
1466080 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1466113 GATTGAATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1487207 original size:253 final size:253
Alignment explanation
Indices: 1486759--1487258 Score: 928
Period size: 253 Copynumber: 2.0 Consensus size: 253
1486749 TATCCCAAGA
*
1486759 AAATTTTTTCTGATGTGGAAGATCAGCCTAAGCTGCAACCACAGAGCATACTAAAATAAACCAAG
1 AAATTTTTTCTGATGTGGAAGATCAGCCTAAGCCGCAACCACAGAGCATACTAAAATAAACCAAG
1486824 AGCGCTGATACCAATTGTTGTGGAATTCAGGTTAATTTCCACCAATAATAACAAATTCACCTTGA
66 AGCGCTGATACCAATTGTTGTGGAATTCAGGTTAATTTCCACCAATAATAACAAATTCACCTTGA
*
1486889 AAACTATTATCTAGGTGACTAGTGTGAAAATGATTGTACTAAAAATCACACCAAGGTAGATTCCC
131 AAACTATTATCTAGGTGACTAGTGTGAAAACGATTGTACTAAAAATCACACCAAGGTAGATTCCC
1486954 AGGAAAGAGGAGGGGTCACAATGGTCCCTCTTAAAACCCACTTTCCTTAGACCCCAAT
196 AGGAAAGAGGAGGGGTCACAATGGTCCCTCTTAAAACCCACTTTCCTTAGACCCCAAT
*
1487012 AAATTTTTTCTGATGTGGAAGATCAGCCTAAGCCGCAACCACAGAGCATATTAAAATAAACCAAG
1 AAATTTTTTCTGATGTGGAAGATCAGCCTAAGCCGCAACCACAGAGCATACTAAAATAAACCAAG
* * * *
1487077 AGCGTTGATACTAATTGTTGTGGAATTCGGGTTAATTTTCACCAATAATAACAAATTCACCTTGA
66 AGCGCTGATACCAATTGTTGTGGAATTCAGGTTAATTTCCACCAATAATAACAAATTCACCTTGA
1487142 AAACTATTATCTAGGTGACTAGTGTGAAAACGATTGTACTAAAAATCACACCAAGGTAGATTCCC
131 AAACTATTATCTAGGTGACTAGTGTGAAAACGATTGTACTAAAAATCACACCAAGGTAGATTCCC
*
1487207 AGGAAAGAGGAGGGGTCACAATGGTCCCTCTTAAAACCCATTTTCCTTAGAC
196 AGGAAAGAGGAGGGGTCACAATGGTCCCTCTTAAAACCCACTTTCCTTAGAC
1487259 AGAACTACCA
Statistics
Matches: 239, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
253 239 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (253 bp):
AAATTTTTTCTGATGTGGAAGATCAGCCTAAGCCGCAACCACAGAGCATACTAAAATAAACCAAG
AGCGCTGATACCAATTGTTGTGGAATTCAGGTTAATTTCCACCAATAATAACAAATTCACCTTGA
AAACTATTATCTAGGTGACTAGTGTGAAAACGATTGTACTAAAAATCACACCAAGGTAGATTCCC
AGGAAAGAGGAGGGGTCACAATGGTCCCTCTTAAAACCCACTTTCCTTAGACCCCAAT
Found at i:1488700 original size:17 final size:18
Alignment explanation
Indices: 1488667--1488705 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1488657 CATATACATC
*
1488667 TAAT-TTATAATGATAAA
1 TAATATTATAACGATAAA
1488684 TAATATTATAACG-TAAA
1 TAATATTATAACGATAAA
1488701 TAATA
1 TAATA
1488706 AACAACATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (18 bp):
TAATATTATAACGATAAA
Found at i:1489216 original size:17 final size:17
Alignment explanation
Indices: 1489194--1489232 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
1489184 ATATGTTGTT
1489194 TATTATTTA-CATTATAA
1 TATTATTTATCATTAT-A
1489211 TATTATTTATCATTATA
1 TATTATTTATCATTATA
1489228 TATTA
1 TATTA
1489233 AATGTACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTATTTATCATTATA
Found at i:1490343 original size:20 final size:20
Alignment explanation
Indices: 1490318--1490355 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1490308 TTTGGTTCAC
1490318 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1490338 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1490356 GGAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:1490365 original size:16 final size:18
Alignment explanation
Indices: 1490318--1490368 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
1490308 TTTGGTTCAC
1490318 GGAATGTAAGATTACCAGTG
1 GGAA-GTAAGATTACCAG-G
1490338 GGAATGTAAGATTACCA-G
1 GGAA-GTAAGATTACCAGG
1490356 GGAA-TAAGATTAC
1 GGAAGTAAGATTAC
1490369 TGGGAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.29
18 5 0.16
20 17 0.55
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGG
Found at i:1492321 original size:21 final size:23
Alignment explanation
Indices: 1492295--1492336 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
1492285 AATTTAAAAA
1492295 AAAAATACA-AA-AATAAAAAGG
1 AAAAATACATAATAATAAAAAGG
1492316 AAAAATACATAATAATAAAAA
1 AAAAATACATAATAATAAAAA
1492337 CAAAAGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 2 0.11
23 8 0.42
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (23 bp):
AAAAATACATAATAATAAAAAGG
Found at i:1492341 original size:21 final size:19
Alignment explanation
Indices: 1492289--1492341 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 19
1492279 TGTCTTAATT
1492289 TAAAAAAAAAATACAAAAA
1 TAAAAAAAAAATACAAAAA
1492308 TAAAAAGGAAAAATACATAATAA
1 TAAAAA--AAAAATACA-AA-AA
1492331 TAAAAACAAAA
1 TAAAAA-AAAA
1492342 GGAAACTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.21
21 9 0.31
22 6 0.21
23 8 0.28
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.13
Consensus pattern (19 bp):
TAAAAAAAAAATACAAAAA
Found at i:1499619 original size:31 final size:31
Alignment explanation
Indices: 1499584--1499651 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1499574 TAACAAATTA
*
1499584 GTCACTAACGTTATCGGTTTGT-GACAAAATG
1 GTCACTAACGTTATCGATTTGTAG-CAAAATG
*
1499615 GTCACTGACGTTATCGATTTGTAGCAAAATG
1 GTCACTAACGTTATCGATTTGTAGCAAAATG
1499646 GTCACT
1 GTCACT
1499652 TCATCATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (31 bp):
GTCACTAACGTTATCGATTTGTAGCAAAATG
Found at i:1500561 original size:31 final size:31
Alignment explanation
Indices: 1500509--1500588 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
1500499 ATAACGGTGG
* *
1500509 AGTGACCATTTTTTTTACAAATCGATAACGTT
1 AGTGACCA-TTTTGTTACAAATCGATAACATT
* *
1500541 AGTGATCATTTTGTTACAAATTGATAACATT
1 AGTGACCATTTTGTTACAAATCGATAACATT
*
1500572 AGTGACCAATTTGTTAC
1 AGTGACCATTTTGTTAC
1500589 TTTTGAAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 35 0.83
32 7 0.17
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (31 bp):
AGTGACCATTTTGTTACAAATCGATAACATT
Found at i:1504291 original size:52 final size:52
Alignment explanation
Indices: 1504213--1504315 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
1504203 ACCTAATCTC
**
1504213 GGTGGAAACTCTGCTAAAGAATTCTTCATGTCTTCAATGTTCAATCAACTAT
1 GGTGGAAACTCTGCTAAAGAATTCTTCATGTCTTCAACCTTCAATCAACTAT
*
1504265 GGTGGAAACTCTGGTAAAGAATTCTTCATGTCTTCAACCTTCAATCAACTA
