Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007838.1 Hibiscus syriacus cultivar Beakdansim tig00110187_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: 3429202
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:1280765 original size:165 final size:165
Alignment explanation
Indices: 1280579--1280908 Score: 552
Period size: 165 Copynumber: 2.0 Consensus size: 165
1280569 TTAGCCAAAA
* *
1280579 GGATTCTTTTTAGGATTTTTGGTATTCCTTTCATCTGATCCATCGTCAGCTCTCCTGATGGCTAA
1 GGATTCTTTTTAGGATTTTTGGTATTCATTTCATCTGATCCATCGTCAGCTCTCCTGAGGGCTAA
* * * *
1280644 TGGTCAGCTGGCAAAGTTCCCTTTATACTGCTGTTCTGACTAGAGTAATATTATCTTTAGATTTT
66 TGGCCAGCTGGCAAAGTTCCCTTTACACTGCTGTTCTGAATAGAGTAATAATATCTTTAGATTTT
1280709 ATGTTGTTAAATCAACTGCTAAACTTCTTGGATTC
131 ATGTTGTTAAATCAACTGCTAAACTTCTTGGATTC
*
1280744 GGATTCTTTTTAGGATTTTTGGTATTCATTTCATCTGATCCATCGTCAGCTCTCCTTAGGGCTAA
1 GGATTCTTTTTAGGATTTTTGGTATTCATTTCATCTGATCCATCGTCAGCTCTCCTGAGGGCTAA
* * *
1280809 TGGCCAGCTGGTAAAGTTCCCTTTCCACTGCTGTTTTGAATAGAGTAATAATATCTTTAGATTTT
66 TGGCCAGCTGGCAAAGTTCCCTTTACACTGCTGTTCTGAATAGAGTAATAATATCTTTAGATTTT
* *
1280874 ATGTTGTTAAATCAGCTGTTAAACTTCTTGGATTC
131 ATGTTGTTAAATCAACTGCTAAACTTCTTGGATTC
1280909 TTACTTGAGG
Statistics
Matches: 153, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
165 153 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (165 bp):
GGATTCTTTTTAGGATTTTTGGTATTCATTTCATCTGATCCATCGTCAGCTCTCCTGAGGGCTAA
TGGCCAGCTGGCAAAGTTCCCTTTACACTGCTGTTCTGAATAGAGTAATAATATCTTTAGATTTT
ATGTTGTTAAATCAACTGCTAAACTTCTTGGATTC
Found at i:1281497 original size:19 final size:20
Alignment explanation
Indices: 1281460--1281499 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1281450 GGTATTGGCT
*
1281460 TCATTTTTTTCCTTGTTTTC
1 TCATTTTGTTCCTTGTTTTC
*
1281480 TCATTTTGTT-CTTTTTTTC
1 TCATTTTGTTCCTTGTTTTC
1281499 T
1 T
1281500 GGCATCACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.05, C:0.17, G:0.05, T:0.72
Consensus pattern (20 bp):
TCATTTTGTTCCTTGTTTTC
Found at i:1288414 original size:4 final size:4
Alignment explanation
Indices: 1288407--1288458 Score: 52
Period size: 4 Copynumber: 12.0 Consensus size: 4
1288397 TTCATAAAAA
1288407 AAAT AAAT AAAT AGACAT GAGAAAT AA-T AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT A-A-AT -A-A-AT AAAT AAAT AAAT AAAT AAAT AAAT
1288455 AAAT
1 AAAT
1288459 TTTATTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
3 3 0.07
4 30 0.70
5 2 0.05
6 3 0.07
7 5 0.12
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1291783 original size:3 final size:3
Alignment explanation
Indices: 1291775--1291807 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
1291765 TGTAAATTCT
1291775 TAA TAA TAA -AA TAA TAA TAA TAA TAA TACA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
1291808 CGAGAACCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1292277 original size:37 final size:37
Alignment explanation
Indices: 1292221--1292316 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
1292211 CGTGCAAAGG
* * *
1292221 TGCATGTGTTTTAACGGTACCATTTAATATTTACATA
1 TGCATGTGTTATAACGGTACAATTTAATATTTACACA
* * *
1292258 TGCAAGTGTTATAATGGTACAATTTTATATTTACACA
1 TGCATGTGTTATAACGGTACAATTTAATATTTACACA
* *
1292295 TGCATGTGTTGTAACAGTACAA
1 TGCATGTGTTATAACGGTACAA
1292317 AATTCTATTA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (37 bp):
TGCATGTGTTATAACGGTACAATTTAATATTTACACA
Found at i:1293533 original size:37 final size:37
Alignment explanation
Indices: 1293476--1293571 Score: 156
Period size: 37 Copynumber: 2.6 Consensus size: 37
1293466 CGTGCAACGG
*
1293476 TGCAAGTGTTTTAACGGTACAATTTTATATTTACACA
1 TGCAAGTGTTATAACGGTACAATTTTATATTTACACA
*
1293513 TGCAAGTGTTATAACAGTACAATTTTATATTTACACA
1 TGCAAGTGTTATAACGGTACAATTTTATATTTACACA
* *
1293550 TACATGTGTTATAACGGTACAA
1 TGCAAGTGTTATAACGGTACAA
1293572 AATTAAAATC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (37 bp):
TGCAAGTGTTATAACGGTACAATTTTATATTTACACA
Found at i:1294306 original size:3 final size:3
Alignment explanation
Indices: 1294298--1294327 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1294288 TGTAAATTGT
1294298 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1294328 ATAACGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1294790 original size:37 final size:37
Alignment explanation
Indices: 1294749--1294834 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 37
1294739 TGCGAAGGTG
1294749 CAAGTGTTATAACGATACAATTTAATATTTACACATA
1 CAAGTGTTATAACGATACAATTTAATATTTACACATA
* * * *
1294786 CAAGTGTTATAATGGTACAATTTTATATTTACACATG
1 CAAGTGTTATAACGATACAATTTAATATTTACACATA
*
1294823 CATGTGTTATAA
1 CAAGTGTTATAA
1294835 AAGTACAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (37 bp):
CAAGTGTTATAACGATACAATTTAATATTTACACATA
Found at i:1294841 original size:37 final size:37
Alignment explanation
Indices: 1294747--1294842 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
1294737 CGTGCGAAGG
*
1294747 TGCAAGTGTTAT-AACGATACAATTTAATATTTACACA
1 TGCAAGTGTTATAAAAG-TACAATTTAATATTTACACA
* ** *
1294784 TACAAGTGTTATAATGGTACAATTTTATATTTACACA
1 TGCAAGTGTTATAAAAGTACAATTTAATATTTACACA
*
1294821 TGCATGTGTTATAAAAGTACAA
1 TGCAAGTGTTATAAAAGTACAA
1294843 AATTCTCTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
37 48 0.96
38 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (37 bp):
TGCAAGTGTTATAAAAGTACAATTTAATATTTACACA
Found at i:1295570 original size:3 final size:3
Alignment explanation
Indices: 1295562--1295594 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1295552 TGTAAATTGT
1295562 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1295595 ATAACTAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1296078 original size:37 final size:37
Alignment explanation
Indices: 1296028--1296124 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
1296018 ACGTGTAACG
*
1296028 GTGCAAGTGTTATAACGCTACAATTTTATATTTACAC
1 GTGCAAGTGTTATAACGGTACAATTTTATATTTACAC
* *
1296065 GTGCAAGCGTTATAACGGTACAATTTTATATTTACAT
1 GTGCAAGTGTTATAACGGTACAATTTTATATTTACAC
* *
1296102 ATGCATGTGTTATAACGGTACAA
1 GTGCAAGTGTTATAACGGTACAA
1296125 AATTAAAATC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (37 bp):
GTGCAAGTGTTATAACGGTACAATTTTATATTTACAC
Found at i:1296859 original size:3 final size:3
Alignment explanation
Indices: 1296851--1296892 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
1296841 TGTAAATTGT
1296851 TAA TAA TAA TAA TAA TAA TAA TTAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
1296893 ATGACAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1297370 original size:37 final size:37
Alignment explanation
Indices: 1297320--1297452 Score: 248
Period size: 37 Copynumber: 3.6 Consensus size: 37
1297310 CGTGCAACGG
1297320 TGCAAGTGTTATAACGGTACAATTTTATATTTACACA
1 TGCAAGTGTTATAACGGTACAATTTTATATTTACACA
*
1297357 TGCAAGTGTTATAACGGTACAATTTTATATTTACGCA
1 TGCAAGTGTTATAACGGTACAATTTTATATTTACACA
1297394 TGCAAGTGTTATAACGGTACAATTTTATATTTACACA
1 TGCAAGTGTTATAACGGTACAATTTTATATTTACACA
*
1297431 TGCATGTGTTATAACGGTACAA
1 TGCAAGTGTTATAACGGTACAA
1297453 AATTAAAATC
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 93 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (37 bp):
TGCAAGTGTTATAACGGTACAATTTTATATTTACACA
Found at i:1298717 original size:37 final size:36
Alignment explanation
Indices: 1298631--1298726 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 36
1298621 CGTGCAACGG
1298631 TGCAAGTGTTATAACGATACAATTTTATATTTACACA
1 TGCAAGTGTTATAACG-TACAATTTTATATTTACACA
** *
1298668 TGCAAGAATTATAACTGTACAATTTTATATTTACACT
1 TGCAAGTGTTATAAC-GTACAATTTTATATTTACACA
**
1298705 TGCTTGTGTTATAACGGTACAA
1 TGCAAGTGTTATAAC-GTACAA
1298727 AATTAAAATC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
37 49 0.98
38 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (36 bp):
TGCAAGTGTTATAACGTACAATTTTATATTTACACA
Found at i:1299466 original size:3 final size:3
Alignment explanation
Indices: 1299458--1299484 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1299448 TGTAAATTGT
1299458 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1299485 ATAACTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1299955 original size:37 final size:37
Alignment explanation
Indices: 1299905--1299989 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
1299895 CATGCAACGG
* * * **
1299905 TGCAAGTATTATAACGGTACACTTTTATATTTACTTA
1 TGCAAGTGTTATAACAGTACAATTTTATATTTACACA
1299942 TGCAAGTGTTATAACAGTACAATTTTATATTTACACA
1 TGCAAGTGTTATAACAGTACAATTTTATATTTACACA
*
1299979 TGCATGTGTTA
1 TGCAAGTGTTA
1299990 GACCATCTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (37 bp):
TGCAAGTGTTATAACAGTACAATTTTATATTTACACA
Found at i:1300186 original size:13 final size:13
Alignment explanation
Indices: 1300170--1300200 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1300160 TTTTTTGTTA
1300170 TTTTTTTACTTTC
