Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_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: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 24
Found at i:5331920 original size:14 final size:14
Alignment explanation
Indices: 5331901--5331927 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5331891 AAAAAATAGA
5331901 AAAATAGAAAAAAT
1 AAAATAGAAAAAAT
5331915 AAAATAGAAAAAA
1 AAAATAGAAAAAA
5331928 AGAAGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.11
Consensus pattern (14 bp):
AAAATAGAAAAAAT
Found at i:5333517 original size:30 final size:30
Alignment explanation
Indices: 5333483--5333557 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
5333473 AAATGGATTT
* * *
5333483 AGTTTAGTGATCAAATTATAAGATTTTG-AA
1 AGTTTAGTGACCAAAGTATAA-ACTTTGAAA
*
5333513 AGTTTGGTGACCAAAGTATAAACTTTGAAA
1 AGTTTAGTGACCAAAGTATAAACTTTGAAA
*
5333543 AGTTTAGGGACCAAA
1 AGTTTAGTGACCAAA
5333558 ATGTAGTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 5 0.13
30 33 0.87
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (30 bp):
AGTTTAGTGACCAAAGTATAAACTTTGAAA
Found at i:5335591 original size:14 final size:14
Alignment explanation
Indices: 5335572--5335618 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
5335562 TATATTGGGA
5335572 TATTGTCTATGGTT
1 TATTGTCTATGGTT
* * *
5335586 TATTGTTTATGATC
1 TATTGTCTATGGTT
5335600 TA-TGATCTATGGTT
1 TATTG-TCTATGGTT
5335614 TATTG
1 TATTG
5335619 GTTAATAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
13 2 0.08
14 21 0.84
15 2 0.08
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.55
Consensus pattern (14 bp):
TATTGTCTATGGTT
Found at i:5335730 original size:45 final size:45
Alignment explanation
Indices: 5335640--5335819 Score: 281
Period size: 45 Copynumber: 4.0 Consensus size: 45
5335630 GTAAACCTGC
* ***
5335640 AAATAAGCTTATGAGCTTATAAAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
*
5335684 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTTGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
* * *
5335729 AAATAAGCTTACGAGCTTTTGGGATAAACGATAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
5335774 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
5335819 A
1 A
5335820 GAAATTTTAT
Statistics
Matches: 123, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 21 0.17
45 102 0.83
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
Found at i:5336415 original size:22 final size:22
Alignment explanation
Indices: 5336390--5336459 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
5336380 GATTGGCATA
*
5336390 AATGCTGACT-GAACTTGGTCTG
1 AATGCTGACTGGAA-TTCGTCTG
* *
5336412 AATGTTGATTGGAATTCGTCTG
1 AATGCTGACTGGAATTCGTCTG
* * * *
5336434 AATGCTGATTAGAAATCGTTTG
1 AATGCTGACTGGAATTCGTCTG
5336456 AATG
1 AATG
5336460 TTGATTAGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 37 0.93
23 3 0.08
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.36
Consensus pattern (22 bp):
AATGCTGACTGGAATTCGTCTG
Found at i:5336464 original size:22 final size:22
Alignment explanation
Indices: 5336407--5336467 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
5336397 ACTGAACTTG
* *
5336407 GTCTGAATGTTGATTGGAATTC
1 GTCTGAATGTTGATTAGAAATC
*
5336429 GTCTGAATGCTGATTAGAAATC
1 GTCTGAATGTTGATTAGAAATC
*
5336451 GTTTGAATGTTGATTAG
1 GTCTGAATGTTGATTAG
5336468 TTTTGGTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (22 bp):
GTCTGAATGTTGATTAGAAATC
Found at i:5337078 original size:19 final size:19
Alignment explanation
Indices: 5337054--5337090 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5337044 AATAAATATA
*
5337054 TAAAGTCAATTTAGTAATT
1 TAAAGTAAATTTAGTAATT
5337073 TAAAGTAAATTTAGTAAT
1 TAAAGTAAATTTAGTAAT
5337091 ATAATGATGA
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:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (19 bp):
TAAAGTAAATTTAGTAATT
Found at i:5337338 original size:16 final size:16
Alignment explanation
Indices: 5337317--5337347 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5337307 TAACTTACAC
5337317 GTCAAGTAAATATCAA
1 GTCAAGTAAATATCAA
5337333 GTCAAGTAAATATCA
1 GTCAAGTAAATATCA
5337348 GTTCAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (16 bp):
GTCAAGTAAATATCAA
Found at i:5351721 original size:21 final size:20
Alignment explanation
Indices: 5351696--5351734 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5351686 TATCAAAGTC
5351696 TTTGTTGAAGCCATGAAATCT
1 TTTGTTGAAGCCAT-AAATCT
*
5351717 TTTGTTGAGGCCATAAAT
1 TTTGTTGAAGCCATAAAT
5351735 TCCTGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
TTTGTTGAAGCCATAAATCT
Found at i:5361368 original size:23 final size:21
Alignment explanation
Indices: 5361316--5361377 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
5361306 TTTTGGTGCA
*
5361316 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
5361336 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
5361357 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
5361378 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:5361398 original size:21 final size:21
Alignment explanation
Indices: 5361359--5361398 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5361349 CCCCCTTTGA
*
5361359 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
* *
5361380 AGGGGAATCGATACGCCCC
1 AGGGGAACCGATACCCCCC
5361399 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.38, G:0.28, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:5368445 original size:2 final size:2
Alignment explanation
Indices: 5368438--5368511 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
5368428 TATGGTAAAC
5368438 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
5368480 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
5368512 CAAAAAAAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5369145 original size:30 final size:31
Alignment explanation
Indices: 5369105--5369164 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
5369095 AAAAGTTCAT
* *
5369105 ATAAAAAATA-TACGATAAATCAGATATCAG
1 ATAAAAAATATTAAGAAAAATCAGATATCAG
* *
5369135 ATAAATAATATTAAGAAAAATCAGGTATCA
1 ATAAAAAATATTAAGAAAAATCAGATATCA
5369165 TGTCATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.25
Consensus pattern (31 bp):
ATAAAAAATATTAAGAAAAATCAGATATCAG
Found at i:5370848 original size:3 final size:3
Alignment explanation
Indices: 5370840--5370870 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5370830 GTGTATACAG
5370840 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
5370871 TAAAACCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:5377813 original size:2 final size:2
Alignment explanation
Indices: 5377806--5377839 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5377796 TTTCTTATTA
5377806 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
5377840 TTATTGTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5380016 original size:2 final size:2
Alignment explanation
Indices: 5380011--5380040 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5380001 AACTTGCATG
5380011 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
5380041 CACAGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5383066 original size:16 final size:16
Alignment explanation
Indices: 5383054--5383125 Score: 117
Period size: 16 Copynumber: 4.5 Consensus size: 16
5383044 ACATGTTTTC
*
5383054 AACCTGACCTGTTATG
1 AACCTGACTTGTTATG
5383070 AACCTGACTTGTTATG
1 AACCTGACTTGTTATG
5383086 AACCTGACTTGTTATG
1 AACCTGACTTGTTATG
* *
5383102 AACCTGACTTGTTTTC
1 AACCTGACTTGTTATG
5383118 AACCTGAC
1 AACCTGAC
5383126 CTATAAATGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.35
Consensus pattern (16 bp):
AACCTGACTTGTTATG
Found at i:5383146 original size:32 final size:32
Alignment explanation
Indices: 5383042--5383127 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
5383032 TGGTATTGCT
*
5383042 TGACATGTTTTCAACCTGACCTGTTATGAACC
1 TGACTTGTTTTCAACCTGACCTGTTATGAACC
* * *
5383074 TGACTTGTTATGAACCTGACTTGTTATGAACC
1 TGACTTGTTTTCAACCTGACCTGTTATGAACC
5383106 TGACTTGTTTTCAACCTGACCT
1 TGACTTGTTTTCAACCTGACCT
5383128 ATAAATGATC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (32 bp):
TGACTTGTTTTCAACCTGACCTGTTATGAACC
Found at i:5383363 original size:14 final size:14
Alignment explanation
Indices: 5383344--5383376 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5383334 TATTATATTA
5383344 ATTATGATTCTTAT
1 ATTATGATTCTTAT
5383358 ATTATGATTCTTAT
1 ATTATGATTCTTAT
*
5383372 GTTAT
1 ATTAT
5383377 AAATCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (14 bp):
ATTATGATTCTTAT
Found at i:5384258 original size:9 final size:9
Alignment explanation
Indices: 5384244--5384273 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
5384234 CATGTACTCT
5384244 TAAATATAA
1 TAAATATAA
5384253 TAAATATAA
1 TAAATATAA
5384262 TAAATATAA
1 TAAATATAA
5384271 TAA
1 TAA
5384274 GTCATTAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAATATAA
Found at i:5386967 original size:53 final size:52
Alignment explanation
Indices: 5386881--5387078 Score: 189
Period size: 53 Copynumber: 3.8 Consensus size: 52
5386871 ATAATAAGGG
* * * *
5386881 TTAGGGTTAGAGAAGATAAACAGAGGCAAAAGATAAAAATACTCAGTTTGGGT
1 TTAGGGTTAGAGAAGATAAACAGAGACAGAAGATGAAGATACTC-GTTTGGGT
* * *** **
5386934 TTAGGGTTAGAGAAGATAAACAGATATAGAAGATGAAGAGGTTCGGTTTTAGT
1 TTAGGGTTAGAGAAGATAAACAGAGACAGAAGATGAAGATACTC-GTTTGGGT
* * * * *
5386987 TTAAGGTTAGAAAATATGAATAGAGACAGAAGATGAAGATACTCGATTTGGGT
1 TTAGGGTTAGAGAAGATAAACAGAGACAGAAGATGAAGATACTCG-TTTGGGT
* * * *
5387040 TTAGGGTTAGAGAAGATGAACAAAAACAAAAGATGAAGA
1 TTAGGGTTAGAGAAGATAAACAGAGACAGAAGATGAAGA
5387079 GGTTAGGTTA
Statistics
Matches: 113, Mismatches: 31, Indels: 2
0.77 0.21 0.01
Matches are distributed among these distances:
52 1 0.01
53 112 0.99
ACGTcount: A:0.43, C:0.06, G:0.27, T:0.24
Consensus pattern (52 bp):