1 GGTGGAAACTCTGCTAAAGAATTCTTCATGTCTTCAACCTTCAATCAACTA
1504316 AGGTCGGCTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (52 bp):
GGTGGAAACTCTGCTAAAGAATTCTTCATGTCTTCAACCTTCAATCAACTAT
Found at i:1505827 original size:182 final size:181
Alignment explanation
Indices: 1505518--1505968 Score: 688
Period size: 182 Copynumber: 2.5 Consensus size: 181
1505508 TTTTTACTAT
* * *
1505518 CGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCAAGACCGGTTTTGTCATATTTTTACCTG-TATATTGTTATGGATCGATAC
* * * *
1505583 ATTTTTATAAAGTATCGACACTTTATTGGTGCTATAACTTCTTTTCTTTTAAATTTCAAAAGTGT
65 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
* *
1505648 CGATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCTCTTTAC
130 CGATACTTATAATAAAATATCGACACTATCAACATATACGGTAGCGCTTTAC
*
1505700 CGGTTTTATCATTTCAAGACCGGTTTTGTCATATTTTTACCTGTCATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCAAGACCGGTTTTGTCATATTTTTACCTGT-ATATTGTTATGGATCGATAC
*
1505765 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAATTTCTTCTCTTTTAAATTCCAAAAGTGT
65 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
* *
1505830 CGATACTTATAATAAAGTATCGACACTATCAACATATATGGTAGCGCTTTAC
130 CGATACTTATAATAAAATATCGACACTATCAACATATACGGTAGCGCTTTAC
* * * * *
1505882 CTGTTTTGTCATTT-ATAGACTGGTTTTGTCATTTTTATTACCTGTTTATTGTTATAGATCGATA
1 CGGTTTTGTCATTTCA-AGACCGGTTTTGTCATATTT-TTACCTGTATATTGTTATGGATCGATA
*
1505946 TATTTTTATAAAGTATCGACACT
64 CATTTTTATAAAGTATCGACACT
1505969 ATCAACATAT
Statistics
Matches: 246, Mismatches: 20, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
181 2 0.01
182 236 0.96
183 8 0.03
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (181 bp):
CGGTTTTGTCATTTCAAGACCGGTTTTGTCATATTTTTACCTGTATATTGTTATGGATCGATACA
TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
GATACTTATAATAAAATATCGACACTATCAACATATACGGTAGCGCTTTAC
Found at i:1506195 original size:113 final size:112
Alignment explanation
Indices: 1505841--1506304 Score: 714
Period size: 112 Copynumber: 4.1 Consensus size: 112
1505831 GATACTTATA
** *
1505841 ATAAAGTATCGACACTATCAACATATATGGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
1505906 TTTGTCATTTTTATTACCTGTT-TATTGTTATAGATCGATATATTTTT
66 TTTGTCATTTTT-TTACCTGTTATATTATTATGGATCAATACATTTTT
*
1505953 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTTATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1506018 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
* * *
1506065 ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1506130 TTTGTCATTTTTTTTACCTGTTATATTATTATGGATAAATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
* * * *
1506178 ATAAAGTATTGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
1506243 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
*
1506290 ATAAAATATCGACAC
1 ATAAAGTATCGACAC
1506305 AAACCGACAA
Statistics
Matches: 328, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
111 9 0.03
112 212 0.65
113 107 0.33
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
Found at i:1506258 original size:225 final size:224
Alignment explanation
Indices: 1505841--1506304 Score: 721
Period size: 225 Copynumber: 2.1 Consensus size: 224
1505831 GATACTTATA
** *
1505841 ATAAAGTATCGACACTATCAACATATATGGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGGT
1 ATAAAGTATCGACACTATCAACATATACAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* ** *
1505906 TTTGTCATTTTTATTACCTGTTTATTGTTATAGATCGATATATTTTTATAAAGTATCGACACTAT
66 TTTGTCATTTTTATTACCTGTTTATTATTATAGATAAATACATTTTTATAAAGTATCGACACTAT
* *
1505971 CAACATATCCGGTAGCGCTTTACCTGTTTTGTTATTTATAGACCGGTTTTGTCATTTTTTTACCT
131 CAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGTTTTGTCATTTTTTTACCT
*
1506036 GTTATATTATTATGGATCGATACATTTTT
196 GTTATATTATTATGGATCAATACATTTTT
* * *
1506065 ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATACAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
1506130 TTTGTCATTTTTTTTACCTGTTATATTATTATGGATAAATACATTTTTATAAAGTATTGACACTT
66 TTTGTCATTTTTATTACCTGTT-TATTATTATAGATAAATACATTTTTATAAAGTATCGACACTA
* *
1506195 TCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGTTTTGTCATTTTTTTACT
130 TCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGTTTTGTCATTTTTTTACC
* *
1506260 TGTTATATTGTTATGGATCAATATATTTTT
195 TGTTATATTATTATGGATCAATACATTTTT
*
1506290 ATAAAATATCGACAC
1 ATAAAGTATCGACAC
1506305 AAACCGACAA
Statistics
Matches: 217, Mismatches: 22, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
224 80 0.37
225 137 0.63
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (224 bp):
ATAAAGTATCGACACTATCAACATATACAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTATTACCTGTTTATTATTATAGATAAATACATTTTTATAAAGTATCGACACTAT
CAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGTTTTGTCATTTTTTTACCT
GTTATATTATTATGGATCAATACATTTTT
Found at i:1513584 original size:21 final size:21
Alignment explanation
Indices: 1513558--1513784 Score: 76
Period size: 21 Copynumber: 11.0 Consensus size: 21
1513548 ATGCAAAATA
1513558 AAAATCGCAACGCGATTCTGG
1 AAAATCGCAACGCGATTCTGG
* ** **
1513579 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTCTGG
* ** * **
1513600 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTCTGG
* * *
1513621 AGAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTCTGG
*
1513641 AAAATCGCAACGCGATTCT-T
1 AAAATCGCAACGCGATTCTGG
** * *
1513661 ACTATCGCAACGAGTATTC-GTA
1 AAAATCGCAACGCG-ATTCTG-G
*
1513683 AAAATCGCAACGCG-TATC-CG
1 AAAATCGCAACGCGAT-TCTGG
* * * *
1513703 TAAATCGCAACGAGAATAC-GT
1 AAAATCGCAACGCG-ATTCTGG
*
1513724 AAAATCGCAACGCG-TATC-CG
1 AAAATCGCAACGCGAT-TCTGG
* * * *
1513744 TAAATCGCAACGAGAATAC-GT
1 AAAATCGCAACGCG-ATTCTGG
1513765 AAAATCGCAACGCGATTCTG
1 AAAATCGCAACGCGATTCTG
1513785 ATTATCGCAA
Statistics
Matches: 148, Mismatches: 48, Indels: 20
0.69 0.22 0.09
Matches are distributed among these distances:
19 1 0.01
20 56 0.38
21 78 0.53
22 13 0.09
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTCTGG
Found at i:1513691 original size:83 final size:81