1 TTTTTTTACTTTC
*
1300183 TTTTTTTATTTTC
1 TTTTTTTACTTTC
1300196 TTTTT
1 TTTTT
1300201 CTTTTATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTACTTTC
Found at i:1300313 original size:15 final size:17
Alignment explanation
Indices: 1300293--1300324 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1300283 CATAATATAA
1300293 TAAATT-CAAG-TAGAT
1 TAAATTGCAAGATAGAT
1300308 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
1300325 AAAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:1314536 original size:214 final size:213
Alignment explanation
Indices: 1313947--1314514 Score: 708
Period size: 214 Copynumber: 2.6 Consensus size: 213
1313937 CCCGACACGA
* *
1313947 TATATATTTAGGAATAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGACACTGT
1 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTGT
* * * * **
1314012 TTTTATTGAATAAAAATATTTTTTTTTATTATTTAGGGTCGGTCGGGTCGGGTTTCTAATTCATA
66 TTTTATTGAATAAAAATA-ATTTTATTATTATTT--CG--GGTCGAGTCGGG-TTGAAATTCATA
*
1314077 TATTTGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGGTCGGTTTGGGTTTAGG
125 TATTCGGGTCGGGTCGGGTGAAACTTTA--TT--T----T--GGTCGGGTC-----GGGTTTAGG
* * *
1314142 GTGAAAAATATCCGACCTGAAAAATATATTATTTTACCT
175 GTGAAAAATACCCGACCCGAAAAATATATAATTTTACCT
*
1314181 TATATATTTAGGAATAATTACAATAATACCTCTCTATATATAATTTTTTTTTTCAATTAAGTCAC
1 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATAA---TTTTTTTCAATTAAGTCAC
* * **
1314246 TGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCTGGTCGAGTCGGGTTTTTAATTCATATA
63 TGTTTTTATTGAATAAAAATAATTTTATTATTATTTCGGGTCGAGTCGGG-TTGAAATTCATATA
1314311 TTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTTTAGGGTGAAAAATACCCGACC
127 TTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTTTAGGGTGAAAAATACCCGACC
1314376 CGAAAAAATATATAATTTTACCT
192 CG-AAAAATATATAATTTTACCT
* *
1314399 TATATATTTAGTAATAATTACAATAATACCCCTCTATATATAA-TTTTTTCAATTAAGTCATTGT
1 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTGT
*
1314463 TTTTATTGAATAAAAATAATTTTATTATTATTTCGGGTCGGGTCGGG-TGAAA
66 TTTTATTGAATAAAAATAATTTTATTATTATTTCGGGTCGAGTCGGGTTGAAA
1314515 CTTTATTTTG
Statistics
Matches: 310, Mismatches: 20, Indels: 30
0.86 0.06 0.08
Matches are distributed among these distances:
212 3 0.01
214 64 0.21
217 26 0.08
218 60 0.19
222 9 0.03
224 1 0.00
228 1 0.00
230 2 0.01
232 50 0.16
234 41 0.13
236 14 0.05
237 39 0.13
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (213 bp):
TATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTGT
TTTTATTGAATAAAAATAATTTTATTATTATTTCGGGTCGAGTCGGGTTGAAATTCATATATTCG
GGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTTTAGGGTGAAAAATACCCGACCCGAA
AAATATATAATTTTACCT
Found at i:1317058 original size:2 final size:2
Alignment explanation
Indices: 1317051--1317083 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1317041 TAAATTACTT
*
1317051 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1317084 TAATTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1318314 original size:9 final size:9
Alignment explanation
Indices: 1318273--1318312 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
1318263 AAAATATTTT
1318273 ATTTTATTA
1 ATTTTATTA
1318282 ATATTTATTA
1 AT-TTTATTA
1318292 ATTTTATTA
1 ATTTTATTA
*
1318301 A-TTAATTA
1 ATTTTATTA
1318309 ATTT
1 ATTT
1318313 AAAACAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 7 0.25
9 12 0.43
10 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTTTATTA
Found at i:1318481 original size:73 final size:73
Alignment explanation
Indices: 1318362--1318582 Score: 352
Period size: 73 Copynumber: 3.0 Consensus size: 73
1318352 CAATCTCTTT
* * * **
1318362 GTTTTCTCCCAACGGTACAAAATTATATTTGCAAAGAAAGAATCAAGAACCGGTTCTCTCTCTTC
1 GTTTTCCCCCAACGGTACAAAATTTTACTTGCAAAGAAAGAATCAAGAACCGGTGATCTCTCTTC
1318427 TCCTCAGA
66 TCCTCAGA
*
1318435 GTTTTCCCCCAACGGTACAAAATTTTACTTGCAAAGAAAGAATCAAGAACCGGTGATCTCTCTTA
1 GTTTTCCCCCAACGGTACAAAATTTTACTTGCAAAGAAAGAATCAAGAACCGGTGATCTCTCTTC
1318500 TCCTCAGA
66 TCCTCAGA
* * * *
1318508 GTTTTCCCCCAACGGTACAAAACTTTACTTGCAAAGAAAGAATCAGGAACCAGTGATCTTTCTTC
1 GTTTTCCCCCAACGGTACAAAATTTTACTTGCAAAGAAAGAATCAAGAACCGGTGATCTCTCTTC
1318573 TCCTCAGA
66 TCCTCAGA
1318581 GT
1 GT
1318583 AGTATAAAAT
Statistics
Matches: 137, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 137 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (73 bp):
GTTTTCCCCCAACGGTACAAAATTTTACTTGCAAAGAAAGAATCAAGAACCGGTGATCTCTCTTC
TCCTCAGA
Found at i:1323687 original size:4 final size:4
Alignment explanation
Indices: 1323678--1323707 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1323668 GAAACATTGG
1323678 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1323708 CTCTTCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1324714 original size:231 final size:231
Alignment explanation
Indices: 1324311--1324769 Score: 891
Period size: 231 Copynumber: 2.0 Consensus size: 231
1324301 ATGTAATTGC
1324311 GTGACTGTGGTTTAAAATTACAAGTAACTGCTCGTTCAATTGTTGAAGCCAAAAAGCGATTTGAG
1 GTGACTGTGGTTTAAAATTACAAGTAACTGCTCGTTCAATTGTTGAAGCCAAAAAGCGATTTGAG
*
1324376 TTTTTGGAAGCTGTTAGTGAGACCATGGGTGCACATCTTCAATACTTCAAACAGGTTATCACATG
66 TTTTTGGAAGCTGTTAGTGAGACCATGGATGCACATCTTCAATACTTCAAACAGGTTATCACATG
1324441 GCAGAATTTCTCAATTTCTTTCTCATTGTTTCTATCACTTGCTAGATGCATTGTTCATGATGAAC
131 GCAGAATTTCTCAATTTCTTTCTCATTGTTTCTATCACTTGCTAGATGCATTGTTCATGATGAAC
1324506 TTTTGTTATTTATGTAGGGCTATGAATTATTGCCAT
196 TTTTGTTATTTATGTAGGGCTATGAATTATTGCCAT
1324542 GTGACTGTGGTTTAAAATTACAAGTAACTGCTCGTTCAATTGTTGAAGCCAAAAAGCGATTTGAG
1 GTGACTGTGGTTTAAAATTACAAGTAACTGCTCGTTCAATTGTTGAAGCCAAAAAGCGATTTGAG
* *
1324607 TTTTTGGAAGCTGTTAGTGAGACTATGGATGCACATCTTCAATACTTCAAACAGGTTATCACGTG
66 TTTTTGGAAGCTGTTAGTGAGACCATGGATGCACATCTTCAATACTTCAAACAGGTTATCACATG
1324672 GCAGAATTTCTCAATTTCTTTCTCATTGTTTCTATCACTTGCTAGATGCATTGTTCATGATGAAC
131 GCAGAATTTCTCAATTTCTTTCTCATTGTTTCTATCACTTGCTAGATGCATTGTTCATGATGAAC
1324737 TTTTGTTATTTATGTAGGGCTATGAATTATTGC
196 TTTTGTTATTTATGTAGGGCTATGAATTATTGC
1324770 ATCAAATGGA
Statistics
Matches: 225, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
231 225 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (231 bp):
GTGACTGTGGTTTAAAATTACAAGTAACTGCTCGTTCAATTGTTGAAGCCAAAAAGCGATTTGAG
TTTTTGGAAGCTGTTAGTGAGACCATGGATGCACATCTTCAATACTTCAAACAGGTTATCACATG
GCAGAATTTCTCAATTTCTTTCTCATTGTTTCTATCACTTGCTAGATGCATTGTTCATGATGAAC
TTTTGTTATTTATGTAGGGCTATGAATTATTGCCAT
Found at i:1325144 original size:43 final size:42
Alignment explanation
Indices: 1325074--1325159 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
1325064 TTTATAGTTT
* *
1325074 TAAAAGATATTATTTAATAATTAAAAATATAATAAATTGTTA
1 TAAAAGATATTATTTAATAATTAAAAATATAAGAAATTATTA
* * *
1325116 TAAAATATATTACTTTAATATTTTAAAATATAAGAAATTATTA
1 TAAAAGATATTA-TTTAATAATTAAAAATATAAGAAATTATTA
1325159 T
1 T
1325160 TATATTGTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 11 0.29
43 27 0.71
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (42 bp):
TAAAAGATATTATTTAATAATTAAAAATATAAGAAATTATTA
Found at i:1333664 original size:8 final size:8
Alignment explanation
Indices: 1333651--1333681 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
1333641 ACATGCTTTT
1333651 GCATGTTA
1 GCATGTTA
1333659 GCATGTTA
1 GCATGTTA
1333667 GCATGTTA
1 GCATGTTA
1333675 GCATGTT
1 GCATGTT
1333682 TACAAGGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (8 bp):
GCATGTTA
Found at i:1334665 original size:165 final size:165
Alignment explanation
Indices: 1334389--1334718 Score: 570
Period size: 165 Copynumber: 2.0 Consensus size: 165
1334379 TTAGCCAAAA
*
1334389 GGATTCTTTTTAGGATTTTTGGTATTCCTTTCATCTGATCCATCCTCACCTCTCCTTAGAGCTAA
1 GGATTCTTTTTAGGATTTTTGGTATTCATTTCATCTGATCCATCCTCACCTCTCCTTAGAGCTAA
* * * *
1334454 TGGTCAGCTGGTAAAGTTCCCTTTCTACTGCTGTTCTGACTAGAGTAATATTATCTTTAGATTTT
66 TGGCCAGCTGGTAAAGTTCCCTTTCCACTGCTGTTCTGAATAGAGTAATAATATCTTTAGATTTT
1334519 ATGTTGTTAAATCAGCTGCTAAACTTCTTGGATTC
131 ATGTTGTTAAATCAGCTGCTAAACTTCTTGGATTC
* *
1334554 GGATTCTTTTTAGGATTTTTGGTATTCATTTCATCTGATCCATCGTCACCTCTCCTTAGGGCTAA
1 GGATTCTTTTTAGGATTTTTGGTATTCATTTCATCTGATCCATCCTCACCTCTCCTTAGAGCTAA
* *
1334619 TGGCCAGCTGGTAAAGTTCCCTTTCCACTGCTGTTTTGAATAGAGTAATAATATCTTTATATTTT
66 TGGCCAGCTGGTAAAGTTCCCTTTCCACTGCTGTTCTGAATAGAGTAATAATATCTTTAGATTTT
*
1334684 ATGTTGTTAAATCAGCTGTTAAACTTCTTGGATTC
131 ATGTTGTTAAATCAGCTGCTAAACTTCTTGGATTC
1334719 TTACCTGAGG
Statistics
Matches: 155, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
165 155 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (165 bp):
GGATTCTTTTTAGGATTTTTGGTATTCATTTCATCTGATCCATCCTCACCTCTCCTTAGAGCTAA
TGGCCAGCTGGTAAAGTTCCCTTTCCACTGCTGTTCTGAATAGAGTAATAATATCTTTAGATTTT
ATGTTGTTAAATCAGCTGCTAAACTTCTTGGATTC
Found at i:1335297 original size:64 final size:64
Alignment explanation
Indices: 1335196--1335323 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
1335186 AAGGCCTCCT