TTAGGGTTAGAGAAGATAAACAGAGACAGAAGATGAAGATACTCGTTTGGGT
Found at i:5387037 original size:106 final size:106
Alignment explanation
Indices: 5386910--5387118 Score: 269
Period size: 106 Copynumber: 2.0 Consensus size: 106
5386900 ACAGAGGCAA
* * * *
5386910 AAGATAAAAATACTCAGTTTGGGTTTAGGGTTAGAGAAGATAAACAGATATAGAAGATGAAGAGG
1 AAGATAAAAATACTCAGTTTGGGTTTAGGGTTAGAGAAGATAAACAAAAACAAAAGATGAAGAGG
* **
5386975 TTCGGTTTTAGTTTAAGG-TTAGAAAATATGAATAGAGACAG
66 TTAGGTTAGAGTTT-AGGATTAGAAAATATGAATAGAGACAG
* * *
5387016 AAGATGAAGATACTC-GATTTGGGTTTAGGGTTAGAGAAGATGAACAAAAACAAAAGATGAAGAG
1 AAGATAAAAATACTCAG-TTTGGGTTTAGGGTTAGAGAAGATAAACAAAAACAAAAGATGAAGAG
* * *
5387080 GTTAGGTTAGGGTTTGGGATTAGAGAATATGAATAGAGA
65 GTTAGGTTAGAGTTTAGGATTAGAAAATATGAATAGAGA
5387119 TAAAAAGTGA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
105 3 0.03
106 85 0.97
ACGTcount: A:0.41, C:0.04, G:0.29, T:0.26
Consensus pattern (106 bp):
AAGATAAAAATACTCAGTTTGGGTTTAGGGTTAGAGAAGATAAACAAAAACAAAAGATGAAGAGG
TTAGGTTAGAGTTTAGGATTAGAAAATATGAATAGAGACAG
Found at i:5387093 original size:53 final size:53
Alignment explanation
Indices: 5386881--5387112 Score: 187
Period size: 53 Copynumber: 4.4 Consensus size: 53
5386871 ATAATAAGGG
* ** * * * *** *
5386881 TTAGGGTTAGAGAAGATAAACAGAGGCAAAAGATAAAAATACTCAGTTTGGGT
1 TTAGGGTTAGAGAAGATGAACAGAAACAGAAGATGAAGAGGTTCGGTTTGGGT
* * * **
5386934 TTAGGGTTAGAGAAGATAAACAGATATAGAAGATGAAGAGGTTCGGTTTTAGT
1 TTAGGGTTAGAGAAGATGAACAGAAACAGAAGATGAAGAGGTTCGGTTTGGGT
* * * * * *** *
5386987 TTAAGGTTAGAAAATATGAATAGAGACAGAAGATGAAGATACTCGATTTGGGT
1 TTAGGGTTAGAGAAGATGAACAGAAACAGAAGATGAAGAGGTTCGGTTTGGGT
* * * *
5387040 TTAGGGTTAGAGAAGATGAACAAAAACAAAAGATGAAGAGGTTAGGTTAGGGT
1 TTAGGGTTAGAGAAGATGAACAGAAACAGAAGATGAAGAGGTTCGGTTTGGGT
*
5387093 TT-GGGATTAGAGAATATGAA
1 TTAGGG-TTAGAGAAGATGAA
5387113 TAGAGATAAA
Statistics
Matches: 139, Mismatches: 39, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
52 3 0.02
53 136 0.98
ACGTcount: A:0.41, C:0.05, G:0.29, T:0.25
Consensus pattern (53 bp):
TTAGGGTTAGAGAAGATGAACAGAAACAGAAGATGAAGAGGTTCGGTTTGGGT
Found at i:5392065 original size:15 final size:15
Alignment explanation
Indices: 5392045--5392077 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5392035 CAAGTAGAAT
5392045 AAAGATGAATGAAAC
1 AAAGATGAATGAAAC
5392060 AAAGATGAATGAAAC
1 AAAGATGAATGAAAC
5392075 AAA
1 AAA
5392078 TGAGTAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.18, T:0.12
Consensus pattern (15 bp):
AAAGATGAATGAAAC
Found at i:5392384 original size:37 final size:36
Alignment explanation
Indices: 5392311--5392405 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 36
5392301 AATAAATAGT
* *
5392311 ATAGGTAAAAAATATAAAATAATAATGTATATATATA
1 ATAGGTAAAAAATA-AAAATAAAAATGAATATATATA
5392348 A-AGGTAAAAAACTAGAAAATAAAAAT-AATATGATATA
1 ATAGGTAAAAAA-TA-AAAATAAAAATGAATAT-ATATA
*
5392385 ATA-GTAATAAATAAAAATAAA
1 ATAGGTAAAAAATAAAAATAAA
5392406 TAAATAAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
35 8 0.16
36 16 0.31
37 26 0.51
38 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.26
Consensus pattern (36 bp):
ATAGGTAAAAAATAAAAATAAAAATGAATATATATA
Found at i:5392399 original size:4 final size:4
Alignment explanation
Indices: 5392390--5392427 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
5392380 ATATAATAGT
5392390 AATA AAT- AA-A AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
5392428 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 4 0.12
4 28 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:5392494 original size:2 final size:2
Alignment explanation
Indices: 5392487--5392577 Score: 91
Period size: 2 Copynumber: 47.0 Consensus size: 2
5392477 ACAAAATAAT
* * * *
5392487 TA TA TA TA TA TA TA TA TA TA AA TA -A TGG GA -A TA TA AA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
*
5392527 AA T- 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
*
5392568 TA TG TA TA TA
1 TA TA TA TA TA
5392578 CAATAAAATA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
1 4 0.05
2 70 0.95
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5392610 original size:18 final size:19
Alignment explanation
Indices: 5392573--5392615 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
5392563 ATATATATGT
*
5392573 ATATACAATAAAATAAATA
1 ATATAAAATAAAATAAATA
5392592 ATATAAAATAAAA-AAATA
1 ATATAAAATAAAATAAATA
5392610 ATATAA
1 ATATAA
5392616 GGGTCAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
ATATAAAATAAAATAAATA
Found at i:5402287 original size:21 final size:21
Alignment explanation
Indices: 5402263--5402302 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5402253 CCCTTTGACC
*
5402263 ATCTTCATCTGATCTTCCAGT
1 ATCTTAATCTGATCTTCCAGT
**
5402284 ATCTTAATCTTCTCTTCCA
1 ATCTTAATCTGATCTTCCA
5402303 TCTTCTTTGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.30, G:0.05, T:0.45
Consensus pattern (21 bp):
ATCTTAATCTGATCTTCCAGT
Found at i:5406196 original size:13 final size:13
Alignment explanation
Indices: 5406135--5406197 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
5406125 CTAAAGAAGT
*
5406135 AAATAAATTAAGCA
1 AAATAAATAAAG-A
5406149 AAATGAAAATAAAGA
1 AAAT--AAATAAAGA
*
5406164 AACAAAAATAAAGA
1 AA-ATAAATAAAGA
* *
5406178 ACATAAATAAATA
1 AAATAAATAAAGA
5406191 AAATAAA
1 AAATAAA
5406198 AATACATAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
13 15 0.38
14 14 0.35
15 3 0.08
16 8 0.20
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.16
Consensus pattern (13 bp):
AAATAAATAAAGA
Found at i:5408406 original size:14 final size:14
Alignment explanation
Indices: 5408377--5408417 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
5408367 CGTTCGTGAA
5408377 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
5408393 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
5408407 CATTCATTTAT
1 CGTTCATTTAT
5408418 ATTCAAACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 16 0.67
15 3 0.12
16 5 0.21
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.54
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:5408741 original size:20 final size:20
Alignment explanation
Indices: 5408718--5408758 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5408708 CGTTTATGTT
* * *
5408718 CGTTCGTTTGTGTTTGTTTA
1 CGTTCGGTTATGTTCGTTTA
5408738 CGTTCGGTTATGTTCGTTTA
1 CGTTCGGTTATGTTCGTTTA
5408758 C
1 C
5408759 CATTTAAATG
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:0.07, C:0.15, G:0.24, T:0.54
Consensus pattern (20 bp):
CGTTCGGTTATGTTCGTTTA
Found at i:5412149 original size:30 final size:30
Alignment explanation
Indices: 5412109--5412178 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
5412099 AAGTGTAAGT
* *
5412109 TTTG-AAAGTTTAGTG-GCCAAATTATAAA
1 TTTGAAAAGTTTAGGGAGCAAAATTATAAA
*
5412137 CTTTGAAAAGTTTAGGGAGTAAAATTATAAA
1 -TTTGAAAAGTTTAGGGAGCAAAATTATAAA
*
5412168 TTTTAAAAGTT
1 TTTGAAAAGTT
5412179 ATATATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.11
30 20 0.57
31 11 0.31
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (30 bp):
TTTGAAAAGTTTAGGGAGCAAAATTATAAA
Found at i:5419513 original size:29 final size:29
Alignment explanation
Indices: 5419467--5419555 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
5419457 AAATTTTTTC
* *
5419467 TAGTGACTAAAATGTAAATTTTGAAAGTT
1 TAGTGGCTAAAATATAAATTTTGAAAGTT
* *
5419496 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGGCTAAAATATAAATTTTG-AAAGTT
* *
5419526 TAG-GGACTAAAATTATAATTTTTAAAAGTT
1 TAGTGG-CTAAAA-TATAAATTTTGAAAGTT
5419556 ATATATTTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 21 0.43
30 20 0.41
31 8 0.16
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (29 bp):
TAGTGGCTAAAATATAAATTTTGAAAGTT
Found at i:5419551 original size:15 final size:17
Alignment explanation
Indices: 5419533--5419564 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5419523 GTTTAGGGAC
5419533 TAAAA-TTATA-ATTTT
1 TAAAAGTTATATATTTT
5419548 TAAAAGTTATATATTTT
1 TAAAAGTTATATATTTT
5419565 AGCCTGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TAAAAGTTATATATTTT
Found at i:5419553 original size:30 final size:30
Alignment explanation
Indices: 5419467--5419555 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 30
5419457 AAATTTTTTC
*
5419467 TAGT-GACTAAAATGTA-AATTTTGAAAGTT
1 TAGTGGACTAAAAT-TATAATTTTAAAAGTT
* *
5419496 TAGTGG-CT-AAAGTATAAACTTTGAAAAGTT
1 TAGTGGACTAAAATTAT-AA-TTTTAAAAGTT
5419526 TAG-GGACTAAAATTATAATTTTTAAAAGTT
1 TAGTGGACTAAAATTATAA-TTTTAAAAGTT
5419556 ATATATTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.04
28 3 0.06
29 10 0.21
30 27 0.56
31 6 0.12
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (30 bp):
TAGTGGACTAAAATTATAATTTTAAAAGTT
Found at i:5422472 original size:24 final size:24
Alignment explanation
Indices: 5422444--5422507 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
5422434 GTTTCCTGAA
*
5422444 TGCACA-AATAGTGTCACGTAGAAT
1 TGCACATAA-AGTGTCACATAGAAT
*
5422468 TGCACATAAAGTGTCACATATAAT
1 TGCACATAAAGTGTCACATAGAAT
*
5422492 TGCACTAGAAAGTGTC
1 TGCAC-ATAAAGTGTC
5422508 GTGTAGAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 24 0.69
25 11 0.31
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
TGCACATAAAGTGTCACATAGAAT
Found at i:5422538 original size:25 final size:25
Alignment explanation
Indices: 5422491--5422539 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5422481 TCACATATAA
** *
5422491 TTGCACTAGAAAGTGTCGTGTAGAG
1 TTGCACTAGAAAGTACCGCGTAGAG
*
5422516 TTGCACTCGAAAGTACCGCGTAGA
1 TTGCACTAGAAAGTACCGCGTAGA
5422540 ATGTACATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (25 bp):
TTGCACTAGAAAGTACCGCGTAGAG
Found at i:5430565 original size:12 final size:12
Alignment explanation
Indices: 5430536--5430567 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
5430526 TATCACAAGC
5430536 CAAATCATTTAA
1 CAAATCATTTAA
5430548 -AAATCATTTAA
1 CAAATCATTTAA
5430559 CAAATCATT