Alignment explanation
Indices: 1513623--1513895 Score: 249
Period size: 82 Copynumber: 3.4 Consensus size: 81
1513613 GATTTTCCAG
* * * * * * *
1513623 AATCGCAACGCGAATATG-AAAATCGCAACGCG-ATTCTTACTATCGCAACGAGTATTCGTAAAA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA-AATCGCAACGAGAATACGT-AAA
1513686 ATCGCAACGCGTATCCGTA
64 ATCGCAACGCGTATCCG-A
1513705 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAAAT
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAAAT
*
1513770 CGCAACGCG-ATTCTGA
66 CGCAACGCGTA-TCCGA
* * * * * ** *
1513786 TTATCGCAACCAGAATACGT-TAATCGCAACGAGAATATGTAAATCGCAACGATAAT-CTGT-AA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATAC-GTAAA
*
1513848 ATCGCAACG-ATAATCCGTA
64 ATCGCAACGCGT-ATCCG-A
1513867 AATCGCAACGAGAAT-C-TATAAATCGCAAC
1 AATCGCAACGAGAATACGTA-AAATCGCAAC
1513896 ACTTAAATTT
Statistics
Matches: 160, Mismatches: 21, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
78 1 0.01
79 1 0.01
80 37 0.23
81 36 0.22
82 50 0.31
83 30 0.19
84 5 0.03
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (81 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAAAT
CGCAACGCGTATCCGA
Found at i:1513740 original size:41 final size:41
Alignment explanation
Indices: 1513623--1513895 Score: 260
Period size: 40 Copynumber: 6.7 Consensus size: 41
1513613 GATTTTCCAG
* * * *
1513623 AATCGCAACGCGAATATG-AAAATCGCAACGCG-ATTCTTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* * *
1513662 CTATCGCAACGAGTATTCGTAAAAATCGCAACGCGTATCCGTA
1 -AATCGCAACGAGAATACGT-AAAATCGCAACGCGTATCCGTA
1513705 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
1513746 AATCGCAACGAGAATACGTAAAATCGCAACGCG-ATTC-TGA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT-A
* * * * * **
1513786 TTATCGCAACCAGAATACGT-TAATCGCAACGAGAATATGTA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* *
1513827 AATCGCAACGATAAT-CTGT-AAATCGCAACG-ATAATCCGTA
1 AATCGCAACGAGAATAC-GTAAAATCGCAACGCGT-ATCCGTA
1513867 AATCGCAACGAGAAT-C-TATAAATCGCAAC
1 AATCGCAACGAGAATACGTA-AAATCGCAAC
1513896 ACTTAAATTT
Statistics
Matches: 196, Mismatches: 26, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.01
39 2 0.01
40 82 0.42
41 75 0.38
42 31 0.16
43 5 0.03
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (41 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
Found at i:1513857 original size:20 final size:20
Alignment explanation
Indices: 1513623--1513895 Score: 207
Period size: 20 Copynumber: 13.4 Consensus size: 20
1513613 GATTTTCCAG
* * *
1513623 AATCGCAACGCGAATATGAA
1 AATCGCAACGAGAATCTGTA
* *
1513643 AATCGCAACGCGATTCT-TA
1 AATCGCAACGAGAATCTGTA
* *
1513662 CTATCGCAACGAGTAT-TCGTAAA
1 -AATCGCAACGAGAATCT-GT--A
* * *
1513685 AATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATCTGTA
1513705 AATCGCAACGAGAATAC-GTAA
1 AATCGCAACGAGAAT-CTGT-A
* * *
1513726 AATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATCTGTA
1513746 AATCGCAACGAGAATAC-GTAA
1 AATCGCAACGAGAAT-CTGT-A
* *
1513767 AATCGCAACGCGATTCTG-A
1 AATCGCAACGAGAATCTGTA
* * *
1513786 TTATCGCAACCAGAATAC-GTT
1 -AATCGCAACGAGAAT-CTGTA
*
1513807 AATCGCAACGAGAATATGTA
1 AATCGCAACGAGAATCTGTA
*
1513827 AATCGCAACGATAATCTGTA
1 AATCGCAACGAGAATCTGTA
* *
1513847 AATCGCAACGATAATCCGTA
1 AATCGCAACGAGAATCTGTA
*
1513867 AATCGCAACGAGAATCTATA
1 AATCGCAACGAGAATCTGTA
1513887 AATCGCAAC
1 AATCGCAAC
1513896 ACTTAAATTT
Statistics
Matches: 204, Mismatches: 33, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.01
20 150 0.74
21 35 0.17
22 15 0.07
23 1 0.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGAGAATCTGTA
Found at i:1514577 original size:12 final size:12
Alignment explanation
Indices: 1514556--1514589 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1514546 ACCACATTTC
*
1514556 CAATACCAAACA
1 CAATATCAAACA
1514568 CAATATCAAACA
1 CAATATCAAACA
*
1514580 CAATCTCAAA
1 CAATATCAAA
1514590 ACCTACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1514747 original size:24 final size:24
Alignment explanation
Indices: 1514715--1514768 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1514705 GTATTCGAAA
1514715 TTTGATCTTGATCAATACCCGGAC
1 TTTGATCTTGATCAATACCCGGAC
* * *
1514739 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGATCAATACCCGGAC
1514763 TTTGAT
1 TTTGAT
1514769 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGATCAATACCCGGAC
Found at i:1517297 original size:19 final size:19
Alignment explanation
Indices: 1517273--1517471 Score: 150
Period size: 19 Copynumber: 11.4 Consensus size: 19
1517263 ACAACGAGAG
1517273 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1517292 AATCGCAA--C---TTGAA
1 AATCGCAATGCGAAATGAA
* *
1517306 AATTGCAACGCGAATATGAA
1 AATCGCAATGCGAA-ATGAA
* * *
1517326 TATCGCAACGCGGAAATGAC
1 AATCGCAATGC-GAAATGAA
*
1517346 TATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1517365 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1517379 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1517398 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1517412 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1517431 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
1517445 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1517464 AATCGCAA
1 AATCGCAA
1517472 CGAAAGAATC
Statistics
Matches: 143, Mismatches: 15, Indels: 44
0.71 0.07 0.22
Matches are distributed among these distances:
14 41 0.29
15 3 0.02
16 7 0.05
17 7 0.05
18 3 0.02
19 52 0.36
20 27 0.19
21 3 0.02
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1517319 original size:33 final size:33
Alignment explanation
Indices: 1517240--1517484 Score: 276
Period size: 33 Copynumber: 7.2 Consensus size: 33
1517230 TCATTTGACT
* * * * *
1517240 ATCGCAACGCGGAAATTACAATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAAA
**
1517274 ATCGCAATGCGAAATGAAAATCGCAACTTGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
* * * *
1517307 ATTGCAACGCGAATATGAATATCGCAACGCGGAAATGA