1335196 TAATCATAGGAAGGAGGAAAAGAGTGCCTTAGGTATTTATTCAACAACATAAAATACATAAGAA
1 TAATCATAGGAAGGAGGAAAAGAGTGCCTTAGGTATTTATTCAACAACATAAAATACATAAGAA
* *
1335260 TAATCATAGGAAGGATGAAAATAGTGCCTTAGGTATTTATTCAACAACATAAAATACATAAGAA
1 TAATCATAGGAAGGAGGAAAAGAGTGCCTTAGGTATTTATTCAACAACATAAAATACATAAGAA
1335324 ACAACCAGGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (64 bp):
TAATCATAGGAAGGAGGAAAAGAGTGCCTTAGGTATTTATTCAACAACATAAAATACATAAGAA
Found at i:1339787 original size:42 final size:43
Alignment explanation
Indices: 1339705--1339811 Score: 148
Period size: 42 Copynumber: 2.5 Consensus size: 43
1339695 TTTAAAAGAT
* * *
1339705 ATTA-TTTAATTATTAAAAATATAATAAATTGTTATAAAATAC
1 ATTATTTTAATTATTTAAAATATAAGAAATTATTATAAAATAC
*
1339747 ATTATTTTAA-TATTTTAAAATATAAGAAATTATTAT-AAATAT
1 ATTATTTTAATTA-TTTAAAATATAAGAAATTATTATAAAATAC
1339789 ATTATTTTAATTATTTAAAATAT
1 ATTATTTTAATTATTTAAAATAT
1339812 TGATATATTC
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
42 31 0.53
43 27 0.47
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (43 bp):
ATTATTTTAATTATTTAAAATATAAGAAATTATTATAAAATAC
Found at i:1341472 original size:17 final size:17
Alignment explanation
Indices: 1341450--1341483 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1341440 AATACATATT
1341450 TATTTAATAA-AAAATTA
1 TATTTAA-AATAAAATTA
1341467 TATTTAAAATAAAATTA
1 TATTTAAAATAAAATTA
1341484 ACACCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATTTAAAATAAAATTA
Found at i:1341609 original size:6 final size:6
Alignment explanation
Indices: 1341598--1341623 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1341588 CAATAATTAT
1341598 ATTAAA ATTAAA ATTAAA ATTAAA AT
1 ATTAAA ATTAAA ATTAAA ATTAAA AT
1341624 CAAATCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTAAA
Found at i:1347296 original size:17 final size:19
Alignment explanation
Indices: 1347274--1347313 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
1347264 TTCATTAAAG
1347274 ATAGATAT-ATAA-AATAA
1 ATAGATATAATAATAATAA
1347291 ATAGATATGAATAATAATAA
1 ATAGATAT-AATAATAATAA
1347311 ATA
1 ATA
1347314 AATGAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
19 4 0.20
20 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
ATAGATATAATAATAATAA
Found at i:1347296 original size:21 final size:20
Alignment explanation
Indices: 1347284--1347321 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1347274 ATAGATATAT
1347284 AAAATAAATAGATATGAATA
1 AAAATAAATAGATATGAATA
*
1347304 ATAATAAATA-A-ATGAATA
1 AAAATAAATAGATATGAATA
1347322 TTTAAATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
AAAATAAATAGATATGAATA
Found at i:1350291 original size:22 final size:23
Alignment explanation
Indices: 1350266--1350308 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1350256 GTTATTTTTA
* *
1350266 CTTT-AAATTTTATAAGTTCATT
1 CTTTAAAATTCTATAAATTCATT
1350288 CTTTAAAATTCTATAAATTCA
1 CTTTAAAATTCTATAAATTCA
1350309 CTTCATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (23 bp):
CTTTAAAATTCTATAAATTCATT
Found at i:1355786 original size:18 final size:19
Alignment explanation
Indices: 1355744--1355787 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1355734 ATATTTGACT
* *
1355744 TTATTTATAATTTTTTACA
1 TTATTTATAATTTTTAAAA
1355763 TCTATTTATAA-TTTTAAAA
1 T-TATTTATAATTTTTAAAA
1355782 TTATTT
1 TTATTT
1355788 TATATTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTTATAATTTTTAAAA
Found at i:1356810 original size:28 final size:26
Alignment explanation
Indices: 1356756--1356807 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1356746 ATTAATTAAA
1356756 AAATATAAAGAGAGTATATTATCTTT
1 AAATATAAAGAGAGTATATTATCTTT
1356782 AAATATATAAGAGA-TA-ATTATACTTT
1 AAATATA-AAGAGAGTATATTAT-CTTT
1356808 TTAGTCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 5 0.21
26 13 0.54
27 6 0.25
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (26 bp):
AAATATAAAGAGAGTATATTATCTTT
Found at i:1358876 original size:89 final size:89
Alignment explanation
Indices: 1358761--1358998 Score: 388
Period size: 89 Copynumber: 2.7 Consensus size: 89
1358751 AAAAAGATAG
*
1358761 CCAACCTAAGGATATTCCTTGGGGCCTATGGGCCTACCCAAGGGTATCCTTAGATCCGTAGGGTT
1 CCAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCCAAGGGTATCCTTAGATCCGTAGGGTT
* *
1358826 ACCATGAGCAC-CTAGCAAAGGGAA
66 ACCATAAGCACAC-AGCAAAGGAAA
* *
1358850 CCAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCCAAGGGTATCTTTAGATTCGTAGGGTT
1 CCAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCCAAGGGTATCCTTAGATCCGTAGGGTT
*
1358915 ACCTTAAGCACACAGCAAAGGAAA
66 ACCATAAGCACACAGCAAAGGAAA
* *
1358939 CCAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCTAAGGATATCCTTAGATCCGTA
1 CCAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCCAAGGGTATCCTTAGATCCGTA
1358999 TGGTCTTACC
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
89 137 0.99
90 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (89 bp):
CCAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCCAAGGGTATCCTTAGATCCGTAGGGTT
ACCATAAGCACACAGCAAAGGAAA
Found at i:1364918 original size:15 final size:15
Alignment explanation
Indices: 1364894--1364926 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1364884 GAGCTCAAGT
1364894 CGAGCCCATTCGATC
1 CGAGCCCATTCGATC
*
1364909 CGAGCTCATTCGATC
1 CGAGCCCATTCGATC
1364924 CGA
1 CGA
1364927 ATATTTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (15 bp):
CGAGCCCATTCGATC
Found at i:1372889 original size:35 final size:34
Alignment explanation
Indices: 1372804--1372890 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
1372794 ATTTGGTATT
*
1372804 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
1372838 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
1372876 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1372891 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:1374603 original size:14 final size:15
Alignment explanation
Indices: 1374557--1374600 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
1374547 TTTTTTTATT
1374557 AAAAAATCATTTTTA
1 AAAAAATCATTTTTA
1374572 AAATATAAT-ATTTTTA
1 AAA-A-AATCATTTTTA
1374588 AAAAAATCATTTT
1 AAAAAATCATTTT
1374601 AAATGACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.12
15 9 0.35
16 11 0.42
17 3 0.12
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAAAATCATTTTTA
Found at i:1374612 original size:31 final size:31
Alignment explanation
Indices: 1374557--1374618 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
1374547 TTTTTTTATT
*
1374557 AAAAAATCATTTTTAAAATATAATATTTTTA
1 AAAAAATCATTTTTAAAATATAATACTTTTA
1374588 AAAAAATCA-TTTT-AAATGACTAATACTTTTA
1 AAAAAATCATTTTTAAAAT-A-TAATACTTTTA
1374619 GGTTTTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 4 0.14
30 5 0.18
31 19 0.68
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (31 bp):
AAAAAATCATTTTTAAAATATAATACTTTTA
Found at i:1375276 original size:13 final size:14
Alignment explanation
Indices: 1375251--1375279 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1375241 CAAAATCTTT
1375251 CAAGAGTAGCAAAA
1 CAAGAGTAGCAAAA
1375265 CAAGAG-AGCAAAA
1 CAAGAGTAGCAAAA
1375278 CA
1 CA
1375280 TGCTCAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.17, G:0.21, T:0.03
Consensus pattern (14 bp):
CAAGAGTAGCAAAA
Found at i:1384541 original size:13 final size:13
Alignment explanation
Indices: 1384523--1384570 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1384513 TAAATTTATT
1384523 ATAAAATAAAAAA
1 ATAAAATAAAAAA
*
1384536 ATAAAATTAAAAA
1 ATAAAATAAAAAA
*
1384549 TTAAAA-AAAAAA
1 ATAAAATAAAAAA
1384561 CA-AAAATAAA
1 -ATAAAATAAA
1384571 TTATCAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 9 0.31
13 20 0.69
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (13 bp):
ATAAAATAAAAAA
Found at i:1385873 original size:36 final size:36
Alignment explanation
Indices: 1385826--1386102 Score: 450
Period size: 36 Copynumber: 7.7 Consensus size: 36
1385816 CGATACATCT
1385826 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCC
1 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCC
*
1385862 TTCCGTTCGACTTGAATCGAAAGTG-CTGATGCCTCC
1 TTCCGTTCGACTTGAATCGGAAGTGTC-GATGCCTCC
*
1385898 TTCCGTTCGACTTGAATCGAAAGTG-CTGATGCCTCC
1 TTCCGTTCGACTTGAATCGGAAGTGTC-GATGCCTCC
* *
1385934 TTCCGTTCGACTTGAATCGAAAGTGTCGATGCCTCA
1 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCC
*
1385970 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCA
1 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCC
*
1386006 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCA
1 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCC
*
1386042 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTCC
1 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCC
*
1386078 TTCCGTTTGACTTGAATCGGAAGTG
1 TTCCGTTCGACTTGAATCGGAAGTG
1386103 CTGATGTTTT
Statistics