1 CAAATCATT
5430568 ATGACAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (12 bp):
CAAATCATTTAA
Found at i:5431447 original size:30 final size:31
Alignment explanation
Indices: 5431411--5431471 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
5431401 TTTTACGTTT
*
5431411 TTGGTCCATA-AAC-CTCTATAAGCTTCCAAA
1 TTGGTCCAAATAACTCTCTA-AAGCTTCCAAA
*
5431441 TTGGTCCAAATAACTTTCTAAAGCTTCCAAA
1 TTGGTCCAAATAACTCTCTAAAGCTTCCAAA
5431472 ACCATCTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
31 14 0.52
32 4 0.15
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (31 bp):
TTGGTCCAAATAACTCTCTAAAGCTTCCAAA
Found at i:5444602 original size:31 final size:29
Alignment explanation
Indices: 5444541--5444616 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 29
5444531 TGGATTACAT
5444541 AACTTTTCAAAATTACACTTTAGTCCCTA
1 AACTTTTCAAAATTACACTTTAGTCCCTA
* *
5444570 AACTTTTCCAAAGTTTATACTTTAG-CCACTA
1 AACTTTT-CAAA-ATTACACTTTAGTCC-CTA
5444601 AAC-TTTCAAAATTACA
1 AACTTTTCAAAATTACA
5444617 TTTTGGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 4 0.10
29 11 0.28
30 9 0.22
31 16 0.40
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (29 bp):
AACTTTTCAAAATTACACTTTAGTCCCTA
Found at i:5451987 original size:253 final size:252
Alignment explanation
Indices: 5451420--5452049 Score: 652
Period size: 253 Copynumber: 2.5 Consensus size: 252
5451410 ATTGGTAAGT
* * * *
5451420 CTTTCGAGCAAGATGATAAGTCGT-T-G-GTCATCTATAAGACCCTCGGGCA-GGATATTTTCAT
1 CTTTCGAGCAAGATGATAAGTC-TCTCGAGCCA-CTATAACACCTTCGGGCATGG--CTTTTCAT
* * **
5451481 AT-G-ATTTATGAA-AAAAAGAGAAAGCAATTTTCAAAGTTTCTCATTTAAGATTTTCAGAATTT
62 ATGGTATTTAT-AAGAGAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAAGATTTTCAGAAAAT
* *
5451543 GAATTTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTCTTACCTAGTAGACTATTTCCAAAATTG
126 GAA-TTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTCTTACCCAGTAGAATATTTCCAAAATTG
* * * *
5451608 ATAAGTCCTTCAGCCATCAGTAAGTCTTTCGAATATGATGACTCCTTAAGGTCATCTGTCAAC
190 ATAAGTCCTTCAGCCATCAATAAGTCTTTCGAATATGATAAATCCTTAAGGTCATCTATCAAC
* *
5451671 CTTTCGAGCAAGATGATAAGTCTCTCGGGCCATCTATAAGACCTTCGGGCATGGCTTTTTCATAT
1 CTTTCGAGCAAGATGATAAGTCTCTCGAGCCA-CTATAACACCTTCGGGCATGGC-TTTTCATAT
** * * *
5451736 -G-ATTT-TGGGGGAAATGAGAAAGCGATTTTAAAAGTTTCTCATTTAAGATTTTCAGAAAATGA
64 GGTATTTATAAGAG-AATGAGAAAGCAATTTTCAAAGTTTCTCATTTAAGATTTTCAGAAAATGA
* * * *
5451798 A-TTTTG-AAAGTAAGAAAGCGATTTCTAAAGTTTCTTACCCAGTAGAATATTTCTATAATTGAT
128 ATTTTTGAAAAGTAAGAAAGCAATTTCCAAAG-TTCTTACCCAGTAGAATATTTCCAAAATTGAT
** * *
5451861 AAGTCCTTCATGCCATCAATAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTCATCTATTAG
192 AAGTCCTTCA-GCCATCAATAAGTCTTTCGA--AT-ATGA-TAAATCCTTAAGGTCATCTATCAA
*
5451926 T
252 C
* *
5451927 CTTT-GAGCATGATGATAAGTC-CTTCGAGCCA-TATAACACCTTCGGGTATGATGC-TTTCATA
1 CTTTCGAGCAAGATGATAAGTCTC-TCGAGCCACTATAACACCTTCGGGCATG--GCTTTTCATA
* *
5451988 TGGTATTTATAAGAGAATGAGAAA--TA-TTTCAAAGTTTCTCATTTAA-ATTTTCAAAAAATGA
63 TGGTATTTATAAGAGAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAAGATTTTCAGAAAATGA
5452049 A
128 A
5452050 AATGAAAAAA
Statistics
Matches: 323, Mismatches: 37, Indels: 38
0.81 0.09 0.10
Matches are distributed among these distances:
250 23 0.07
251 81 0.25
252 40 0.12
253 107 0.33
254 6 0.02
255 42 0.13
256 24 0.07
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (252 bp):
CTTTCGAGCAAGATGATAAGTCTCTCGAGCCACTATAACACCTTCGGGCATGGCTTTTCATATGG
TATTTATAAGAGAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAAGATTTTCAGAAAATGAATT
TTTGAAAAGTAAGAAAGCAATTTCCAAAGTTCTTACCCAGTAGAATATTTCCAAAATTGATAAGT
CCTTCAGCCATCAATAAGTCTTTCGAATATGATAAATCCTTAAGGTCATCTATCAAC
Found at i:5452060 original size:15 final size:15
Alignment explanation
Indices: 5452040--5452084 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
5452030 TTAAATTTTC
5452040 AAAAAATGAAAATGA
1 AAAAAATGAAAATGA
5452055 AAAAAATAAGAAAA-GA
1 AAAAAAT--GAAAATGA
5452071 AAATAAATGAAAAT
1 AAA-AAATGAAAAT
5452085 TAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 12 0.46
16 5 0.19
17 9 0.35
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (15 bp):
AAAAAATGAAAATGA
Found at i:5454744 original size:23 final size:23
Alignment explanation
Indices: 5454718--5454815 Score: 110
Period size: 23 Copynumber: 4.3 Consensus size: 23
5454708 GAGTTGAGGG
5454718 TTCTATGCGGTCCTTCGAGACAA
1 TTCTATGCGGTCCTTCGAGACAA
* *
5454741 TTCTATGTGGTCCTTC-AGGACAT
1 TTCTATGCGGTCCTTCGA-GACAA
* *
5454764 TTCTACGCGGTCCTTCGGGACAA
1 TTCTATGCGGTCCTTCGAGACAA
* * *
5454787 TACTATGTGGTCCTTCAAGAC-A
1 TTCTATGCGGTCCTTCGAGACAA
5454809 TTCTATG
1 TTCTATG
5454816 TGGCACTTCG
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
22 8 0.13
23 53 0.87
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.34
Consensus pattern (23 bp):
TTCTATGCGGTCCTTCGAGACAA
Found at i:5454774 original size:46 final size:46
Alignment explanation
Indices: 5454718--5454810 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
5454708 GAGTTGAGGG
* * *
5454718 TTCTATGCGGTCCTTCGAGACAATTCTATGTGGTCCTTCAGGACAT
1 TTCTACGCGGTCCTTCGAGACAATACTATGTGGTCCTTCAAGACAT
*
5454764 TTCTACGCGGTCCTTCGGGACAATACTATGTGGTCCTTCAAGACAT
1 TTCTACGCGGTCCTTCGAGACAATACTATGTGGTCCTTCAAGACAT
5454810 T
1 T
5454811 CTATGTGGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCGAGACAATACTATGTGGTCCTTCAAGACAT
Found at i:5457678 original size:16 final size:17
Alignment explanation
Indices: 5457653--5457700 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
5457643 ATTATTTTAT
5457653 AAAT-TTTAATAATTAA
1 AAATATTTAATAATTAA
5457669 AAA-ATTTAATAA--AA
1 AAATATTTAATAATTAA
5457683 AAATATCTT-ATAATTAA
1 AAATAT-TTAATAATTAA
5457700 A
1 A
5457701 GAATCATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 13 0.48
17 3 0.11
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATTTAATAATTAA
Found at i:5463240 original size:74 final size:74
Alignment explanation
Indices: 5463156--5463306 Score: 275
Period size: 74 Copynumber: 2.0 Consensus size: 74
5463146 ATAATTATAT
5463156 ATTTGATCCTCAATATTTATAAATTATATCAATTTGGTCATAATTTTAATTCAATTTAATAAATT
1 ATTTGATCCTCAATATTTATAAATTATATCAATTTGGTCATAATTTTAATTCAATTTAATAAATT
5463221 TAATATCCA
66 TAATATCCA
* * *
5463230 ATTTGGTCCTCAATATTTGTAAATTCTATCAATTTGGTCATAATTTTAATTCAATTTAATAAATT
1 ATTTGATCCTCAATATTTATAAATTATATCAATTTGGTCATAATTTTAATTCAATTTAATAAATT
5463295 TAATATCCA
66 TAATATCCA
5463304 ATT
1 ATT
5463307 AGGTGGTGAC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.46
Consensus pattern (74 bp):
ATTTGATCCTCAATATTTATAAATTATATCAATTTGGTCATAATTTTAATTCAATTTAATAAATT
TAATATCCA
Found at i:5463786 original size:24 final size:24
Alignment explanation
Indices: 5463727--5463796 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
5463717 TTTGTGATTT
*
5463727 ATAAATATATACATTTTAAAATATA
1 ATAAATATA-ATATTTTAAAATATA
* *
5463752 GTTAATATAATA-TTTAAAATAATA
1 ATAAATATAATATTTTAAAAT-ATA
*
5463776 ATAAATTTAATATTTTAAAAT
1 ATAAATATAATATTTTAAAAT
5463797 TAAATTCAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 8 0.22
24 14 0.38
25 15 0.41
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (24 bp):
ATAAATATAATATTTTAAAATATA
Found at i:5463821 original size:21 final size:20
Alignment explanation
Indices: 5463770--5463830 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
5463760 AATATTTAAA
*
5463770 ATAATAATAAATTTAATATT
1 ATAAAAATAAATTTAATATT
* * *
5463790 TTAAAATTAAATTCAATATGT
1 ATAAAAATAAATTTAATAT-T
5463811 ATAAAAATAAATTTAATATT
1 ATAAAAATAAATTTAATATT
5463831 TTTTAAAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAAAAATAAATTTAATATT
Found at i:5463838 original size:21 final size:20
Alignment explanation
Indices: 5463775--5463839 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
5463765 TTAAAATAAT
5463775 AATAAATTTAATA-TTTTAA
1 AATAAATTTAATATTTTTAA
* * *
5463794 AATTAAATTCAATATGTATAAA
1 AA-TAAATTTAATAT-TTTTAA
5463816 AATAAATTTAATATTTTTTAA
1 AATAAATTTAATA-TTTTTAA
5463837 AAT
1 AAT
5463840 GATTTTGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.06
20 10 0.28
21 17 0.47
22 7 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
AATAAATTTAATATTTTTAA
Found at i:5467691 original size:23 final size:23
Alignment explanation
Indices: 5467662--5467728 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
5467652 TTCCACATAT
*
5467662 TTGTCCCTAAGGACCACATAGGA
1 TTGTCCCGAAGGACCACATAGGA
5467685 TTGTCCCGAAGGACCACATAGGA
1 TTGTCCCGAAGGACCACATAGGA
5467708 TTGTCCCGAAGGACCACATAG
1 TTGTCCCGAAGGACCACATAG
5467729 AACCCTCGAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAGGA
Found at i:5471996 original size:20 final size:20
Alignment explanation
Indices: 5471952--5471997 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
5471942 CTTACCTTAG
*
5471952 GTATCGGTACTATATGAATA
1 GTATCGGTACTATATCAATA
*
5471972 ATATCGGTACTAT-TCATATA
1 GTATCGGTACTATATCA-ATA
5471992 GTATCG
1 GTATCG
5471998 ATAATGTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (20 bp):
GTATCGGTACTATATCAATA
Found at i:5480505 original size:19 final size:19
Alignment explanation
Indices: 5480481--5480534 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
5480471 TATGCTTGTA
*
5480481 GTATCGATACACTTTTACG
1 GTATCGATACACATTTACG
*
5480500 GTATCGATACCCATTTACG
1 GTATCGATACACATTTACG
*
5480519 GTATCGATACCCATTT
1 GTATCGATACACATTT
5480535 TCGATTCTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (19 bp):
GTATCGATACACATTTACG
Found at i:5484191 original size:32 final size:29
Alignment explanation
Indices: 5484155--5484214 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 29
5484145 TATCTTATTT
5484155 CTTATGATCACATAACTTATTATCACACATAG
1 CTTATGATCACATAA--T-TTATCACACATAG
*
5484187 CTTATGGTCACATAATTTATCACACATA
1 CTTATGATCACATAATTTATCACACATA
5484215 CATGTATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.44
30 1 0.04
32 14 0.52
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.35