1 ATCGCAATGCGAA-ATGAAAATCGCAACG-AG-AA--A
*
1517345 CTATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 --ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
* *
1517380 ATCGTAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1517413 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1517446 ATCGCAATGCGAAATGAAAATCGCAACGA-AAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAA-A
1517479 ATCGCA
1 ATCGCA
1517485 CTCGTTGTGA
Statistics
Matches: 183, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
32 2 0.01
33 127 0.69
34 22 0.12
35 2 0.01
36 2 0.01
37 1 0.01
38 2 0.01
39 14 0.08
40 11 0.06
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:1517417 original size:14 final size:14
Alignment explanation
Indices: 1517362--1517484 Score: 68
Period size: 14 Copynumber: 7.7 Consensus size: 14
1517352 AATGCGAAAT
1517362 GAAAATCGCAACGA
1 GAAAATCGCAACGA
* *
1517376 GAGAATCGTAATGCGAAA
1 GAAAATCGCAA--CG--A
1517394 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
*
1517409 GAGAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
1517427 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
1517442 GAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
1517460 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
1517475 -AAGAATCGCA
1 GAA-AATCGCA
1517485 CTCGTTGTGA
Statistics
Matches: 87, Mismatches: 6, Indels: 32
0.70 0.05 0.26
Matches are distributed among these distances:
13 2 0.02
14 37 0.43
15 3 0.03
16 6 0.07
17 6 0.07
18 3 0.03
19 30 0.34
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1517640 original size:14 final size:14
Alignment explanation
Indices: 1517621--1517657 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1517611 CATCAATTAA
1517621 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1517635 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1517649 ACAAATCAA
1 ACAAATCAA
1517658 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1517798 original size:82 final size:84
Alignment explanation
Indices: 1517624--1517800 Score: 331
Period size: 83 Copynumber: 2.1 Consensus size: 84
1517614 CAATTAAACA
1517624 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
1517689 ATTTCCTCATCTACTATTG
66 ATTTCCTCATCTACTATTG
*
1517708 AATCAACTTTTACAAATCATCTTTTAC-AATGAATTAAACAATCAAAAAATAAGCAATAATTC-T
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
1517771 ATTTCCTCATCTACTATTG
66 ATTTCCTCATCTACTATTG
1517790 AATCAACTTTT
1 AATCAACTTTT
1517801 GTAGCCATAC
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
82 31 0.34
83 34 0.37
84 27 0.29
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (84 bp):
AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
ATTTCCTCATCTACTATTG
Found at i:1519174 original size:42 final size:42
Alignment explanation
Indices: 1519089--1519177 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
1519079 GTGAATCGGG
* * *
1519089 CTCTTGAATGGTGGGAGGGACCTCTTCAATGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAAGGATGACAGGGGC
* *
1519131 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTCAAGG-ATGACAGGGGC
1519173 CTCTT
1 CTCTT
1519178 TAATGATAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 32 0.80
43 4 0.10
ACGTcount: A:0.20, C:0.19, G:0.36, T:0.25
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAAGGATGACAGGGGC
Found at i:1519666 original size:14 final size:14
Alignment explanation
Indices: 1519647--1519704 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
1519637 GCGAAATGAA
1519647 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1519661 AATCGCAACGAGAAATG
1 AATCGCAACGAG--A-G
*
1519678 AAAATCGCAACGATAG
1 --AATCGCAACGAGAG
1519694 AATCGCAACGA
1 AATCGCAACGA
1519705 CAAAATCGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 23 0.61
16 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1519676 original size:33 final size:33
Alignment explanation
Indices: 1519629--1519704 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
1519619 AAAAATGACT
*
1519629 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGAGAAATGAAAATCGCAACGAGAGA
*
1519662 ATCGCAACGAGAAATGAAAATCGCAACGATAGA
1 ATCGCAACGAGAAATGAAAATCGCAACGAGAGA
1519695 ATCGCAACGA
1 ATCGCAACGA
1519705 CAAAATCGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGAAATGAAAATCGCAACGAGAGA
Found at i:1519685 original size:19 final size:19
Alignment explanation
Indices: 1519605--1519690 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
1519595 CACGAAACTT
*
1519605 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAAC--GAGAAATG
** *
1519626 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGAGAAATG
1519645 AAAATCGCAACGAG--A-G
1 AAAATCGCAACGAGAAATG
1519661 --AATCGCAACGAGAAATG
1 AAAATCGCAACGAGAAATG
1519678 AAAATCGCAACGA
1 AAAATCGCAACGA
1519691 TAGAATCGCA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
14 12 0.23
16 2 0.04
17 2 0.04
19 28 0.53
21 9 0.17
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGAGAAATG
Found at i:1519711 original size:14 final size:14
Alignment explanation
Indices: 1519678--1519717 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1519668 ACGAGAAATG
*
1519678 AAAATCGCAACGAT
1 AAAATCGCAACGAC
*
1519692 AGAATCGCAACGAC
1 AAAATCGCAACGAC
*
1519706 AAAATCGTAACG
1 AAAATCGCAACG
1519718 CGAAACCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1519729 original size:47 final size:47
Alignment explanation
Indices: 1519647--1519736 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 47
1519637 GCGAAATGAA
* * **
1519647 AATCGCAACGAGAGAATCGCAACGAGAAATGAAAATCGCAACGATAG
1 AATCGCAACGACAAAATCGCAACGAGAAACCAAAATCGCAACGATAG
* *
1519694 AATCGCAACGACAAAATCGTAACGCGAAACCAAAATCGCAACG
1 AATCGCAACGACAAAATCGCAACGAGAAACCAAAATCGCAACG
1519737 CGAAACTATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (47 bp):
AATCGCAACGACAAAATCGCAACGAGAAACCAAAATCGCAACGATAG
Found at i:1519750 original size:19 final size:19
Alignment explanation