Matches: 233, Mismatches: 6, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
35 1 0.00
36 231 0.99
37 1 0.00
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.31
Consensus pattern (36 bp):
TTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCC
Found at i:1385916 original size:72 final size:72
Alignment explanation
Indices: 1385800--1386108 Score: 455
Period size: 72 Copynumber: 4.3 Consensus size: 72
1385790 AAAGACAAAC
* * * * *
1385800 ACTTGAAACAAAAGTGC-GATACATCTTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTT
1 ACTTGAATCGAAAGTGCTGATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTT
1385864 CCGTTCG
66 CCGTTCG
* *
1385871 ACTTGAATCGAAAGTGCTGATGCCTCCTTCCGTTCGACTTGAATCGAAAGTG-CTGATGCCTCCT
1 ACTTGAATCGAAAGTGCTGATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTC-GATGCCTCCT
1385935 TCCGTTCG
65 TCCGTTCG
*
1385943 ACTTGAATCGAAAGTG-TCGATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCAT
1 ACTTGAATCGAAAGTGCT-GATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCT
1386007 TCCGTTCG
65 TCCGTTCG
* *
1386015 ACTTGAATCGGAAGTG-TCGATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTCCT
1 ACTTGAATCGAAAGTGCT-GATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCT
*
1386079 TCCGTTTG
65 TCCGTTCG
*
1386087 ACTTGAATCGGAAGTGCTGATG
1 ACTTGAATCGAAAGTGCTGATG
1386109 TTTTCTTTCG
Statistics
Matches: 220, Mismatches: 13, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
71 17 0.08
72 201 0.91
73 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (72 bp):
ACTTGAATCGAAAGTGCTGATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTT
CCGTTCG
Found at i:1385950 original size:108 final size:108
Alignment explanation
Indices: 1385800--1386108 Score: 462
Period size: 108 Copynumber: 2.9 Consensus size: 108
1385790 AAAGACAAAC
* * * * *
1385800 ACTTGAAACAAAAGTGC-GATACATCTTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTT
1 ACTTGAATCGAAAGTGCTGATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTT
* *
1385864 CCGTTCGACTTGAATCGAAAGTGCTGATGCCTCCTTCCGTTCG
66 CCGTTCGACTTGAATCGGAAGTGCTGATGCCTCATTCCGTTCG
* * *
1385907 ACTTGAATCGAAAGTGCTGATGCCTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCCTCATT
1 ACTTGAATCGAAAGTGCTGATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTT
1385972 CCGTTCGACTTGAATCGGAAGTG-TCGATGCCTCATTCCGTTCG
66 CCGTTCGACTTGAATCGGAAGTGCT-GATGCCTCATTCCGTTCG
* *
1386015 ACTTGAATCGGAAGTG-TCGATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTCCT
1 ACTTGAATCGAAAGTGCT-GATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCT
*
1386079 TCCGTTTGACTTGAATCGGAAGTGCTGATG
65 TCCGTTCGACTTGAATCGGAAGTGCTGATG
1386109 TTTTCTTTCG
Statistics
Matches: 183, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
107 17 0.09
108 165 0.90
109 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (108 bp):
ACTTGAATCGAAAGTGCTGATGCCTCATTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTT
CCGTTCGACTTGAATCGGAAGTGCTGATGCCTCATTCCGTTCG
Found at i:1387601 original size:21 final size:20
Alignment explanation
Indices: 1387568--1387633 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
1387558 CCAAGTAACC
*
1387568 AACAACCATAACAAACTAAT
1 AACAACAATAACAAACTAAT
*
1387588 AACAACTAATAACAAGCTAAT
1 AACAAC-AATAACAAACTAAT
* *
1387609 AATAAACCATAACAAACTAAT
1 AA-CAACAATAACAAACTAAT
1387630 AACA
1 AACA
1387634 CTCTAACATT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 7 0.18
21 28 0.74
22 3 0.08
ACGTcount: A:0.61, C:0.21, G:0.02, T:0.17
Consensus pattern (20 bp):
AACAACAATAACAAACTAAT
Found at i:1390226 original size:21 final size:21
Alignment explanation
Indices: 1390175--1390227 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1390165 ATTCTGACTA
1390175 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
1390196 TCACGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1390217 TCGCAATGCGA
1 TCGCATTGCGA
1390228 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1390242 original size:20 final size:20
Alignment explanation
Indices: 1390217--1390302 Score: 154
Period size: 20 Copynumber: 4.3 Consensus size: 20
1390207 TTTTCCTAAT
1390217 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1390237 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1390257 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1390277 TCGCAACGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
1390297 TCGCAA
1 TCGCAA
1390303 CGTGAATCTG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1390319 original size:20 final size:20
Alignment explanation
Indices: 1390296--1390382 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
1390286 GAATATGTAA
* *
1390296 ATCGCAACGTGAATCTGACT
1 ATCGCAACGAGATTCTGACT
*
1390316 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
1390336 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
1390356 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
1390376 ATCGCAA
1 ATCGCAA
1390383 TACTGAATTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:1390320 original size:40 final size:40
Alignment explanation
Indices: 1390236--1390364 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 40
1390226 GAATACGTAA
* * * * *
1390236 ATCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GTA-A
1 ATCGCAACGCGAATATGTAAATCGCAACGAGAAT-CTG-ACT
*
1390276 ATCGCAACGCGAATATGTAAATCGCAACGTGAATCTGACT
1 ATCGCAACGCGAATATGTAAATCGCAACGAGAATCTGACT
* * * *
1390316 ATCGCAACGCGATTCTG-ACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGAATATGTA-AATCGCAACGAGAATCTGACT
1390356 ATCGCAACG
1 ATCGCAACG
1390365 AGATTCTGAC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
39 3 0.04
40 73 0.96
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (40 bp):
ATCGCAACGCGAATATGTAAATCGCAACGAGAATCTGACT
Found at i:1391251 original size:24 final size:24
Alignment explanation
Indices: 1391224--1391277 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1391214 GTATTCGAAA
1391224 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1391248 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1391272 TTTGAT
1 TTTGAT
1391278 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1393738 original size:20 final size:19
Alignment explanation
Indices: 1393713--1393781 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
1393703 CAACGCGGAA
1393713 ATCGCAACGCAAATATGACT
1 ATCGCAACGCAAA-ATGACT
*
1393733 ATCGCAACATG-GAAATGACT
1 ATCGCAAC--GCAAAATGACT
1393753 ATCGCAACGCGAAAATGACT
1 ATCGCAACGC-AAAATGACT
1393773 ATCGCAACG
1 ATCGCAACG
1393782 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.02
20 39 0.91
21 2 0.05
22 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCAAAATGACT
Found at i:1393791 original size:34 final size:34
Alignment explanation
Indices: 1393694--1393837 Score: 141
Period size: 33 Copynumber: 4.1 Consensus size: 34
1393684 GACATTCATT
*
1393694 TGACTATCGCAACGCG-GAAATCGCAACGC-AAATA
1 TGACTATCGCAACGAGAG-AATCGCAACGCGAAA-A
*
1393728 TGACTATCGCAACATGGAAATGACTATCGCAACGCGAAAA
1 TGACTATCGCAAC---GAGA-GA--ATCGCAACGCGAAAA
*
1393768 TGACTATCGCAACGAGAGAATCGCAATGCG-AAA
1 TGACTATCGCAACGAGAGAATCGCAACGCGAAAA
** *
1393801 TGAAAATCGCAACGAGAGAATCGCAATGCGAAAA
1 TGACTATCGCAACGAGAGAATCGCAACGCGAAAA
1393835 TGA
1 TGA
1393838 AAATCGTAAC
Statistics
Matches: 95, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
33 31 0.33
34 29 0.31
36 2 0.02
37 4 0.04
38 1 0.01
39 1 0.01
40 24 0.25
41 3 0.03
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (34 bp):
TGACTATCGCAACGAGAGAATCGCAACGCGAAAA
Found at i:1393792 original size:14 final size:14
Alignment explanation
Indices: 1393773--1393826 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1393763 GAAAATGACT
1393773 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1393787 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
1393806 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1393820 ATCGCAA
1 ATCGCAA
1393827 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1393841 original size:34 final size:34
Alignment explanation
Indices: 1393753--1393848 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
1393743 GGAAATGACT
* **
1393753 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
1393787 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
1393820 ATCGCAATGCGAAAATGAAAATCGTAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
1393849 CGAATTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:1393906 original size:34 final size:34
Alignment explanation
Indices: 1393863--1393958 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 34
1393853 TTTAGTTTCG
1393863 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
*
1393897 CGTTGCGATTTTCA-TTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** ** * *
1393930 TTTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
1393959 AGTCTGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.53