Consensus pattern (29 bp):
CTTATGATCACATAATTTATCACACATAG
Found at i:5487742 original size:18 final size:18
Alignment explanation
Indices: 5487719--5487793 Score: 87
Period size: 18 Copynumber: 3.9 Consensus size: 18
5487709 ATATAGAATT
*
5487719 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
5487737 TGTCCCGAAGGACCATTGTATA
1 TGTCCCGAAGGACCA----CTA
*
5487759 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
5487777 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
5487794 GTATATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 32 0.67
22 16 0.33
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:5487763 original size:22 final size:21
Alignment explanation
Indices: 5487735--5487799 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
5487725 GTAGGACCAC
5487735 TATGTCCCGAAGGACCATTGTA
1 TATGTCCCGAAGGACCA-TGTA
* *
5487757 TATGTCCCGAATGACCA---C
1 TATGTCCCGAAGGACCATGTA
5487775 TATGTCCCGAAGGACCACTGTA
1 TATGTCCCGAAGGACCA-TGTA
5487797 TAT
1 TAT
5487800 CCCTCGACTC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 16 0.46
22 19 0.54
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (21 bp):
TATGTCCCGAAGGACCATGTA
Found at i:5487774 original size:40 final size:40
Alignment explanation
Indices: 5487719--5487799 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
5487709 ATATAGAATT
* *
5487719 TGTCCCGTAGGACCACTATGTCCCGAAGGACCATTGTATA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGTATA
*
5487759 TGTCCCGAATGACCACTATGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGTATA
5487799 T
1 T
5487800 CCCTCGACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGTATA
Found at i:5492220 original size:22 final size:22
Alignment explanation
Indices: 5492195--5492261 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
5492185 GCGTAGAATT
*
5492195 TGTCCCGAATGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
5492217 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
5492239 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
5492261 T
1 T
5492262 CCCTCGACTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGTATA
Found at i:5493993 original size:27 final size:27
Alignment explanation
Indices: 5493950--5494043 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 27
5493940 GAAAGCAAAG
5493950 ATAAAATAGTA-AGTAAAAAAAACAAATA
1 ATAAAATA-TATA-TAAAAAAAACAAATA
*
5493978 ATAAAATATATATAAAAAAGAA-AAAAA
1 ATAAAATATATATAAAAAA-AACAAATA
* * *
5494005 AGAAAATAAATAAAACAAATAAACAAAATA
1 ATAAAATATATATAA-AAA-AAAC-AAATA
5494035 ATAATAATA
1 ATAA-AATA
5494044 AAGTACGAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
27 25 0.47
28 16 0.30
29 1 0.02
30 7 0.13
31 4 0.08
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.18
Consensus pattern (27 bp):
ATAAAATATATATAAAAAAAACAAATA
Found at i:5494019 original size:9 final size:9
Alignment explanation
Indices: 5493973--5494079 Score: 51
Period size: 9 Copynumber: 11.3 Consensus size: 9
5493963 TAAAAAAAAC
5493973 AAAT-AATA
1 AAATAAATA
*
5493981 AAATATATA
1 AAATAAATA
*
5493990 TAAA-AAAGA
1 -AAATAAATA
* *
5493999 AAAAAAAGA
1 AAATAAATA
5494008 AAATAAATA
1 AAATAAATA
*
5494017 AAACAAATA
1 AAATAAATA
5494026 AACA-AAATA
1 AA-ATAAATA
5494035 ATAAT-AATA
1 A-AATAAATA
*
5494044 AAGTACGAATA
1 AAATA--AATA
5494055 ATATATATATATA
1 A-A-ATA-A-ATA
5494068 AAATAAATA
1 AAATAAATA
5494077 AAA
1 AAA
5494080 AAGTAAATAT
Statistics
Matches: 78, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
8 9 0.12
9 46 0.59
10 6 0.08
11 8 0.10
12 3 0.04
13 6 0.08
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:5494171 original size:2 final size:2
Alignment explanation
Indices: 5494164--5494209 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
5494154 TAAAGATAAT
5494164 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
5494206 TA TA
1 TA TA
5494210 GTAACAATAC
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):
TA
Found at i:5494372 original size:2 final size:2
Alignment explanation
Indices: 5494365--5494399 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5494355 CTTGTGTAGA
5494365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5494400 ATAATAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5494604 original size:2 final size:2
Alignment explanation
Indices: 5494597--5494621 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5494587 GAACATACGC
5494597 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5494622 CAAAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5494640 original size:14 final size:15
Alignment explanation
Indices: 5494617--5494645 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5494607 ATATATATAT
5494617 ATATACAAAATAATA
1 ATATACAAAATAATA
5494632 ATATA-AAAATAATA
1 ATATACAAAATAATA
5494646 CAAGTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
ATATACAAAATAATA
Found at i:5494656 original size:12 final size:11
Alignment explanation
Indices: 5494628--5494668 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
5494618 TATACAAAAT
* *
5494628 AATAATATAAA
1 AATAATACAAG
5494639 AATAATACAAG
1 AATAATACAAG
5494650 TAATAATACAAG
1 -AATAATACAAG
5494662 AATAATA
1 AATAATA
5494669 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:5494669 original size:14 final size:13
Alignment explanation
Indices: 5494619--5494669 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 13
5494609 ATATATATAT
5494619 ATACAAAATAATA
1 ATACAAAATAATA
*
5494632 ATA-TAAA-AATA
1 ATACAAAATAATA
*
5494643 ATAC-AAGTAATA
1 ATACAAAATAATA
5494655 ATACAAGAATAATA
1 ATACAA-AATAATA
5494669 A
1 A
5494670 AAAGAAAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 9 0.29
12 11 0.35
13 4 0.13
14 7 0.23
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.24
Consensus pattern (13 bp):
ATACAAAATAATA
Found at i:5494772 original size:12 final size:12
Alignment explanation
Indices: 5494750--5494794 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
5494740 GAATAAAAGA
5494750 AAAATATAATAGT
1 AAAA-ATAATAGT
*
5494763 AAAAATAATAAT
1 AAAAATAATAGT
*
5494775 AAATATAATAGT
1 AAAAATAATAGT
*
5494787 AATAATAA
1 AAAAATAA
5494795 GAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:5494778 original size:24 final size:24
Alignment explanation
Indices: 5494688--5494794 Score: 80
Period size: 24 Copynumber: 4.3 Consensus size: 24
5494678 AGAAAGTAAA
*
5494688 AAAATATAATAAT-AATAAAATA-T
1 AAAA-ATAATAATAAATATAATAGT
5494711 AAAAAT-ATACATATATATATAAATAAGT
1 AAAAATAATA-ATA-A-ATAT-AAT-AGT
*
5494739 AGAATAA-AAGAA-AAATATAATAGT
1 A-AA-AATAATAATAAATATAATAGT
5494763 AAAAATAATAATAAATATAATAGT
1 AAAAATAATAATAAATATAATAGT
*
5494787 AATAATAA
1 AAAAATAA
5494795 GAATGCAAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
21 3 0.04
22 6 0.09
23 10 0.15
24 24 0.35
25 6 0.09
26 7 0.10
27 2 0.03
28 3 0.04
29 3 0.04
30 4 0.06
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (24 bp):
AAAAATAATAATAAATATAATAGT
Found at i:5495384 original size:37 final size:36
Alignment explanation
Indices: 5495343--5495447 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 36
5495333 GTGCTTGTGG
*
5495343 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
5495380 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTA-TTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
5495417 ATCCTATTTTAAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTT-AGGAGTTTAAATCCTAGTAG
5495448 GACTAAAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 4 0.07
37 54 0.92
38 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:5496500 original size:106 final size:106
Alignment explanation
Indices: 5496175--5497641 Score: 2159
Period size: 106 Copynumber: 13.9 Consensus size: 106
5496165 GCATTGTTCT
* * * * *
5496175 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
** * * *
5496239 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
5496281 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
** * * *
5496340 TTAGCCG-CCTCTTCGTCGTGAAGTTGAGCTTGTGTT-TCCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGT-C-TG
* * * ** *
5496382 G-GTACAAGATCCTTCACTAAGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
5496446 CCAGCGGTCCCTTCGTCGTGAAGTTGAAATTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5496487 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
5496552 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5496593 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTG-TTAGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA-TTGACA
5496657 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5496698 GAGTCCAAAATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
5496763 CCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
5496804 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
5496869 CCAGCGGTCCCTTCGTCGTGAAGTTGAAATTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
5496910 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
5496975 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
5497016 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
5497081 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5497122 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
5497187 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5497228 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
5497293 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
**
5497334 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
5497399 CCAGCTGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5497440 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
5497505 TCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
5497546 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
5497610 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
5497642 TGTTATCTTG
Statistics
Matches: 1242, Mismatches: 103, Indels: 33
0.90 0.07 0.02