Indices: 1519705--1519742 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1519695 ATCGCAACGA
*
1519705 CAAAATCGTAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
1519724 CAAAATCGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
1519743 TATAATCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.08
Consensus pattern (19 bp):
CAAAATCGCAACGCGAAAC
Found at i:1519789 original size:14 final size:14
Alignment explanation
Indices: 1519770--1519826 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1519760 TTTGGTTTCG
*
1519770 CGTTGCGATTCTAT
1 CGTTGCGATTCTCT
1519784 CGTTGCGATTTTCATTTCT
1 CGTTGCGA--TTC---TCT
1519803 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1519817 CGTTGCGATT
1 CGTTGCGATT
1519827 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 21 0.57
16 3 0.08
17 3 0.08
19 10 0.27
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1519795 original size:33 final size:33
Alignment explanation
Indices: 1519765--1519844 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1519755 GCAATTTTGG
1519765 TTTCGCGTTGCGATTCTATCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTATCGTTGCGATTTTCA
* *
1519798 TTTCTCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTATCGTTGCGATTTTCA
1519831 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1519845 AGTCATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTATCGTTGCGATTTTCA
Found at i:1519807 original size:19 final size:19
Alignment explanation
Indices: 1519783--1519868 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
1519773 TGCGATTCTA
1519783 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
1519802 TCGTTGCGA--TTC---TC
1 TCGTTGCGATTTTCATTTC
1519816 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
* **
1519835 GCGTTGCGATAGTCATTTTTC
1 TCGTTGCGATTTTCA--TTTC
*
1519856 ACGTTGCGATTTT
1 TCGTTGCGATTTT
1519869 AAGTTTCGTG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
14 11 0.20
16 3 0.06
17 3 0.06
19 23 0.43
21 14 0.26
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.48
Consensus pattern (19 bp):
TCGTTGCGATTTTCATTTC
Found at i:1520140 original size:95 final size:92
Alignment explanation
Indices: 1519995--1520187 Score: 305
Period size: 95 Copynumber: 2.1 Consensus size: 92
1519985 GAATACACAG
* * * *
1519995 TTTAGTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTTACTTCAACCAAAAGACAAAAAAAAGACAAATACTACTTCACAGTGTTAAAGAATAAACAGTT
1520060 TAGCAGAATTGACAGCAACCGAATAAA
66 TAGCAGAATTGACAGCAACCGAATAAA
1520087 TTTACTTCAACCAAAAGACAAAGCAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACA
1 TTTACTTCAACCAAAAGACAAA--AAAAAGACAAATACT-ACTTCACAGTGTTAAAGAATAAACA
* *
1520152 GTTTAGCAGTATTGGCAGCAACCGAATAAA
63 GTTTAGCAGAATTGACAGCAACCGAATAAA
1520182 TTTACT
1 TTTACT
1520188 AAGCAATCTA
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
92 21 0.23
94 14 0.15
95 57 0.62
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.23
Consensus pattern (92 bp):
TTTACTTCAACCAAAAGACAAAAAAAAGACAAATACTACTTCACAGTGTTAAAGAATAAACAGTT
TAGCAGAATTGACAGCAACCGAATAAA
Found at i:1522282 original size:20 final size:20
Alignment explanation
Indices: 1522257--1522351 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
1522247 CTTTAAAAAT
1522257 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1522277 CGCGTTGCGATTTTTACGGATA
1 CGCGTTGCGA--TTTACGGATA
* * * * *
1522299 CTCATTGCGATAGTAAGAAT-
1 CGCGTTGCGAT-TTACGGATA
*** *
1522319 CGCGTTGCGATTTATATATT
1 CGCGTTGCGATTTACGGATA
1522339 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1522352 TCATATTCGC
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.07
20 33 0.55
21 5 0.08
22 18 0.30
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1522357 original size:20 final size:20
Alignment explanation
Indices: 1522318--1522370 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1522308 ATAGTAAGAA
1522318 TCGCGTTGCGATTTATATAT
1 TCGCGTTGCGATTTATATAT
1522338 TCGCGTTGCGATTT-TCATAT
1 TCGCGTTGCGATTTAT-ATAT
*
1522358 TCGCGTTGTGATT
1 TCGCGTTGCGATT
1522371 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTATATAT
Found at i:1522402 original size:21 final size:20
Alignment explanation
Indices: 1522378--1522435 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
1522368 ATTCTGGAAA
*
1522378 ATCGCAATGCGAATTTGTACT
1 ATCGCATTGCGAATTTGTA-T
*
1522399 ATCGCATTGCG-ATTTTTAT
1 ATCGCATTGCGAATTTGTAT
* *
1522418 TTCGCATTGCGATTTTGT
1 ATCGCATTGCGAATTTGT
1522436 TGGTCATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 11 0.35
20 10 0.32
21 10 0.32
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (20 bp):
ATCGCATTGCGAATTTGTAT
Found at i:1524157 original size:2 final size:2
Alignment explanation
Indices: 1524150--1524190 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1524140 GGAGTTTGAA
1524150 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1524191 TGGTGGGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1529686 original size:3 final size:3
Alignment explanation
Indices: 1529678--1529758 Score: 83
Period size: 3 Copynumber: 26.7 Consensus size: 3
1529668 TCATTTAAAT
** **
1529678 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* *
1529727 TTA TTA ATA TTA ATA -TA TATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT
1529759 TAATAAATAT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
2 2 0.03
3 56 0.88
4 6 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1531142 original size:3 final size:3
Alignment explanation
Indices: 1531124--1531190 Score: 70
Period size: 3 Copynumber: 23.0 Consensus size: 3
1531114 TATTTTAATC
*
1531124 ATT ATTT ATT -TT ATT ATT ATT ATT ATT ATT -TT ATT GTT -TT AATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
*
1531168 ATT ATT -TC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
1531191 TATAAAAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
2 7 0.13
3 43 0.78
4 5 0.09
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:1531154 original size:20 final size:20