34 25 0.47
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:1394083 original size:14 final size:14
Alignment explanation
Indices: 1394064--1394100 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1394054 CATCAATTAA
1394064 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1394078 ACAAATCATCTTTT
1 ACAAATCAACATTT
1394092 ACAAATCAA
1 ACAAATCAA
1394101 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1395583 original size:42 final size:42
Alignment explanation
Indices: 1395504--1395596 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1395494 CCTCTTCAAC
* * *
1395504 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
1395546 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
1395588 GATGACAGG
1 GATGACAGG
1395597 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:1396101 original size:20 final size:20
Alignment explanation
Indices: 1396076--1396164 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 20
1396066 GAAACTTAAA
1396076 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1396096 ACCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1396116 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1396136 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
1396156 ATTGCAACG
1 ATCGCAACG
1396165 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1396261 original size:20 final size:20
Alignment explanation
Indices: 1396209--1396365 Score: 135
Period size: 20 Copynumber: 8.5 Consensus size: 20
1396199 GATTCTTTCG
** *
1396209 TTGCGATAGTCAAATTCACA
1 TTGCGATAGTCATTTTCGCA
1396229 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1396249 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1396269 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
1396283 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1396302 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
1396316 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1396336 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1396356 TTGCGATAGT
1 TTGCGATAGT
1396366 AAACTATTCT
Statistics
Matches: 116, Mismatches: 7, Indels: 28
0.77 0.05 0.19
Matches are distributed among these distances:
14 14 0.12
16 12 0.10
17 6 0.05
18 5 0.04
19 7 0.06
20 72 0.62
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1396340 original size:34 final size:34
Alignment explanation
Indices: 1396188--1396342 Score: 152
Period size: 34 Copynumber: 4.4 Consensus size: 34
1396178 GCGATTTTCA
*
1396188 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAA
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
* *
1396222 ATTCACATTGCGATAGTCATTTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGAT--TC--TTTCG--TTGCGATAGTCAT
* * **
1396262 TTTCGCGTTGCGATT-TTGTTGTTGCGATTTTCA-
1 TTTCGCATTGCGATTCTT-TCGTTGCGATAGTCAT
*
1396295 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
*
1396329 TTTCGCGTTGCGAT
1 TTTCGCATTGCGAT
1396343 AGTCATTTTC
Statistics
Matches: 97, Mismatches: 15, Indels: 18
0.75 0.12 0.14
Matches are distributed among these distances:
33 26 0.27
34 36 0.37
35 2 0.02
36 4 0.04
38 6 0.06
40 23 0.24
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.43
Consensus pattern (34 bp):
TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
Found at i:1398288 original size:20 final size:20
Alignment explanation
Indices: 1398230--1398296 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
1398220 GAAATTTAAA
**
1398230 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
1398250 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
1398270 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
1398290 ATCGCAA
1 ATCGCAA
1398297 TGCAAGAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:1398497 original size:20 final size:20
Alignment explanation
Indices: 1398472--1398566 Score: 172
Period size: 20 Copynumber: 4.8 Consensus size: 20
1398462 CAGTTTAGCA
1398472 GTATTCGCATTGCGATTTAC
1 GTATTCGCATTGCGATTTAC
*
1398492 GTATTCGCATTGTGATTTAC
1 GTATTCGCATTGCGATTTAC
1398512 GTATTCGCATTGCGATTTAC
1 GTATTCGCATTGCGATTTAC
*
1398532 ATATTCGCATTGCGATTTAC
1 GTATTCGCATTGCGATTTAC
1398552 GTATTCGCATTGCGA
1 GTATTCGCATTGCGA
1398567 ATTAGGAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
GTATTCGCATTGCGATTTAC
Found at i:1398889 original size:15 final size:15
Alignment explanation
Indices: 1398869--1398898 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1398859 TAAAAGAGAT
1398869 TTTGAATTAATACTA
1 TTTGAATTAATACTA
1398884 TTTGAATTAATACTA
1 TTTGAATTAATACTA
1398899 CTCTTACAAT
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:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
TTTGAATTAATACTA
Found at i:1412323 original size:29 final size:29
Alignment explanation
Indices: 1412288--1412369 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1412278 AAACTAAATT
*
1412288 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1412317 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1412346 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1412370 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1414556 original size:166 final size:166
Alignment explanation
Indices: 1414333--1414664 Score: 607
Period size: 167 Copynumber: 2.0 Consensus size: 166
1414323 GCTATCTAAG
1414333 AAGGAGATGGTGAAAGGACTACCTCACATCAACATCCTGACCAACTCTGTGAAGGGTGTCTAG-C
1 AAGGAGATGGTGAAAGGACTACCTCACATCAACATCCTGACCAACTCTGTGAAGGGTGTCTAGTC
*
1414397 GGGAAACAATTCAGGAAAAGCTTTCCAAAGGAGTCAGAGACAAGAGCTACGAAGCCACTTGAG-T
66 GGGAAACAATTCAGGAAAAGCTTTCCAAAGGAGTCAGAGACAAGAGCTAAGAAGCCACTTGAGCT
1414461 CATCCATACCGATGTGTGTGGACCGATCAAGCCAAGTT
131 CATCCATACCGA--TGTGTGGACCGATCAAGCCAAGTT
1414499 AAGGAG-TGGTGAAAGGACTACCTCACATCAACCATCCTGACCAACTCTGTGAAGGGTGTCTAGT
1 AAGGAGATGGTGAAAGGACTACCTCACATCAA-CATCCTGACCAACTCTGTGAAGGGTGTCTAGT
1414563 CGGGAAACAATTCAGGAAAAGCTTTCCAAAGGAGTCAGAGACAAGAGCTAAGAAGCCACTTGAGC
65 CGGGAAACAATTCAGGAAAAGCTTTCCAAAGGAGTCAGAGACAAGAGCTAAGAAGCCACTTGAGC
1414628 TCATCCATACCGATGTGTGGACCGATCAAGCCAAGTT
130 TCATCCATACCGATGTGTGGACCGATCAAGCCAAGTT
1414665 CTCGTAACAA
Statistics
Matches: 162, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
165 25 0.15
166 61 0.38
167 63 0.39
168 13 0.08
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (166 bp):
AAGGAGATGGTGAAAGGACTACCTCACATCAACATCCTGACCAACTCTGTGAAGGGTGTCTAGTC
GGGAAACAATTCAGGAAAAGCTTTCCAAAGGAGTCAGAGACAAGAGCTAAGAAGCCACTTGAGCT
CATCCATACCGATGTGTGGACCGATCAAGCCAAGTT
Found at i:1417128 original size:29 final size:29
Alignment explanation
Indices: 1417093--1417174 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1417083 AAACTAAATT
*
1417093 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1417122 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1417151 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1417175 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1420098 original size:20 final size:20
Alignment explanation
Indices: 1420073--1420137 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
1420063 ATACAGTTTA
1420073 TACAGGCTGAGTCTGAAGAG
1 TACAGGCTGAGTCTGAAGAG
1420093 TACAGGCTGAGTCTGAAGAG
1 TACAGGCTGAGTCTGAAGAG
* *
1420113 TACAGGATGAGTCTGAAAAG
1 TACAGGCTGAGTCTGAAGAG
1420133 TACAG
1 TACAG
1420138 ACTGTTCTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (20 bp):
TACAGGCTGAGTCTGAAGAG
Found at i:1421637 original size:23 final size:23
Alignment explanation
Indices: 1421603--1421664 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1421593 TGTTAGTTGT
* * *
1421603 CAAACATCAAACAAATATGTTTT
1 CAAACATTAAACAAACATGTTTG
*
1421626 TAAACATTAAACAAACATGTTTG
1 CAAACATTAAACAAACATGTTTG
*
1421649 CAAACACTAAACAAAC
1 CAAACATTAAACAAAC
1421665 GAACACCTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (23 bp):
CAAACATTAAACAAACATGTTTG
Found at i:1423224 original size:2 final size:2
Alignment explanation
Indices: 1423217--1423246 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1423207 TATCTTAAAT
*
1423217 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1423247 AATTAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1426257 original size:29 final size:29
Alignment explanation
Indices: 1426209--1426268 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
1426199 TCAGTAAAGC
* *
1426209 TTCTGTTAATGTCAATATAACGCTATTGT
1 TTCTGTTAATGCCAACATAACGCTATTGT
*
1426238 TTCTGTTAATGCCAACATAATGCTATTGT
1 TTCTGTTAATGCCAACATAACGCTATTGT
1426267 TT
1 TT
1426269 GAAATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (29 bp):
TTCTGTTAATGCCAACATAACGCTATTGT
Found at i:1426628 original size:32 final size:32
Alignment explanation
Indices: 1426592--1426652 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1426582 AATAGGAACA
*
1426592 AATTGAGCAACACTGACTCG-TTATTCCTTAAT
1 AATTGAGCAACACCGACT-GATTATTCCTTAAT
1426624 AATTGAGCAACACCGACTGATTATTCCTT
1 AATTGAGCAACACCGACTGATTATTCCTT