Matches are distributed among these distances:
99 3 0.00
100 70 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 140 0.11
106 1013 0.82
107 4 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:5498505 original size:22 final size:22
Alignment explanation
Indices: 5498479--5498555 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
5498469 TTATGTTTGG
5498479 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
5498501 TCAAAGGTTTGGCATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
5498523 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
5498545 TCAACGGTTTG
1 TCAAAGGTTTG
5498556 ATGAGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:5499181 original size:16 final size:14
Alignment explanation
Indices: 5499159--5499235 Score: 57
Period size: 16 Copynumber: 5.0 Consensus size: 14
5499149 TTTTTGTCCC
5499159 TTTTTCTTTTTGATT
1 TTTTTCTTTTTG-TT
5499174 TTTGTTCTTTCTT-TT
1 TTT-TTCTTT-TTGTT
5499189 TTTCCTTCTTTTTTGCTT
1 TTT--TTC-TTTTTG-TT
5499207 TTTTTCTTTTTTGTT
1 TTTTTC-TTTTTGTT
**
5499222 TTTCCCTTTTTGTT
1 TTTTTCTTTTTGTT
5499236 CTGATTGAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
14 8 0.15
15 14 0.26
16 21 0.40
17 5 0.09
18 5 0.09
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.78
Consensus pattern (14 bp):
TTTTTCTTTTTGTT
Found at i:5499199 original size:32 final size:32
Alignment explanation
Indices: 5499162--5499233 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 32
5499152 TTGTCCCTTT
5499162 TTCTTTTTGATTTTTGTTCTTTCTT-TTTTTCC
1 TTCTTTTTGATTTTT-TTCTTTCTTGTTTTTCC
* *
5499194 TTCTTTTTTGCTTTTTTTCTTTTTTGTTTTTCC
1 TTC-TTTTTGATTTTTTTCTTTCTTGTTTTTCC
5499227 --CTTTTTG
1 TTCTTTTTG
5499234 TTCTGATTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
30 6 0.17
31 1 0.03
32 11 0.31
33 18 0.50
ACGTcount: A:0.01, C:0.15, G:0.07, T:0.76
Consensus pattern (32 bp):
TTCTTTTTGATTTTTTTCTTTCTTGTTTTTCC
Found at i:5502489 original size:19 final size:20
Alignment explanation
Indices: 5502461--5502498 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5502451 TGCAGATGAT
*
5502461 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
5502480 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
5502499 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:5503671 original size:27 final size:27
Alignment explanation
Indices: 5503628--5503776 Score: 75
Period size: 27 Copynumber: 5.6 Consensus size: 27
5503618 GAAATCAAAG
5503628 ATAAAATAGTA-AGTAAAAAAAACAAATA
1 ATAAAATA-TATA-TAAAAAAAACAAATA
* *
5503656 ATAAAATATATATAAAAAGAA-AAAGA
1 ATAAAATATATATAAAAAAAACAAATA
*
5503682 A-AAAGA-A-A-ATAAATAAAACAAATAA
1 ATAAA-ATATATATAAAAAAAACAAAT-A
* * *
5503707 ACAAAATA-ATAATAACAAAATACGAATA
1 ATAAAATATAT-ATAA-AAAAAACAAATA
* * *
5503735 AT-ATATATAAATAAAATAAATA-AAAAA
1 ATAAAATATATATAAAA-AAA-ACAAATA
5503762 AT-AAATATATATAAA
1 ATAAAATATATATAAA
5503777 TTAATAAATT
Statistics
Matches: 93, Mismatches: 16, Indels: 25
0.69 0.12 0.19
Matches are distributed among these distances:
23 8 0.09
24 4 0.04
25 7 0.08
26 13 0.14
27 36 0.39
28 17 0.18
29 8 0.09
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.20
Consensus pattern (27 bp):
ATAAAATATATATAAAAAAAACAAATA
Found at i:5503697 original size:4 final size:4
Alignment explanation
Indices: 5503688--5503790 Score: 50
Period size: 4 Copynumber: 24.0 Consensus size: 4
5503678 AAGAAAAAGA
* *
5503688 AAAT AAAT AAAAC AAAT AAAC AAA- ATAAT -AAT AACA- AAAT ACGAAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AA-AT AAAT A--AAT
* * *
5503734 AATAT ATAT AAAT AAAAT AAAT AAAA AAAT AAAT ATATAT AAAT TAAT
1 AA-AT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT
5503782 AAATT AAAT
1 AAA-T AAAT
5503791 GACGAAAAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
3 5 0.06
4 48 0.62
5 17 0.22
6 7 0.09
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:5503782 original size:18 final size:18
Alignment explanation
Indices: 5503731--5503785 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
5503721 ACAAAATACG
*
5503731 AATA-ATATATATAAATA
1 AATATATATAAATAAATA
* *
5503748 AA-ATAAATAAAAAAATA
1 AATATATATAAATAAATA
*
5503765 AATATATATAAATTAATA
1 AATATATATAAATAAATA
5503783 AAT
1 AAT
5503786 TAAATGACGA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 1 0.03
17 14 0.47
18 15 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATATATATAAATAAATA
Found at i:5503790 original size:27 final size:27
Alignment explanation
Indices: 5503655--5503784 Score: 77
Period size: 27 Copynumber: 4.6 Consensus size: 27
5503645 AAAAACAAAT
* *
5503655 AATAAAATATATATAAAAAGAA-AAAGAAA
1 AATAAAATA-A-ATAAAAA-AATAAATATA
* *
5503684 AAGAAAATAAATAAAACAAATAAACA-A
1 AATAAAATAAATAAAA-AAATAAATATA
* *
5503711 AATAATAATAACAAAATACGAATAATATATATA
1 AATAA-AATAA-ATAA-A--AA-AATAAATATA
5503744 AATAAAATAAATAAAAAAATAAATATA
1 AATAAAATAAATAAAAAAATAAATATA
* *
5503771 TAT-AAATTAATAAA
1 AATAAAATAAATAAA
5503785 TTAAATGACG
Statistics
Matches: 82, Mismatches: 10, Indels: 21
0.73 0.09 0.19
Matches are distributed among these distances:
26 10 0.12
27 24 0.29
28 13 0.16
29 11 0.13
30 2 0.02
31 4 0.05
32 12 0.15
33 6 0.07
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (27 bp):
AATAAAATAAATAAAAAAATAAATATA
Found at i:5503856 original size:2 final size:2
Alignment explanation
Indices: 5503849--5503887 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5503839 TAATTACAAA
5503849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5503888 GTAACAATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5504411 original size:12 final size:12
Alignment explanation
Indices: 5504389--5504433 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
5504379 GAATAAAAGG
5504389 AAAATATAATAGT
1 AAAA-ATAATAGT
*
5504402 AAAAATAATAAT
1 AAAAATAATAGT
*
5504414 AAATATAATAGT
1 AAAAATAATAGT
*
5504426 AATAATAA
1 AAAAATAA
5504434 GAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:5504483 original size:20 final size:20
Alignment explanation
Indices: 5504458--5504519 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
5504448 TAAATATATA
5504458 TATATATATGGGTAATAACG
1 TATATATATGGGTAATAACG
* *
5504478 TATATAAAT-AG-AGAT-A--
1 TATATATATGGGTA-ATAACG
5504494 TATATATATGGGTAATAACG
1 TATATATATGGGTAATAACG
5504514 TATATA
1 TATATA
5504520 AATAGAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 8 0.25
17 3 0.09
18 4 0.12
19 3 0.09
20 14 0.44
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.35
Consensus pattern (20 bp):
TATATATATGGGTAATAACG
Found at i:5504502 original size:36 final size:36
Alignment explanation
Indices: 5504455--5504527 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
5504445 AAATAAATAT
5504455 ATATATATATATGGGTAATAACGTATATAAATAGAG
1 ATATATATATATGGGTAATAACGTATATAAATAGAG
5504491 ATATATATATATGGGTAATAACGTATATAAATAGAG
1 ATATATATATATGGGTAATAACGTATATAAATAGAG
5504527 A
1 A
5504528 AAAATTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.33
Consensus pattern (36 bp):
ATATATATATATGGGTAATAACGTATATAAATAGAG
Found at i:5505069 original size:37 final size:37
Alignment explanation
Indices: 5505028--5505132 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
5505018 GTGCTTGTGG
* *
5505028 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* *
5505065 ATCCTATTTTTAGGAGTTTAAATCCTAGTAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* *
5505102 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
5505133 GACGAAAAGG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:5512146 original size:14 final size:14
Alignment explanation
Indices: 5512127--5512164 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
5512117 TGCCAAGGCG
5512127 AGTTTTATCTTGCA
1 AGTTTTATCTTGCA
5512141 AGTTTTATCTTGCA
1 AGTTTTATCTTGCA
5512155 AGTTTTATCT
1 AGTTTTATCT
5512165 GACGTAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (14 bp):
AGTTTTATCTTGCA
Found at i:5513564 original size:19 final size:20
Alignment explanation
Indices: 5513532--5513569 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5513522 ACTACTATAT
5513532 TACTTGCATCGA-TTGTGTA
1 TACTTGCATCGATTTGTGTA
5513551 TACTTGCA-CAGATTTGTGT
1 TACTTGCATC-GATTTGTGT
5513570 GTCACAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.06
19 10 0.59
20 6 0.35
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (20 bp):
TACTTGCATCGATTTGTGTA
Found at i:5514187 original size:3 final size:3
Alignment explanation
Indices: 5514181--5514210 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5514171 TGATTGGAAA
5514181 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5514211 TCTTGAATCA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5515437 original size:16 final size:16
Alignment explanation
Indices: 5515399--5515448 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
5515389 TTCTTCTACT
*
5515399 TTATTTATT-TTCTCA
1 TTATTTATTATTTTCA
*
5515414 TAATTTA-T-TTTT-A
1 TTATTTATTATTTTCA
5515427 TTATTTATTATTTTCA
1 TTATTTATTATTTTCA
5515443 TTATTT
1 TTATTT
5515449 CTAAATCCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 7 0.24
14 5 0.17
15 10 0.34
16 7 0.24
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTATTATTTTCA
Found at i:5520819 original size:32 final size:31
Alignment explanation
Indices: 5520764--5520838 Score: 123
Period size: 32 Copynumber: 2.4 Consensus size: 31
5520754 TAAGGGGACC
* *
5520764 CTTGGGTAGGCTCTGTGGCCCCGAGATCTTT
1 CTTGGGTAGGCTCCGTGGCCCCGAGAACTTT
5520795 CTTGGGTAGGTCTCCGTGGCCCCGAGAACTTT
1 CTTGGGTAGG-CTCCGTGGCCCCGAGAACTTT
5520827 CTTGGGTAGGCT
1 CTTGGGTAGGCT
5520839 ATCAGGCCCC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 12 0.29
32 29 0.71
ACGTcount: A:0.11, C:0.25, G:0.33, T:0.31
Consensus pattern (31 bp):
CTTGGGTAGGCTCCGTGGCCCCGAGAACTTT
Found at i:5523733 original size:15 final size:15
Alignment explanation
Indices: 5523697--5523735 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5523687 TAAATTTAGG