Alignment explanation
Indices: 1531111--1531190 Score: 92
Period size: 20 Copynumber: 4.0 Consensus size: 20
1531101 TTTTATTTCC
*
1531111 TTTTATT-TTAATCATTATTTA
1 TTTTATTATT-ATTATTA-TTA
1531132 TTTTATTATTATTATTATTA
1 TTTTATTATTATTATTATTA
*
1531152 TTTTATTGTT-TTAATTATTA
1 TTTTATTATTATT-ATTATTA
*
1531172 TTTCATTATTATTATTATT
1 TTTTATTATTATTATTATT
1531191 TATAAAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.04
20 33 0.63
21 15 0.29
22 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.69
Consensus pattern (20 bp):
TTTTATTATTATTATTATTA
Found at i:1531231 original size:14 final size:14
Alignment explanation
Indices: 1531191--1531231 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 14
1531181 TATTATTATT
1531191 TATAA-AAATAA-A
1 TATAATAAATAATA
1531203 TA-AATAAAT-ATA
1 TATAATAAATAATA
1531215 TATAATAAATAATA
1 TATAATAAATAATA
1531229 TAT
1 TAT
1531232 TTATTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.12
12 9 0.36
13 7 0.28
14 6 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TATAATAAATAATA
Found at i:1531503 original size:17 final size:17
Alignment explanation
Indices: 1531481--1531518 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1531471 ATATTTTATT
1531481 TATATTTTATATATAAA
1 TATATTTTATATATAAA
* *
1531498 TATATTTTTTATATAAT
1 TATATTTTATATATAAA
1531515 TATA
1 TATA
1531519 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:1532296 original size:2 final size:2
Alignment explanation
Indices: 1532187--1532277 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
1532177 ATGTTCTTAA
1532187 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
1532229 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
1532271 AT AT AT A
1 AT AT AT A
1532278 AAATGATTTA
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:1532996 original size:37 final size:36
Alignment explanation
Indices: 1532924--1532997 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
1532914 GTTGAAAAAT
*
1532924 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
* *
1532960 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATT-AAAATCATAAA
1532997 A
1 A
1532998 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 8 0.24
37 21 0.64
38 4 0.12
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:1535809 original size:16 final size:16
Alignment explanation
Indices: 1535788--1535819 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1535778 TGTGTCGTTG
1535788 GTGGAGGTTCGGTCGA
1 GTGGAGGTTCGGTCGA
*
1535804 GTGGAGGTTTGGTCGA
1 GTGGAGGTTCGGTCGA
1535820 CAACGGCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.50, T:0.28
Consensus pattern (16 bp):
GTGGAGGTTCGGTCGA
Found at i:1536367 original size:23 final size:23
Alignment explanation
Indices: 1536348--1536425 Score: 147
Period size: 23 Copynumber: 3.4 Consensus size: 23
1536338 TATTAGGTAT
*
1536348 CGCTTATATAATGTAATAGGTAG
1 CGCTTATATAATGTAATAAGTAG
1536371 CGCTTATATAATGTAATAAGTAG
1 CGCTTATATAATGTAATAAGTAG
1536394 CGCTTATATAATGTAATAAGTAG
1 CGCTTATATAATGTAATAAGTAG
1536417 CGCTTATAT
1 CGCTTATAT
1536426 TGACCTATTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (23 bp):
CGCTTATATAATGTAATAAGTAG
Found at i:1537250 original size:182 final size:182
Alignment explanation
Indices: 1536937--1537312 Score: 637
Period size: 182 Copynumber: 2.1 Consensus size: 182
1536927 TTTACTACTG
1536937 GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
1 GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
* * *
1537002 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCG
66 TTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAATGTCG
** *
1537067 ATACTTATAATAAAATATCGACACTTTCAACATATCCGGTAGCTCTTTACC-
131 ATACTTATAATAAAATATCGACACAATCAACATATCCGGTAGCGCTTTACCT
* *
1537118 GATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACA
1 G-TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
1537183 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAATGTC
65 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAATGTC
* * *
1537248 GATACTTATAATAAAGTATCGAGACAATCAACATATCTGGTAGCGCTTTACCT
130 GATACTTATAATAAAATATCGACACAATCAACATATCCGGTAGCGCTTTACCT
1537301 GTTTTGTCATTT
1 GTTTTGTCATTT
1537313 GTTTACCTGT
Statistics
Matches: 182, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
181 1 0.01
182 180 0.99
183 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
TTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAATGTCG
ATACTTATAATAAAATATCGACACAATCAACATATCCGGTAGCGCTTTACCT
Found at i:1537501 original size:112 final size:112
Alignment explanation
Indices: 1537301--1537518 Score: 391
Period size: 112 Copynumber: 1.9 Consensus size: 112
1537291 CGCTTTACCT
*
1537301 GTTTTGTCATTTGTTTACCTGTTATATTGTTATGGATCGATACATTGTTATAAAGTATCGACACT
1 GTTTTGTCATTTGTTTACCTGTTATATTGTTATAGATCGATACATTGTTATAAAGTATCGACACT
* *
1537366 TTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
66 TTCAATATATCAGGTAGCCCTTTACCTGTTTTGTCATTTATAGACCG
*
1537413 GTTTTGTCATTTGTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTGTTTACCTGTTATATTGTTATAGATCGATACATTGTTATAAAGTATCGACACT
*
1537478 TTCAATATATCAGGTAGCCCTTTATCTGTTTTGTCATTTAT
66 TTCAATATATCAGGTAGCCCTTTACCTGTTTTGTCATTTAT
1537519 CATTTTTTAC
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 101 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (112 bp):
GTTTTGTCATTTGTTTACCTGTTATATTGTTATAGATCGATACATTGTTATAAAGTATCGACACT
TTCAATATATCAGGTAGCCCTTTACCTGTTTTGTCATTTATAGACCG
Found at i:1537535 original size:98 final size:99
Alignment explanation
Indices: 1537419--1537616 Score: 328
Period size: 98 Copynumber: 2.0 Consensus size: 99
1537409 ACCGGTTTTG
1537419 TCATTTGTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTCAAT
1 TCATTTGTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTCAAT
*
1537484 ATATCAGGTAGCCCTTTA-TCTGTTTTGTCATTTA
66 ATATCAGGTAGCCCTTTACT-TGTTTTGCCATTTA
* *
1537518 TCATTT-TTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGATACTTTCAAT
1 TCATTTGTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTCAAT
* *
1537582 ATATCCGGTAGCGCTTTACTTGTTTTGCCATTTA
66 ATATCAGGTAGCCCTTTACTTGTTTTGCCATTTA
1537616 T
1 T
1537617 AGACCGATTT
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
98 86 0.92
99 7 0.08
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (99 bp):
TCATTTGTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTCAAT
ATATCAGGTAGCCCTTTACTTGTTTTGCCATTTA
Found at i:1537616 original size:210 final size:211
Alignment explanation
Indices: 1537307--1537686 Score: 654
Period size: 210 Copynumber: 1.8 Consensus size: 211
1537297 ACCTGTTTTG
1537307 TCATTTGTTTACCTGTTATATTGTTATGGATCGATACATTGTTATAAAGTATCGACACTTTCAAT
1 TCATTTGTTTACCTGTTATATTGTTATGGATCGATACATTGTTATAAAGTATCGACACTTTCAAT
* *
1537372 ATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTGTTTACCTGTTA
66 ATATCCGGTAGCGCTTTACCTGTTTTGCCATTTATAGACCGATTTTGTCATTTGTTTACCTGTTA
* *
1537437 TATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCAGGTAGCCCTTTA
131 TATTGTTATAGATCAATACATTTTTATAAAGCATCGACACTTTCAATATATCAGGTAGCCCTTTA
1537502 TCTGTTTTGTCATTTA
196 TCTGTTTTGTCATTTA
* *
1537518 TCATTT-TTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGATACTTTCAAT
1 TCATTTGTTTACCTGTTATATTGTTATGGATCGATACATTGTTATAAAGTATCGACACTTTCAAT
* *
1537582 ATATCCGGTAGCGCTTTACTTGTTTTGCCATTTATAGACCGATTTTGTCATTTTTTTACCTGTTA
66 ATATCCGGTAGCGCTTTACCTGTTTTGCCATTTATAGACCGATTTTGTCATTTGTTTACCTGTTA
* * *
1537647 TATTGTTATGGATTAATATATTTTTATAAAGCATCGACAC
131 TATTGTTATAGATCAATACATTTTTATAAAGCATCGACAC
1537687 AAACCGACAA
Statistics
Matches: 158, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
210 152 0.96
211 6 0.04
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (211 bp):
TCATTTGTTTACCTGTTATATTGTTATGGATCGATACATTGTTATAAAGTATCGACACTTTCAAT
ATATCCGGTAGCGCTTTACCTGTTTTGCCATTTATAGACCGATTTTGTCATTTGTTTACCTGTTA
TATTGTTATAGATCAATACATTTTTATAAAGCATCGACACTTTCAATATATCAGGTAGCCCTTTA
TCTGTTTTGTCATTTA
Found at i:1545608 original size:15 final size:15
Alignment explanation
Indices: 1545556--1545624 Score: 68
Period size: 15 Copynumber: 4.4 Consensus size: 15
1545546 ATTTTGTAGC
1545556 ATTTTTATATTTAAT
1 ATTTTTATATTTAAT
* *
1545571 GTATTTAATATCTTAAT
1 AT-TTTTATAT-TTAAT
*
1545588 ATTTTTTATATTTTAT
1 A-TTTTTATATTTAAT
1545604 ATTTTTA-ATTTAAAT
1 ATTTTTATATTT-AAT
1545619 ATTTTT
1 ATTTTT
1545625 TTAAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
14 4 0.09
15 15 0.34
16 12 0.27
17 12 0.27
18 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (15 bp):
ATTTTTATATTTAAT
Found at i:1545620 original size:31 final size:33
Alignment explanation
Indices: 1545557--1545625 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
1545547 TTTTGTAGCA
* *
1545557 TTTTTATATTTAATGTATTTAATATCTTAATAT
1 TTTTTATATTTAATATATTTAATATCTAAATAT
* *
1545590 TTTTTATATTTTATATTTTTAAT-T-TAAATAT
1 TTTTTATATTTAATATATTTAATATCTAAATAT
1545621 TTTTT
1 TTTTT
1545626 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 11 0.34
32 1 0.03
33 20 0.62
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (33 bp):
TTTTTATATTTAATATATTTAATATCTAAATAT
Found at i:1553272 original size:24 final size:24
Alignment explanation
Indices: 1553221--1553283 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
1553211 GTCATAACCA
* *
1553221 TTTTTTTTTAAAACAATTAAGTAT
1 TTTTTTTTAAAAACAATTAAGTAC
*
1553245 TTTTTTTTAAAAAACAATTATG-AC
1 TTTTTTTT-AAAAACAATTAAGTAC
1553269 TTTTATTTTGAAAAA
1 TTTT-TTTT-AAAAA
1553284 TTGAGTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (24 bp):
TTTTTTTTAAAAACAATTAAGTAC
Found at i:1556114 original size:25 final size:25
Alignment explanation
Indices: 1556083--1556182 Score: 191
Period size: 25 Copynumber: 4.0 Consensus size: 25
1556073 AGTTAGGGGA
1556083 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1556108 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1556133 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
1556158 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1556183 GGGTTGTTGG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:1557042 original size:20 final size:20
Alignment explanation
Indices: 1557017--1557057 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1557007 AAACATATTT
*
1557017 TATTTTTACCTTAACTTAAA
1 TATTTTAACCTTAACTTAAA
* *
1557037 TATTTTAATCTTATCTTAAA
1 TATTTTAACCTTAACTTAAA
1557057 T
1 T
1557058 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTTAACCTTAACTTAAA
Found at i:1557093 original size:20 final size:22
Alignment explanation
Indices: 1557068--1557116 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
1557058 TTAAAAATAT
1557068 ATATTTTTATCTTA-ACTTA-A
1 ATATTTTTATCTTATACTTATA
* *
1557088 ATATTTTTATTTTATTCTTATA
1 ATATTTTTATCTTATACTTATA
1557110 ATATTTT
1 ATATTTT
1557117 AAAATTAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.52
21 4 0.16
22 8 0.32
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATTTTTATCTTATACTTATA
Found at i:1557106 original size:26 final size:26
Alignment explanation
Indices: 1557026--1557107 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
1557016 TTATTTTTAC
* *
1557026 CTTAACTTAAATATTTTAATCTTA-T
1 CTTAACTTAAATATTTTTATTTTATT
* * * *
1557051 CTTAAATTTAAAAATATATATTTT-TAT
1 CTT-AACTTAAATATTTTTATTTTAT-T
1557078 CTTAACTTAAATATTTTTATTTTATT
1 CTTAACTTAAATATTTTTATTTTATT
1557104 CTTA
1 CTTA
1557108 TAATATTTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
25 3 0.07
26 35 0.81
27 5 0.12
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.55
Consensus pattern (26 bp):
CTTAACTTAAATATTTTTATTTTATT
Found at i:1557138 original size:23 final size:24
Alignment explanation
Indices: 1557110--1557164 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
1557100 TATTCTTATA
1557110 ATATTTTAAAATTAAGAT-AAAAT
1 ATATTTTAAAATTAAGATGAAAAT
** *
1557133 ATATTTTTTAGTTAAGATGAAAAT
1 ATATTTTAAAATTAAGATGAAAAT
*
1557157 AAATTTTA
1 ATATTTTA