1426653 CTAAGCTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (32 bp):
AATTGAGCAACACCGACTGATTATTCCTTAAT
Found at i:1435612 original size:16 final size:15
Alignment explanation
Indices: 1435578--1435608 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1435568 TTCAAGATAC
1435578 ATCAAGAGAATAAAA
1 ATCAAGAGAATAAAA
1435593 ATCAAGAGAATAAAA
1 ATCAAGAGAATAAAA
1435608 A
1 A
1435609 ATCATCTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.13, T:0.13
Consensus pattern (15 bp):
ATCAAGAGAATAAAA
Found at i:1436826 original size:228 final size:228
Alignment explanation
Indices: 1436577--1437232 Score: 1026
Period size: 228 Copynumber: 2.9 Consensus size: 228
1436567 AACCAAATGA
* * * * *
1436577 AGGGTCGACTCCTTTTGGATGTTGTAGTCGGCCAAAGTTCGACCGTCCTCAAGTTGCTTCCCGGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGTTGCTTCCCGGC
* * *
1436642 GAAGATGAGCCTCTGCTGGTCCGGTGGGATACCTTCCTTGTCTTGGATTTTGGCCTTGACGTTGT
66 GAAGATGAGCCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
* * * * * *
1436707 CGATGGTGTCGGAGCTCTCGACTTCCAAGGTGATGGTTTTTCCGGTCAGGGTTTTCACGAAGATT
131 CAATGGTGTCGGAGCTCTCGACCTCCAGGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGATT
1436772 TGCATGCCTCCACGAAGACGGAGGACGAGGTGG
196 TGCATGCCTCCACGAAGACGGAGGACGAGGTGG
* *
1436805 AGGGTCGACTCCTTCTGGATGTTGTAGTCCGCCAAGGTGCGGCCGTCCTCGAGTTGCTTCCCGGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGTTGCTTCCCGGC
1436870 GAAGATGAGCCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
66 GAAGATGAGCCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
*
1436935 CAATGGTGTCGGAGCTCTCGACCTCTAGGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGATT
131 CAATGGTGTCGGAGCTCTCGACCTCCAGGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGATT
1437000 TGCATGCCTCCACGAAGACGGAGGACGAGGTGG
196 TGCATGCCTCCACGAAGACGGAGGACGAGGTGG
* * * *
1437033 AGGGTTGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGTTTTCCGGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGTTGCTTCCCGGC
* * * * *
1437098 GAAGATGAGACGT-TGTTGGTCTGGAGGGATCCCTTCCTTGTCTTGGATCTTCGCCTTGACGTTA
66 GAAGATGAG-CCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTG
* * *
1437162 TCAATGGTGTCGGAGCTCTCGACCTCGAGGGTGATTGTCTTGCCGGTCAGGGTCTTAACGAAGAT
130 TCAATGGTGTCGGAGCTCTCGACCTCCAGGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGAT
*
1437227 CTGCAT
195 TTGCAT
1437233 CTTGTTTGGC
Statistics
Matches: 396, Mismatches: 31, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
228 394 0.99
229 2 0.01
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (228 bp):
AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGTTGCTTCCCGGC
GAAGATGAGCCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
CAATGGTGTCGGAGCTCTCGACCTCCAGGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGATT
TGCATGCCTCCACGAAGACGGAGGACGAGGTGG
Found at i:1438701 original size:13 final size:13
Alignment explanation
Indices: 1438650--1438719 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
1438640 ATCGACTATT
1438650 ATATATTTTACGAAA
1 ATATATTTTA--AAA
1438665 ATAT-TTTATAAAA
1 ATATATTT-TAAAA
* *
1438678 TTTAAATTTTAAAA
1 -ATATATTTTAAAA
1438692 ATATATTTTATAAA
1 ATATATTTTA-AAA
*
1438706 A-ATATTTTAGAA
1 ATATATTTTAAAA
1438718 AT
1 AT
1438720 CTTTAAGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
12 3 0.07
13 19 0.42
14 14 0.31
15 9 0.20
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (13 bp):
ATATATTTTAAAA
Found at i:1438705 original size:15 final size:15
Alignment explanation
Indices: 1438665--1438710 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1438655 TTTTACGAAA
1438665 ATATTTTAT-AAAAT
1 ATATTTTATAAAAAT
* *
1438679 TTAAATTT-TAAAAAT
1 AT-ATTTTATAAAAAT
1438694 ATATTTTATAAAAAT
1 ATATTTTATAAAAAT
1438709 AT
1 AT
1438711 TTTAGAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATTTTATAAAAAT
Found at i:1438709 original size:42 final size:43
Alignment explanation
Indices: 1438650--1438732 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 43
1438640 ATCGACTATT
* *
1438650 ATATATTTTACGAAAATATTTTATAAA-ATTTAAATTTTAAAA
1 ATATATTTTACAAAAATATTTTAGAAATATTTAAATTTTAAAA
* * *
1438692 ATATATTTTATAAAAATATTTTAGAAATCTTTAAGTTTTAA
1 ATATATTTTACAAAAATATTTTAGAAATATTTAAATTTTAA
1438733 CATTATATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 24 0.69
43 11 0.31
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (43 bp):
ATATATTTTACAAAAATATTTTAGAAATATTTAAATTTTAAAA
Found at i:1439422 original size:17 final size:17
Alignment explanation
Indices: 1439400--1439439 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1439390 TCATTTGAAA
1439400 ATTTTAAATCATTAT-AT
1 ATTTTAAAT-ATTATCAT
*
1439417 ATTTTAAATATTTTCAT
1 ATTTTAAATATTATCAT
1439434 ATTTTA
1 ATTTTA
1439440 TATGATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTAAATATTATCAT
Found at i:1439499 original size:25 final size:25
Alignment explanation
Indices: 1439464--1439512 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1439454 TCTGTCATAC
*
1439464 TAAAATATTATAAATTCATTATTTT
1 TAAAATATTATAAATTCATCATTTT
*
1439489 TAAAATTTTATAAATTCATCATTT
1 TAAAATATTATAAATTCATCATTT
1439513 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (25 bp):
TAAAATATTATAAATTCATCATTTT
Found at i:1439517 original size:23 final size:24
Alignment explanation
Indices: 1439464--1439518 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
1439454 TCTGTCATAC
*
1439464 TAAAATATTATAAATTCATTATTTT
1 TAAAATATTATAAATTCATCA-TTT
*
1439489 TAAAATTTTATAAATTCATCA-TT
1 TAAAATATTATAAATTCATCATTT
1439512 TAAAATA
1 TAAAATA
1439519 AAATAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 8 0.30
25 19 0.70
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAAATATTATAAATTCATCATTT
Found at i:1439865 original size:2 final size:2
Alignment explanation
Indices: 1439860--1439905 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1439850 TATATATTGG
1439860 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
1439902 AT AT
1 AT AT
1439906 TGTCAATAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1449501 original size:34 final size:34
Alignment explanation
Indices: 1449458--1449534 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
1449448 TTTTATAGGG
1449458 ACAGGCAGCGGTATTTGCAGACCTTTCCCCAGCA
1 ACAGGCAGCGGTATTTGCAGACCTTTCCCCAGCA
1449492 ACAGGCAGCGGTATTTGCAGACCTTTCCCCAGCA
1 ACAGGCAGCGGTATTTGCAGACCTTTCCCCAGCA
1449526 ACAGGCAGC
1 ACAGGCAGC
1449535 TTAGAATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (34 bp):
ACAGGCAGCGGTATTTGCAGACCTTTCCCCAGCA
Found at i:1450326 original size:20 final size:20
Alignment explanation
Indices: 1450301--1450353 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1450291 CGTTGCATTT
1450301 TCGCAACGCGATTATTTCTA
1 TCGCAACGCGATTATTTCTA
1450321 TCGCAACGCGATTATTTCTA
1 TCGCAACGCGATTATTTCTA
*
1450341 TCGCAATGCGATT
1 TCGCAACGCGATT
1450354 TTCCAATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (20 bp):
TCGCAACGCGATTATTTCTA
Found at i:1450371 original size:21 final size:21
Alignment explanation
Indices: 1450341--1450414 Score: 114
Period size: 21 Copynumber: 3.5 Consensus size: 21
1450331 ATTATTTCTA
1450341 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
*
1450362 TCGCATTGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
*
1450383 TCGCATTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1450404 TCGCAATGCGA
1 TCGCAATGCGA
1450415 ATAAGTAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 46 0.92
22 4 0.08
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1450451 original size:21 final size:20
Alignment explanation
Indices: 1450404--1450455 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1450394 TTTTCCCAAT
*
1450404 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
1450424 TCACAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
1450445 TCGCAATGCGA
1 TCGCAATGCGA
1450456 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1450469 original size:20 final size:20
Alignment explanation
Indices: 1450444--1450558 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1450434 AATTTGGAAA
*
1450444 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1450464 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1450485 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1450505 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * ** *
1450525 TTCGCGACTAGATACTAACT
1 ATCGCAACGCGATACTGACT
* *
1450545 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1450559 ATACATAATC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.03
20 59 0.77
21 14 0.18
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1450486 original size:41 final size:41
Alignment explanation
Indices: 1450441--1450578 Score: 156
Period size: 41 Copynumber: 3.4 Consensus size: 41
1450431 GCGAATTTGG
*
1450441 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
*