*
5523697 ATTTTTACTTTGATT
1 ATTTTTATTTTGATT
*
5523712 A-TTTTATTTTTATT
1 ATTTTTATTTTGATT
5523726 ATTTTTATTT
1 ATTTTTATTT
5523736 ATTTAGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
ATTTTTATTTTGATT
Found at i:5544528 original size:23 final size:23
Alignment explanation
Indices: 5544502--5544574 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
5544492 ATACTTTACA
*
5544502 ATATAAGCACTACTTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
5544525 ATATAAACGCTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
*
5544548 ATATAAGCGA-TACCTATTACATC
1 ATATAAGC-ACTACCTATTACATT
5544571 ATAT
1 ATAT
5544575 TTTACCAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:5545024 original size:23 final size:23
Alignment explanation
Indices: 5544989--5545061 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
5544979 ATACTTTACA
* *
5544989 ATATAAGCACTACATATTACATT
1 ATATAAGCGCTACCTATTACATT
*
5545012 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
5545035 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
5545058 ATAT
1 ATAT
5545062 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:5545030 original size:487 final size:489
Alignment explanation
Indices: 5544105--5545362 Score: 2172
Period size: 487 Copynumber: 2.6 Consensus size: 489
5544095 TTATAATATG
* * * * *
5544105 TTGAAAGTATTCATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAAATTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAATTTATGT
*
5544170 TTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
65 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
* * *
5544234 CAAAATATTATTTGATTGTTTTGATATTTTAT--AA-A--ATTTAGAATTTAAATATAATAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAT
*
5544294 TAACCAAAGATAATAATAAATATGTAATATATATGTTTTTTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* * *
5544359 ATCTTAACGTAAAAAATAAATCATTATACGCCTATAATTACTAAATTAATATCTTAAAGCTCACT
260 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
* * *
5544424 CAAAAGATAACCTTAAATTAATGTTTTTCACAGTAAAAACAGTATAGACACTTTTATATAAATGA
325 CAAAAGATAACCTTAAATTAATGTTTTTCACAGTAAAAAAAGTATAGACACTTTTATAAAAAGGA
*
5544489 TAAATACTTTACAATATAAGCACTACTTATTACATTATATAAACGCTACCTATTACATTATATAA
390 TAAATACTTTACAATATAAGCACTACATATTACATTATATAAACGCTACCTATTACATTATATAA
5544554 GCGATACCTATTACATCATA-TTTTACCAATTATA
455 GCGATACCTATTACATCATATTTTTACCAATTATA
5544588 TTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTATTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAATTTATGTT
* *
5544652 TCAATTTTTTTAATAGTATTTCATGTTTTCCACCTACAATATTTATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
5544717 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
5544782 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* * *
5544847 CCGCAACGTAAAAAATAAATTATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
*
5544912 AAAAGATAACCTTAAATTAATGTTTTTCACAGTAAAAAAAGTATGGACACTTTTATAAAAAGGAT
326 AAAAGATAACCTTAAATTAATGTTTTTCACAGTAAAAAAAGTATAGACACTTTTATAAAAAGGAT
*
5544977 AGATACTTTACAATATAAGCACTACATATTACATTATATAAACGCTACCTATTACATTATATAAG
391 AAATACTTTACAATATAAGCACTACATATTACATTATATAAACGCTACCTATTACATTATATAAG
* *
5545042 CGCTACCTATTACATCATATTTTTACCTATTATA
456 CGATACCTATTACATCATATTTTTACCAATTATA
*
5545076 TTGAAAGTGTGCATACTTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAATTTATGTT
5545141 TCAATTTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
66 TCAA--TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
5545206 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
129 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
*
5545271 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTTTTTTTAATTTAATAATAATATA
194 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
*
5545336 TATTGTAACGTAAAAAATAAATCATTA
259 TATCGTAACGTAAAAAATAAATCATTA
5545363 AACACTTTAT
Statistics
Matches: 731, Mismatches: 34, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
481 42 0.06
482 94 0.13
483 14 0.02
484 2 0.00
485 1 0.00
487 289 0.40
488 35 0.05
489 45 0.06
491 209 0.29
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (489 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTTCACAGTAAAAAAAGTATAGACACTTTTATAAAAAGGAT
AAATACTTTACAATATAAGCACTACATATTACATTATATAAACGCTACCTATTACATTATATAAG
CGATACCTATTACATCATATTTTTACCAATTATA
Found at i:5548709 original size:120 final size:120
Alignment explanation
Indices: 5548496--5548738 Score: 432
Period size: 120 Copynumber: 2.0 Consensus size: 120
5548486 TTTTTCTTCC
*
5548496 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCACT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCACT
5548561 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
* *
5548616 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCACT
* * *
5548681 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
5548736 ATT
1 ATT
5548739 TTGGGTTCCG
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 117 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCACT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:5548878 original size:303 final size:303
Alignment explanation
Indices: 5548331--5550050 Score: 3156
Period size: 303 Copynumber: 5.7 Consensus size: 303
5548321 TTAAAATTAG
*
5548331 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
5548396 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATTTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
5548461 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
*
5548526 AAAAAGTGTCGACATAGGTTGTAGACCTATTCACTAATAAAACCGGTATACTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
5548591 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
5548634 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
5548699 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTTTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
5548764 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
*
5548829 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAATCGGTATACTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
5548894 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
5548937 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* ** *
5549002 ATACTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTTTGATGTATAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
5549067 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTAGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
*
5549132 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAATCGGTATACTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
5549197 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
*
5549240 CGACACAAAATTAAAAAGTGTCGATGTAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
5549305 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
5549370 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
*
5549435 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCAGTTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
5549500 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
* *
5549543 CGACATAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * *
5549608 ATACCGGTTATATCACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGCAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
* *
5549673 AACTTTTTGACAAGGTATCAACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
*
5549738 AAAAAGTATCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
5549803 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
5549846 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * * * *
5549911 ATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGATTCCGATGTTTTTTCAA--T
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TGTAAATGT
*
5549974 CGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAAT
128 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAAT
5550039 ATTAAAAAGTGT
193 ATTAAAAAGTGT
5550051 GAAAACTTTG
Statistics
Matches: 1373, Mismatches: 41, Indels: 5
0.97 0.03 0.00
Matches are distributed among these distances:
303 1296 0.94
304 74 0.05
306 3 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (303 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
Found at i:5549012 original size:120 final size:120
Alignment explanation
Indices: 5548799--5549045 Score: 431
Period size: 120 Copynumber: 2.1 Consensus size: 120
5548789 TTTTTCTTCC
*
5548799 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
*
5548864 AATAAAATCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
*
5548919 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
* * * *
5548984 CATAAAACCGGTATATTTATACTGGTTATATTACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
5549039 ATTCTGG
1 ATTCTGG
5549046 GTTTTGATGT
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:5549315 original size:120 final size:120
Alignment explanation
Indices: 5549102--5549348 Score: 422
Period size: 120 Copynumber: 2.1 Consensus size: 120
5549092 TTTTTCTTCC
* *
5549102 ATTCTAGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
*
5549167 AATAAAATCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
**
5549222 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATGTAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
* * *
5549287 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
5549342 ATTCTGG
1 ATTCTGG
5549349 GTTCCGATGT
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:5549618 original size:120 final size:120
Alignment explanation
Indices: 5549405--5549647 Score: 405
Period size: 120 Copynumber: 2.0 Consensus size: 120
5549395 TTTTTCTTCC
*
5549405 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
*
5549470 AATAAAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCAGTTATATCACAAAATTATCTAGTACATTATA
* *
5549525 ATTCTGGACATAAAGTACCGACATAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
* * * * *