1557165 TTTCTTAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (24 bp):
ATATTTTAAAATTAAGATGAAAAT
Found at i:1557202 original size:29 final size:29
Alignment explanation
Indices: 1557126--1557202 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
1557116 TAAAATTAAG
* **
1557126 ATAAAATATATTTTTTAGTTAAGATGAAA
1 ATAAAATATATTTTTAAACTAAGATGAAA
* * *
1557155 ATAAATTTTATTTCTTAAACTAA-ATGAGA
1 ATAAAATATATTT-TTAAACTAAGATGAAA
1557184 ATAAAATATATATTTTAAA
1 ATAAAATATAT-TTTTAAA
1557203 ATTAAAATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
29 30 0.79
30 8 0.21
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (29 bp):
ATAAAATATATTTTTAAACTAAGATGAAA
Found at i:1557265 original size:30 final size:28
Alignment explanation
Indices: 1557215--1557498 Score: 126
Period size: 30 Copynumber: 10.5 Consensus size: 28
1557205 TAAAATTAAA
*
1557215 AAGAATAT-ATATTT--TAAGTTAAAAT
1 AAGAATATAATATTTAATAAGTTAAGAT
*
1557240 AAGAATAATTAATATTTAATAAGTTATGAT
1 AAGAAT-A-TAATATTTAATAAGTTAAGAT
* * **
1557270 AAGAATATAACTTTTTTAATAACTTAATTT
1 AAGAATATAA--TATTTAATAAGTTAAGAT
1557300 AAGAATATAATATATGTAATAAGTTAAGAT
1 AAGAATATAATAT-T-TAATAAGTTAAGAT
* * **
1557330 AAAAATAAAATATATTTTTAA---AA-ATT
1 AAGAATATAATAT-TTAATAAGTTAAGA-T
*
1557356 AAG-ATATTAA-A---AATTAAGATAAGAGT
1 AAGAATA-TAATATTTAA-TAAGTTAAGA-T
*
1557382 AA-AATAT-AT-TTT-TTAAGTTAAGAT
1 AAGAATATAATATTTAATAAGTTAAGAT
* **
1557406 AAGAATAAAATATATTTTTTAAGTTAAGAT
1 AAGAAT-ATA-ATATTTAATAAGTTAAGAT
*
1557436 AAGAATAT-AT-TTT--T-AGTTAAAAT
1 AAGAATATAATATTTAATAAGTTAAGAT
*
1557459 AAGAATA-AAAATTTAATAAGTTAAGAT
1 AAGAATATAATATTTAATAAGTTAAGAT
* *
1557486 AAAAATAAAATAT
1 AAGAATATAATAT
1557499 ATTTTTTAAT
Statistics
Matches: 197, Mismatches: 29, Indels: 63
0.68 0.10 0.22
Matches are distributed among these distances:
22 3 0.02
23 16 0.08
24 8 0.04
25 26 0.13
26 20 0.10
27 17 0.09
28 17 0.09
29 10 0.05
30 80 0.41
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (28 bp):
AAGAATATAATATTTAATAAGTTAAGAT
Found at i:1557367 original size:15 final size:15
Alignment explanation
Indices: 1557347--1557376 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1557337 AAATATATTT
1557347 TTAAAAATTAAGATA
1 TTAAAAATTAAGATA
1557362 TTAAAAATTAAGATA
1 TTAAAAATTAAGATA
1557377 AGAGTAAAAT
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:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (15 bp):
TTAAAAATTAAGATA
Found at i:1557389 original size:76 final size:75
Alignment explanation
Indices: 1557299--1557516 Score: 217
Period size: 76 Copynumber: 2.8 Consensus size: 75
1557289 TAACTTAATT
*
1557299 TAAGAATATAATATATGTAATAAGTTAAGATAAAAATAAAATATATTTTTAAAAATTAAGATATT
1 TAAGAATAAAATATAT-TAATAAGTTAAGATAAAAATAAAATATATTTTTAAAAATTAAGATATT
*
1557364 AAAAATTAAGA
65 AAAAATTAAAA
* ** *
1557375 TAAGAGTAAAATATATTTTTTAAGTTAAGATAAGAATAAAATATATTTTTTAAGTTAAGA-TAAG
1 TAAGAATAAAATATA-TTAATAAGTTAAGATAAAAATAAAATATA-TTTTTAA---AA-ATTAAG
*** *
1557439 AATATATTTTTAGTTAAAA
60 ---ATATTAAAAATTAAAA
* *
1557458 TAAGAATAAAA-AT-TTAATAAGTTAAGATAAAAATAAAATATATTTTTTAATATTAAGAT
1 TAAGAATAAAATATATTAATAAGTTAAGATAAAAATAAAATATATTTTTAAAAATTAAGAT
1557517 GTGAATTTAA
Statistics
Matches: 116, Mismatches: 16, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
73 2 0.02
75 1 0.01
76 43 0.37
77 8 0.07
79 6 0.05
80 32 0.28
81 1 0.01
82 2 0.02
83 21 0.18
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.38
Consensus pattern (75 bp):
TAAGAATAAAATATATTAATAAGTTAAGATAAAAATAAAATATATTTTTAAAAATTAAGATATTA
AAAATTAAAA
Found at i:1557398 original size:25 final size:24
Alignment explanation
Indices: 1557369--1557449 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 24
1557359 ATATTAAAAA
1557369 TTAAGATAAGAGTAAAATATATTTTTT
1 TTAAGATAAGA-TAAAATATA--TTTT
1557396 AAGTTAAGATAAGAATAAAATATATTTT
1 ---TTAAGATAAG-ATAAAATATATTTT
*
1557424 TTAAGTTAAGATAAGAATATATTTT
1 TTAAGATAAGATAA-AATATATTTT
1557449 T
1 T
1557450 AGTTAAAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
24 4 0.08
25 20 0.42
28 4 0.08
30 19 0.40
31 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (24 bp):
TTAAGATAAGATAAAATATATTTT
Found at i:1557448 original size:23 final size:23
Alignment explanation
Indices: 1557399--1557492 Score: 73
Period size: 25 Copynumber: 3.8 Consensus size: 23
1557389 ATTTTTTAAG
*
1557399 TTAAGATAAGAATAA-AATATATTTT
1 TTAAGTTAAG-ATAAGAATATA--TT
1557424 TTAAGTTAAGATAAGAATATATT
1 TTAAGTTAAGATAAGAATATATT
* * *
1557447 TTTAGTTAAAATAAGAATAAAAATT
1 TTAAGTTAAGATAAGAAT--ATATT
*
1557472 TAATAAGTTAAGATAAAAATA
1 T--TAAGTTAAGATAAGAATA
1557493 AAATATATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
23 18 0.32
24 4 0.07
25 21 0.37
27 14 0.25
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (23 bp):
TTAAGTTAAGATAAGAATATATT
Found at i:1557498 original size:55 final size:54
Alignment explanation
Indices: 1557369--1557504 Score: 141
Period size: 55 Copynumber: 2.5 Consensus size: 54
1557359 ATATTAAAAA
* * * ***
1557369 TTAAGATAAGAGTAAAATATATTTTTTAAGTTAAGATAAGAATAAAATATATTTT
1 TTAAGATAAAAATAAAATATA-TTTTTAAGTTAAAATAAGAATAAAATATATAAG
* * *
1557424 TTAAG-TTAAGATAAGAATATATTTTT-AGTTAAAATAAGAATAAAAATTTAATAAG
1 TTAAGATAAAAATAA-AATATATTTTTAAGTTAAAATAAGAAT-AAAATAT-ATAAG
1557479 TTAAGATAAAAATAAAATATATTTTT
1 TTAAGATAAAAATAAAATATATTTTT
1557505 TAATATTAAG
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
53 14 0.21
54 16 0.24
55 29 0.44
56 7 0.11
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (54 bp):
TTAAGATAAAAATAAAATATATTTTTAAGTTAAAATAAGAATAAAATATATAAG
Found at i:1558566 original size:24 final size:24
Alignment explanation
Indices: 1558534--1558586 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1558524 CTGGCGGTCC
*
1558534 GTGACATTAGCGTCGAATGTCTTA
1 GTGACATTAGCGTCGAATATCTTA
*
1558558 GTGACATTAGCGTCGAATATTTTA
1 GTGACATTAGCGTCGAATATCTTA
1558582 GTGAC
1 GTGAC
1558587 CAATTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (24 bp):
GTGACATTAGCGTCGAATATCTTA
Done.