1450482 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATACTTAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATA-ATAC
** * * * *
1450524 --TTTCGCGACT-AGATACTAACTTTCGCAACGAGATAATAC
1 AAAATCGC-AATGCGATACTGACTTTCGCAACGCGATAATAC
*
1450563 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
1450579 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
39 3 0.04
40 28 0.35
41 45 0.57
42 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:1450776 original size:22 final size:22
Alignment explanation
Indices: 1450745--1450788 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1450735 CACTCTCTCA
*
1450745 CCCATCTCCGACGAAATTCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1450767 CCCATTTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1450789 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.41, G:0.14, T:0.23
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1451131 original size:20 final size:20
Alignment explanation
Indices: 1451101--1451205 Score: 102
Period size: 20 Copynumber: 5.7 Consensus size: 20
1451091 TAGTTTCGAT
*
1451101 AATGAAAATCGCAATGCAGA
1 AATGAAAATCGCAACGCAGA
**
1451121 AATGACTATCGCAACG-AGA
1 AATGAAAATCGCAACGCAGA
1451140 GAATGAAAATCGCAACGC-GA
1 -AATGAAAATCGCAACGCAGA
1451160 AATGAAAATCGCAACG-AG-
1 AATGAAAATCGCAACGCAGA
*
1451178 -AT---AATCGCGACGC-GA
1 AATGAAAATCGCAACGCAGA
1451193 AATGAAAATCGCA
1 AATGAAAATCGCA
1451206 TTGCGATTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
14 10 0.14
16 2 0.03
17 2 0.03
19 26 0.38
20 29 0.42
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGCAGA
Found at i:1451173 original size:39 final size:37
Alignment explanation
Indices: 1451101--1451205 Score: 119
Period size: 33 Copynumber: 2.9 Consensus size: 37
1451091 TAGTTTCGAT
* **
1451101 AATGAAAATCGCAATGCAGAAATGACTATCGCAACGAGAG
1 AATGAAAATCGCAACGC-GAAATGAAAATCGCAAC--GAG
1451141 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAG
1 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAG
*
1451178 -AT---AATCGCGACGCGAAATGAAAATCGCA
1 AATGAAAATCGCAACGCGAAATGAAAATCGCA
1451206 TTGCGATTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
33 25 0.41
36 2 0.03
37 3 0.05
39 15 0.25
40 16 0.26
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (37 bp):
AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAG
Found at i:1451242 original size:19 final size:19
Alignment explanation
Indices: 1451218--1451254 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1451208 GCGATTATCT
1451218 CGTTGCGATTCTCATTTCG
1 CGTTGCGATTCTCATTTCG
*
1451237 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1451255 AACCAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTCTCATTTCG
Found at i:1453407 original size:154 final size:154
Alignment explanation
Indices: 1453127--1453436 Score: 620
Period size: 154 Copynumber: 2.0 Consensus size: 154
1453117 TTCACTGTTT
1453127 AAATATCATGTCTGTTTATTTACTGATATTTGTATTTAATTATTTAGCGGACCGATAAGGTGGAT
1 AAATATCATGTCTGTTTATTTACTGATATTTGTATTTAATTATTTAGCGGACCGATAAGGTGGAT
1453192 GCTTTACGTCAAGTTTTTATTGCACGACAGAGTTCACGCATCAGACGGCGTGCACGTGCTATTAA
66 GCTTTACGTCAAGTTTTTATTGCACGACAGAGTTCACGCATCAGACGGCGTGCACGTGCTATTAA
1453257 GTCTCCAAACACCCCAATAGTGCG
131 GTCTCCAAACACCCCAATAGTGCG
1453281 AAATATCATGTCTGTTTATTTACTGATATTTGTATTTAATTATTTAGCGGACCGATAAGGTGGAT
1 AAATATCATGTCTGTTTATTTACTGATATTTGTATTTAATTATTTAGCGGACCGATAAGGTGGAT
1453346 GCTTTACGTCAAGTTTTTATTGCACGACAGAGTTCACGCATCAGACGGCGTGCACGTGCTATTAA
66 GCTTTACGTCAAGTTTTTATTGCACGACAGAGTTCACGCATCAGACGGCGTGCACGTGCTATTAA
1453411 GTCTCCAAACACCCCAATAGTGCG
131 GTCTCCAAACACCCCAATAGTGCG
1453435 AA
1 AA
1453437 GACACCGCAA
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 156 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (154 bp):
AAATATCATGTCTGTTTATTTACTGATATTTGTATTTAATTATTTAGCGGACCGATAAGGTGGAT
GCTTTACGTCAAGTTTTTATTGCACGACAGAGTTCACGCATCAGACGGCGTGCACGTGCTATTAA
GTCTCCAAACACCCCAATAGTGCG
Found at i:1453543 original size:21 final size:21
Alignment explanation
Indices: 1453519--1453585 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1453509 TCATTCCTTG
1453519 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1453540 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1453561 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1453582 AGAG
1 AGAG
1453586 CTCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1453543 original size:42 final size:42
Alignment explanation
Indices: 1453467--1453585 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
1453457 GACTCGCCTG
* * * * * * *
1453467 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCTTGAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1453509 TCATTCCTTG-AGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTTGAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* *
1453551 TCATCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATCCTTGAAGA-GTCCCCTCCCACCGTTCAAGAG
1453586 CTCGATTCAC
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
41 5 0.08
42 53 0.83
43 6 0.09
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCCTTGAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1455111 original size:18 final size:18
Alignment explanation
Indices: 1455072--1455111 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1455062 AAACAGACTG
* *
1455072 TCGCAACACGAAACTGAC
1 TCGCAACACGAAACTAAA
*
1455090 TCGCAACGCGAAACTAAA
1 TCGCAACACGAAACTAAA
1455108 TCGC
1 TCGC
1455112 TTTGCGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.33, G:0.17, T:0.12
Consensus pattern (18 bp):
TCGCAACACGAAACTAAA
Found at i:1455170 original size:33 final size:33
Alignment explanation
Indices: 1455113--1455238 Score: 207
Period size: 33 Copynumber: 3.8 Consensus size: 33
1455103 CTAAATCGCT
* * *
1455113 TTGCGATTTTAATTTTCGCTTTGCGATTCCCTCG
1 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1455147 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1455180 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1455213 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1455239 GGTCAATGAT
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
33 77 0.88
34 11 0.12
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1455171 original size:19 final size:19
Alignment explanation
Indices: 1455147--1455238 Score: 96
Period size: 19 Copynumber: 5.4 Consensus size: 19
1455137 GATTCCCTCG
1455147 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1455166 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1455180 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1455199 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
1455213 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1455232 TTGCGAT
1 TTGCGAT
1455239 GGTCAATGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 12 0.20
16 14 0.24
17 14 0.24
19 19 0.32
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1455185 original size:14 final size:14
Alignment explanation
Indices: 1455133--1455220 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1455123 AATTTTCGCT
*
1455133 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
1455147 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1455164 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
1455180 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
1455197 CATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
1455213 TTGCGATT
1 TTGCGATT
1455221 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 12 0.21
19 12 0.21
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1456117 original size:50 final size:50
Alignment explanation
Indices: 1456059--1456158 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1456049 ATAAGTTACG
1456059 ATTTAAAGAAATAATACATGCATGGTTTCTTTTCTTGTAGTACCACTGTT
1 ATTTAAAGAAATAATACATGCATGGTTTCTTTTCTTGTAGTACCACTGTT
1456109 ATTTAAAGAAATAATACATGCATGGTTTCTTTTCTTGTAGTACCACTGTT
1 ATTTAAAGAAATAATACATGCATGGTTTCTTTTCTTGTAGTACCACTGTT
1456159 GAATAGAGGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (50 bp):
ATTTAAAGAAATAATACATGCATGGTTTCTTTTCTTGTAGTACCACTGTT
Found at i:1457761 original size:24 final size:24
Alignment explanation
Indices: 1457727--1457780 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1457717 CTGAAACATC
* *
1457727 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1457751 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1457775 ATCAAA
1 ATCAAA
1457781 TTTCGAATAC
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1458576 original size:33 final size:33
Alignment explanation
Indices: 1458534--1458656 Score: 147
Period size: 33 Copynumber: 3.7 Consensus size: 33
1458524 TCATTTGACC
* * *
1458534 ATCGCAATGCGAAATGCAAATTGCAACGATAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1458567 ATCGCAATGCGAAATGAAAAAGGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1458600 ATCACAATGCGAAATGAAAATCGTAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1458633 ATCGCAAAGCGAAAATTAAAATCG