5549590 CATAAAACTGGTATATTTATACCGGTTATATCACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCAGTTATATCACAAAATTATCTAGTACATTATA
5549645 ATT
1 ATT
5549648 ATGGGTTCCG
Statistics
Matches: 114, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 114 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCAGTTATATCACAAAATTATCTAGTACATTATA
Found at i:5549922 original size:120 final size:120
Alignment explanation
Indices: 5549708--5549955 Score: 424
Period size: 120 Copynumber: 2.1 Consensus size: 120
5549698 TTTTTCTTCC
*
5549708 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTATCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTATCGACATAGGTTGTAGACCTATTCGCT
*
5549773 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGATTATATTACAAAATTATCTAGTACATTATA
* *
5549828 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTATCGACATAGGTTGTAGACCTATTCGCT
* * *
5549893 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGATTATATTACAAAATTATCTAGTACATTATA
*
5549948 ATTATGGA
1 ATTCTGGA
5549956 TTCCGATGTT
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTATCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCGATTATATTACAAAATTATCTAGTACATTATA
Found at i:5551268 original size:3 final size:3
Alignment explanation
Indices: 5551260--5551310 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
5551250 ACTTGTTTGG
* * *
5551260 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
5551308 ATC
1 ATC
5551311 GTCAGCTTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.27, C:0.33, G:0.02, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:5551311 original size:12 final size:12
Alignment explanation
Indices: 5551260--5551327 Score: 82
Period size: 12 Copynumber: 5.7 Consensus size: 12
5551250 ACTTGTTTGG
*
5551260 ATCATCATCATC
1 ATCATCATCTTC
*
5551272 ATCATCATCATC
1 ATCATCATCTTC
5551284 ATCATCATCTTC
1 ATCATCATCTTC
*
5551296 ATCGTCATCTTC
1 ATCATCATCTTC
* *
5551308 ATCGTCAGCTTC
1 ATCATCATCTTC
*
5551320 ATCTTCAT
1 ATCATCAT
5551328 TGACCGTTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.25, C:0.32, G:0.04, T:0.38
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:5553104 original size:200 final size:200
Alignment explanation
Indices: 5552778--5553939 Score: 1975
Period size: 200 Copynumber: 5.8 Consensus size: 200
5552768 CATTAAACAA
* * * * * *
5552778 TGTCGATACA-TATTATATACCAATTCTCCCATAAAATCGGTATACTTATACCGGTTAGATTGAA
1 TGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAA
* *
5552842 AAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGG
65 AAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGG
* * * *
5552907 ATTGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATTGACAAAAACTA
130 ATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTA
5552972 CAAAAG
195 CAAAAG
* *
5552978 TTTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCAGTTAGATTGAAA
1 TGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
5553043 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
*
5553108 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
131 TCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
5553173 AAAAG
196 AAAAG
* * *
5553178 TGTCGACACATTATTTATACCTATTCTCTCATAAAGCTGGTATACTTGTACCGGTTAGATTGAAA
1 TGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
*
5553243 AATTACCTATTACATTATACTCATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
5553308 TCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
131 TCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
*
5553373 AGAAG
196 AAAAG
* * *
5553378 TGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGATATACTTGTACCGGTTAGATTGAAA
1 TGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
*
5553443 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
* *
5553508 TCGATACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
131 TCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
5553573 AAAAG
196 AAAAG
* *
5553578 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTATACCGGTTAGATTGAAA
1 TGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
**
5553643 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCAGATCGACACTTTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
* *
5553708 TTGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
131 TCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
5553773 AAAAG
196 AAAAG
* *
5553778 TGTCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAA
1 TGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
* * *
5553843 TATTACCTATTACATTATACTTTTGGGTTTTGATGTTTATGGGATCGACACTTTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
5553908 TCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 TCGACACTTTATGGTTGCACCCTGTTTGCCAT
5553940 ATTGTAAATT
Statistics
Matches: 909, Mismatches: 52, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
200 905 1.00
201 4 0.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (200 bp):
TGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
TCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
AAAAG
Found at i:5556031 original size:33 final size:33
Alignment explanation
Indices: 5555994--5556059 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
5555984 CATCTTAATA
*
5555994 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
5556027 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
5556060 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:5556118 original size:21 final size:21
Alignment explanation
Indices: 5556093--5556157 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
5556083 CCCCTTATGC
* *
5556093 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
5556114 CTCTCAAGTTTCTCTTCAACT
1 CTCTCAAGTTTCTCTTCGACT
*
5556135 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
5556156 CT
1 CT
5556158 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.18, C:0.31, G:0.09, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:5558588 original size:20 final size:20
Alignment explanation
Indices: 5558563--5558600 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5558553 GGTAACGTTT
5558563 TACCGGTTTTATCATATTGA
1 TACCGGTTTTATCATATTGA
5558583 TACCGGTTTTATCATATT
1 TACCGGTTTTATCATATT
5558601 TTTACATGGT
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:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (20 bp):
TACCGGTTTTATCATATTGA
Found at i:5558650 original size:181 final size:181
Alignment explanation
Indices: 5558346--5558818 Score: 687
Period size: 181 Copynumber: 2.6 Consensus size: 181
5558336 CGTACTTACG
*
5558346 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCA-TTTGATACCGGTTT
* * *
5558411 TATCATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
65 TATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
5558476 ATGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
5558527 AAAGTATCGACACTTTCTATATATCCGGTAACGTTTTACCGGTTTTATCATATTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCAT-TTGATACCGGTTT
* *
5558592 TATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
65 TATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * *
5558657 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATTCTTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * * *
5558709 AAAGTACCGACACTTTAAATGTATCAGGTAGCGCTTTACCGGTTTTATCATTTCAATACCAGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-GATACCGGTTT
* * * *
5558774 TGTCATAGTTTTACCTGTTATATCATTTTGGATCGATACATTTTT
65 TATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTTTT
5558819 AATTTGGATC
Statistics
Matches: 262, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
180 1 0.00
181 167 0.64
182 94 0.36
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTGATACCGGTTTT
ATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:5559738 original size:17 final size:17
Alignment explanation
Indices: 5559712--5559744 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
5559702 TTTTATTTTT
5559712 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
5559730 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
5559745 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:5559746 original size:17 final size:19
Alignment explanation
Indices: 5559705--5559746 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
5559695 TTTGATATTT
*
5559705 TATTTTTAATTTATTTAAG
1 TATTTTAAATTTATTTAAG
5559724 TA-TTTAAATTT-TTTAA-
1 TATTTTAAATTTATTTAAG
5559740 TATTTTA
1 TATTTTA
5559747 TTTAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 9 0.43
18 8 0.38
19 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTAAATTTATTTAAG
Found at i:5561236 original size:18 final size:19
Alignment explanation
Indices: 5561213--5561248 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5561203 GAGCCCATTT
5561213 TTACTGACCTTT-TTATGG
1 TTACTGACCTTTATTATGG
*
5561231 TTACTGACGTTTATTATG
1 TTACTGACCTTTATTATG
5561249 AGTGGTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (19 bp):
TTACTGACCTTTATTATGG
Found at i:5562862 original size:18 final size:18
Alignment explanation
Indices: 5562841--5562879 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5562831 TGTTACATAC
5562841 ATTCCATTTGATACAACA
1 ATTCCATTTGATACAACA
*
5562859 ATTCCATTTGATACAATA
1 ATTCCATTTGATACAACA
5562877 ATT
1 ATT
5562880 TTTTGTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (18 bp):
ATTCCATTTGATACAACA
Found at i:5566130 original size:7 final size:7
Alignment explanation
Indices: 5566118--5566143 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5566108 TATTAAGTGA
5566118 CATGTGT
1 CATGTGT
5566125 CATGTGT
1 CATGTGT
5566132 CATGTGT
1 CATGTGT
5566139 CATGT
1 CATGT
5566144 TAGAGTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42
Consensus pattern (7 bp):
CATGTGT
Found at i:5566187 original size:16 final size:16
Alignment explanation
Indices: 5566166--5566206 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