1 ATCGCAATGCG-AAATGAAAATCG
1458657 TTGCGACAGT
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
33 66 0.86
34 11 0.14
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1459130 original size:20 final size:20
Alignment explanation
Indices: 1459105--1459161 Score: 98
Period size: 19 Copynumber: 2.9 Consensus size: 20
1459095 ATTCATTTGA
1459105 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1459125 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
*
1459144 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1459162 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1459221 original size:19 final size:19
Alignment explanation
Indices: 1459199--1459244 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1459189 GATTTTCTCG
1459199 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1459218 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1459237 TTGCGATT
1 TTGCGATT
1459245 CTCTCGTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1459390 original size:14 final size:14
Alignment explanation
Indices: 1459371--1459404 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1459361 CATCAATTAA
1459371 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1459385 ACAAATCATCTTTT
1 ACAAATCAACATTT
1459399 ACAAAT
1 ACAAAT
1459405 ATATTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1461276 original size:20 final size:19
Alignment explanation
Indices: 1461253--1461320 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
1461243 GAAACTTAAA
1461253 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
1461273 ATCGCAACACGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1461293 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1461312 ATCGCAACG
1 ATCGCAACG
1461321 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 14 0.36
20 24 0.62
21 1 0.03
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1461328 original size:14 final size:14
Alignment explanation
Indices: 1461309--1461366 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1461299 ATGCGAAATG
1461309 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1461323 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1461339 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1461355 AAAATCGCAACG
1 AAAATCGCAACG
1461367 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1461351 original size:32 final size:33
Alignment explanation
Indices: 1461293--1461371 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1461283 GGAAATGGCT
1461293 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1461326 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1461358 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1461372 CACAACTCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1461478 original size:19 final size:20
Alignment explanation
Indices: 1461456--1461498 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1461446 CATTTTCATT
1461456 TTGCGAT-GCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
* *
1461475 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTTCGCG
1461495 TTGC
1 TTGC
1461499 AAAAGTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:1461963 original size:18 final size:18
Alignment explanation
Indices: 1461937--1461981 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1461927 GTCGATCAGA
*
1461937 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1461955 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1461973 TGATGGCTC
1 TGATGGCTC
1461982 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1463436 original size:20 final size:20
Alignment explanation
Indices: 1463388--1463446 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1463378 AATAGTTTCT
** *
1463388 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1463408 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1463428 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1463447 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1463736 original size:22 final size:22
Alignment explanation
Indices: 1463708--1463751 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1463698 AGATGGAGAT
1463708 AGACGGATTTCGCCGGAAATGG
1 AGACGGATTTCGCCGGAAATGG
* *
1463730 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAAATGG
1463752 GTGAGAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.16, G:0.39, T:0.20
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAAATGG
Found at i:1463931 original size:21 final size:20
Alignment explanation
Indices: 1463907--1463959 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
1463897 CAATACTTAT
1463907 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
*
1463928 TCGCAATGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
1463949 TCGCATTGCGA
1 TCGCATTGCGA
1463960 TAGAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 24 0.83
22 4 0.14
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:1466036 original size:2 final size:2
Alignment explanation
Indices: 1466029--1466089 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1466019 GATTATTGCG
1466029 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1466071 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1466090 CCTATTACAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1466536 original size:180 final size:180
Alignment explanation
Indices: 1466231--1466586 Score: 554
Period size: 180 Copynumber: 2.0 Consensus size: 180
1466221 CCTGTTTGAT
1466231 TTGATTAATTTGTACCATTATGTCTTATGATACATAATTTTAAACCATTCAAGCTTAAATAGGAT
1 TTGATTAATTTGTACCATTATGTCTTATGATACATAATTTTAAACCATTCAAGCTTAAATAGGAT
* * *
1466296 GTGAATGGAGTAAAACTTTGCAGCTTAAAGCTTTGTCTAGACTTAGGGATGAATAATTGATCCGA
66 GTGAATGAAGTAAAACTTTACAGCTTAAAGCTTTGTCTAGACTTAGGGATGAACAATTGATCCGA
* * * * *
1466361 ATCTTATGGATTTTGATTCAATTCAAATATATTGGGTTGATTTTTTTAAA
131 ATCTTATGGATTTTGATTCAACTAAAATATACTAGGTTGACTTTTTTAAA
* *
1466411 TTGATTAATTTGTACCATTTTGTCTTATGATACATAATTTTAAACCATTCAAGCTTAAATTGGAT
1 TTGATTAATTTGTACCATTATGTCTTATGATACATAATTTTAAACCATTCAAGCTTAAATAGGAT
* * *
1466476 TTGAATGAAGTAAAAACTTTATAGCTT-AAGCTTTGTCTTA-ACTTAGGGATGGACAATTGATCC
66 GTGAATGAAGT-AAAACTTTACAGCTTAAAGCTTTGTC-TAGACTTAGGGATGAACAATTGATCC
*
1466539 GATTCTTATGGATTTTGATTCAACTAAAATATACTAGGTTGACTTTTT
129 GAATCTTATGGATTTTGATTCAACTAAAATATACTAGGTTGACTTTTT
1466587 AAAAAACCCA
Statistics
Matches: 160, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
180 145 0.91
181 15 0.09
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (180 bp):
TTGATTAATTTGTACCATTATGTCTTATGATACATAATTTTAAACCATTCAAGCTTAAATAGGAT
GTGAATGAAGTAAAACTTTACAGCTTAAAGCTTTGTCTAGACTTAGGGATGAACAATTGATCCGA
ATCTTATGGATTTTGATTCAACTAAAATATACTAGGTTGACTTTTTTAAA
Found at i:1480790 original size:18 final size:18
Alignment explanation
Indices: 1480754--1480787 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1480744 GTAATATATA
1480754 AATATTAATATACTTAAT
1 AATATTAATATACTTAAT
*
1480772 AATATTATTATA-TTAA
1 AATATTAATATACTTAA
1480788 ATATAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
AATATTAATATACTTAAT
Found at i:1480805 original size:27 final size:26
Alignment explanation
Indices: 1480755--1480805 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1480745 TAATATATAA
* * *
1480755 ATATTAATATACTTAATAATATTATT
1 ATATTAATATAATTAAAAACATTATT
1480781 ATATTAAATATAATTAAAAACATTA
1 ATATT-AATATAATTAAAAACATTA
1480806 AATCATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATTAATATAATTAAAAACATTATT
Found at i:1480900 original size:15 final size:15
Alignment explanation
Indices: 1480880--1480914 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1480870 TAAAAGGGTG
*
1480880 TAATTATCTTTCTAA
1 TAATTATATTTCTAA
*
1480895 TAATTATATTTTTAA
1 TAATTATATTTCTAA
1480910 TAATT
1 TAATT
1480915 CTTTTAGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATTATATTTCTAA
Found at i:1481171 original size:20 final size:19
Alignment explanation
Indices: 1481123--1481173 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1481113 TAAATAACTA
1481123 AAATATAGT-T-TTAAAAT
1 AAATATAGTATATTAAAAT
*
1481140 -AATATGAATATATTAAAAAT
1 AAATAT-AGTATATT-AAAAT
1481160 AAATATAGTATATT
1 AAATATAGTATATT
1481174 CCATAAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 5 0.19
17 2 0.07
18 1 0.04
19 2 0.07
20 12 0.44
21 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
AAATATAGTATATTAAAAT
Found at i:1486020 original size:23 final size:23
Alignment explanation
Indices: 1485994--1486037 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1485984 TGAACATGTA
1485994 AATTTCATATTTGGTGGCTAATG
1 AATTTCATATTTGGTGGCTAATG
1486017 AATTTCATATTTGGTGGCTAA
1 AATTTCATATTTGGTGGCTAA
1486038 CTTGTACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.43
Consensus pattern (23 bp):
AATTTCATATTTGGTGGCTAATG
Done.