5566156 AAGAATTTTT
5566166 ATTTTAAAAAAATAAA
1 ATTTTAAAAAAATAAA
5566182 ATTTT-AAAAAATAAA
1 ATTTTAAAAAAATAAA
*
5566197 ATCTTAAAAA
1 ATTTTAAAAA
5566207 TCTTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTTTAAAAAAATAAA
Found at i:5566227 original size:22 final size:24
Alignment explanation
Indices: 5566179--5566236 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
5566169 TTAAAAAAAT
*
5566179 AAAATTTTAAAAAATAAAATCTTA
1 AAAATTTTAAAAAATAAAATCTCA
*
5566203 AAAATCTTAAAAAA-AAAA-CTCA
1 AAAATTTTAAAAAATAAAATCTCA
*
5566225 AAACTTTTAAAA
1 AAAATTTTAAAA
5566237 CTTTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 13 0.43
23 4 0.13
24 13 0.43
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAATTTTAAAAAATAAAATCTCA
Found at i:5568377 original size:43 final size:42
Alignment explanation
Indices: 5568327--5568660 Score: 337
Period size: 43 Copynumber: 7.8 Consensus size: 42
5568317 CTATAGGTCA
*
5568327 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAATGTTG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA-GTTC
* * * * *
5568370 ATATCTATAGCGGCGTTTTTAGAACAAACGCTGTAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGTTC
* *
5568412 GAGATCTATAGCGGCGTTTATGGAACAAATGCCGCAAAAGGTT-
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA-GTTC
* * * * * *
5568455 AGATATTTAGCGGCATTTTTGGATACAAACGCCGCTATAGGTC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGTTC
* * * * **
5568498 AAGATCTACAGTGGTGTTTTTGGAACAAACGCCACAAAAGGAC
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGTTC
* ** *
5568541 AGATCTATAGCGGAGTTTTTAAAACAAACGCCGCAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGTTC
* * *
5568583 AGATCTATAGCGGCATTTTTAGATACAAACGCCGCAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGTTC
* *
5568626 AGATCAATAGCGGCGTTGTTGGATACAAACGCCGC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGC
5568661 TAATTACCAT
Statistics
Matches: 240, Mismatches: 45, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
42 78 0.32
43 143 0.60
44 19 0.08
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (42 bp):
AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGTTC
Found at i:5568420 original size:86 final size:86
Alignment explanation
Indices: 5568321--5568659 Score: 389
Period size: 86 Copynumber: 4.0 Consensus size: 86
5568311 AAGCCGCTAT
* * *
5568321 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAATGTTGATATCTATAGCGGCGT
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA-GGTCAGATCTATAGCGGCGT
*
5568386 TTTTAGA-ACAAACGCTGTAAA
65 TTTTAGATACAAACGCCGTAAA
* * * * * * *
5568407 AGGTCGAGATCTATAGCGGCGTTTATGGAACAAATGCCGCAAAAGGTTAGATATTTAGCGGCATT
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTT
* *
5568472 TTTGGATACAAACGCCGCT-AT
66 TTTAGATACAAACGCCG-TAAA
* * * * * *
5568493 AGGTCAAGATCTACAGTGGTGTTTTTGGAACAAACGCCACAAAAGGACAGATCTATAGCGGAGTT
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTT
* *
5568558 TTTA-AAACAAACGCCGCAAA
66 TTTAGATACAAACGCCGTAAA
* * *
5568578 AGGTC-AGATCTATAGCGGCATTTTTAGATACAAACGCCGCAAAAGGTCAGATCAATAGCGGCGT
1 AGGTCAAGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGT
* *
5568642 TGTTGGATACAAACGCCG
65 TTTTAGATACAAACGCCG
5568660 CTAATTACCA
Statistics
Matches: 207, Mismatches: 41, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
84 18 0.09
85 71 0.34
86 117 0.57
87 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (86 bp):
AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTT
TTTAGATACAAACGCCGTAAA
Found at i:5568575 original size:128 final size:128
Alignment explanation
Indices: 5568321--5568658 Score: 392
Period size: 128 Copynumber: 2.6 Consensus size: 128
5568311 AAGCCGCTAT
* * * * *
5568321 AGGTCAAGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAATGTTGATATCTATAGCGGCG
1 AGGTC-AGATATATAGCGGCATTTTTGGATACAAACGCCGCAAAA-GGTCAGATCTATAGCGGCG
* *** * * ** *
5568385 TTTTTAGAACAAACGCTGTAAAAGGTCGAGATCTATAGCGGCGTTTATGGAACAAATGCCGCAAA
64 TTTTTGGAACAAACGCCACAAAAGGACGAGATCTATAGCGGAGTTTATAAAACAAACGCCGCAAA
* * * * * * *
5568450 AGGTTAGATATTTAGCGGCATTTTTGGATACAAACGCCGCTATAGGTCAAGATCTACAGTGGTGT
1 AGGTCAGATATATAGCGGCATTTTTGGATACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCGT
*
5568515 TTTTGGAACAAACGCCACAAAAGGAC-AGATCTATAGCGGAGTTTTTAAAACAAACGCCGCAAA
65 TTTTGGAACAAACGCCACAAAAGGACGAGATCTATAGCGGAGTTTATAAAACAAACGCCGCAAA
* * *
5568578 AGGTCAGATCTATAGCGGCATTTTTAGATACAAACGCCGCAAAAGGTCAGATCAATAGCGGCGTT
1 AGGTCAGATATATAGCGGCATTTTTGGATACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTT
*
5568643 GTTGGATACAAACGCC
66 TTTGGA-ACAAACGCC
5568659 GCTAATTACC
Statistics
Matches: 173, Mismatches: 33, Indels: 7
0.81 0.15 0.03
Matches are distributed among these distances:
127 18 0.10
128 105 0.61
129 50 0.29
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (128 bp):
AGGTCAGATATATAGCGGCATTTTTGGATACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTT
TTTGGAACAAACGCCACAAAAGGACGAGATCTATAGCGGAGTTTATAAAACAAACGCCGCAAA
Found at i:5571541 original size:41 final size:40
Alignment explanation
Indices: 5571491--5572033 Score: 444
Period size: 41 Copynumber: 13.2 Consensus size: 40
5571481 CGGCAGAAAT
*
5571491 GCCATTAAAGTACGGATCTTTGGCGGCGTTTGTATAAAAAC
1 GCCACTAAAGTAC-GATCTTTGGCGGCGTTTGTATAAAAAC
* **
5571532 GCCACTAAAGTACGAGTCTTTGGTGGCGTTTGTATAAAATT
1 GCCACTAAAGTACGA-TCTTTGGCGGCGTTTGTATAAAAAC
5571573 GCCACTAAAGTACGGATCTTTGGCGGCGTTTGTATAAAAAC
1 GCCACTAAAGTAC-GATCTTTGGCGGCGTTTGTATAAAAAC
**
5571614 GCCACTAAAGTACGAGTCTTTGGCGGCGTTTGTATAAAATT
1 GCCACTAAAGTACGA-TCTTTGGCGGCGTTTGTATAAAAAC
* *
5571655 GCCACTAAAGTACGAGTCTTTGGTGGCGTTTGCATAAAAAC
1 GCCACTAAAGTACGA-TCTTTGGCGGCGTTTGTATAAAAAC
* * *
5571696 GCCACTAAAGTGCGAGTCTTTGGCAGCGTTTGTATAGAAAC
1 GCCACTAAAGTACGA-TCTTTGGCGGCGTTTGTATAAAAAC
* * *
5571737 ACCACTAAAGTACGAGTCTTTGGCGCCGTTTGTATAGAAAC
1 GCCACTAAAGTACGA-TCTTTGGCGGCGTTTGTATAAAAAC
* * * * * *
5571778 GCCACTATAGTACGAACATTTAGCGGCATTTGTGCTTAAAAC
1 GCCACTAAAGTACGATC-TTTGGCGGCGTTTGT-ATAAAAAC
* * * * * *
5571820 GCCACTAAAGTACTATATTTAGTGGCGTTTATACAAAAAC
1 GCCACTAAAGTACGATCTTTGGCGGCGTTTGTATAAAAAC
** * * ** * * *
5571860 ATCGCTAAAGTATGAGAATTTAGCGGCGTTTGTGCTTAAAAC
1 GCCACTAAAGTACGA-TCTTTGGCGGCGTTTGT-ATAAAAAC
* * * * * *
5571902 GCCACTAAAGAATA-G-TATTTAGTGGCATTTATATAGAAAC
1 GCCACTAAAG--TACGATCTTTGGCGGCGTTTGTATAAAAAC
* * * * * * *
5571942 GCCACTAAAGTATGAGCATTTAGCGGCATTTGTGCTTAAAAT
1 GCCACTAAAGTACGATC-TTTGGCGGCGTTTGT-ATAAAAAC
* * * *
5571984 GCCACTAAAGTAC-AGTATTTAGCGGCATTTATATAAAAAC
1 GCCACTAAAGTACGA-TCTTTGGCGGCGTTTGTATAAAAAC
*
5572024 GTCACTAAAG
1 GCCACTAAAG
5572034 CACAAGTATT
Statistics
Matches: 410, Mismatches: 78, Indels: 29
0.79 0.15 0.06
Matches are distributed among these distances:
38 2 0.00
39 1 0.00
40 49 0.12
41 307 0.75
42 48 0.12
43 1 0.00
44 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (40 bp):
GCCACTAAAGTACGATCTTTGGCGGCGTTTGTATAAAAAC
Found at i:5571847 original size:164 final size:163
Alignment explanation
Indices: 5571487--5572033 Score: 566
Period size: 164 Copynumber: 3.3 Consensus size: 163
5571477 TTAGCGGCAG
* * * * * *
5571487 AAATGCCATTAAAGTACGGATCTTTGGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
1 AAATGCCACTAAAGTACAG-TATTTAGTGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCTT
* * *
5571552 TGGTGGCGTTTGTATAAAATTGCCACTAAAGTACG-GATCTTTGGCGGCGTTTGTATAAAAACGC
65 TGGCGGCGTTTGTATAAAA-CGCCACTAAAGTACGAG-TCTTTGGCGGCGTTTGTATAGAAACGC
* * * *
5571616 CACTAAAGTACGAGTC-TTTGGCGGCGTTTGT--ATA
128 CACTAAAGTACGA-ACATTTAGCGGCATTTGTGCTTA
* * ** *
5571650 AAATTGCCACTAAAGTACGAGTCTTTGGTGGCGTTTGCATAAAAACGCCACTAAAGTGCGAGTCT
1 AAA-TGCCACTAAAGTAC-AGTATTTAGTGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCT
* * *
5571715 TTGGCAGCGTTTGTATAGAAACACCACTAAAGTACGAGTCTTTGGCGCCGTTTGTATAGAAACGC
64 TTGGCGGCGTTTGTATA-AAACGCCACTAAAGTACGAGTCTTTGGCGGCGTTTGTATAGAAACGC
*
5571780 CACTATAGTACGAACATTTAGCGGCATTTGTGCTTA
128 CACTAAAGTACGAACATTTAGCGGCATTTGTGCTTA
* * ** * * **
5571816 AAACGCCACTAAAGTACTA-TATTTAGTGGCGTTTATACAAAAACATCGCTAAAGTATGAGAATT
1 AAATGCCACTAAAGTAC-AGTATTTAGTGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCTT
* * ** * * * * *
5571880 TAGCGGCGTTTGTGCTTAAAACGCCACTAAAG-AATAGTATTTAGTGGCATTTATATAGAAACGC
65 TGGCGGCGTTTGT--ATAAAACGCCACTAAAGTACGAGTCTTTGGCGGCGTTTGTATAGAAACGC
* *
5571944 CACTAAAGTATGAGCATTTAGCGGCATTTGTGCTTA
128 CACTAAAGTACGAACATTTAGCGGCATTTGTGCTTA
* * *
5571980 AAATGCCACTAAAGTACAGTATTTAGCGGCATTTATATAAAAACGTCACTAAAG
1 AAATGCCACTAAAGTACAGTATTTAGTGGCGTTTATATAAAAACGCCACTAAAG
5572034 CACAAGTATT
Statistics
Matches: 323, Mismatches: 51, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
163 5 0.02
164 279 0.86
165 32 0.10
166 7 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (163 bp):
AAATGCCACTAAAGTACAGTATTTAGTGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCTTT
GGCGGCGTTTGTATAAAACGCCACTAAAGTACGAGTCTTTGGCGGCGTTTGTATAGAAACGCCAC
TAAAGTACGAACATTTAGCGGCATTTGTGCTTA
Found at i:5572063 original size:41 final size:40
Alignment explanation
Indices: 5571897--5572050 Score: 119
Period size: 41 Copynumber: 3.8 Consensus size: 40
5571887 GTTTGTGCTT
* * * **
5571897 AAAACGCCACTAAAGAATAGTATTTAGTGGCATTTATATA
1 AAAACGTCACTAAAGCACAGTATTTACCGGCATTTATATA
* * * * * * * * *
5571937 GAAACGCCACTAAAGTATGAGCATTTAGCGGCATTTGTGCTT
1 AAAACGTCACTAAAGCA-CAGTATTTACCGGCATTTAT-ATA
* * * *
5571979 AAAATGCCACTAAAGTACAGTATTTAGCGGCATTTATATA
1 AAAACGTCACTAAAGCACAGTATTTACCGGCATTTATATA
5572019 AAAACGTCACTAAAGCACAAGTATTTACCGGC
1 AAAACGTCACTAAAGCAC-AGTATTTACCGGC
5572051 GTTTGCTAAA
Statistics
Matches: 92, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
40 31 0.34
41 45 0.49
42 16 0.17
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (40 bp):
AAAACGTCACTAAAGCACAGTATTTACCGGCATTTATATA
Found at i:5575282 original size:106 final size:106
Alignment explanation
Indices: 5574007--5575281 Score: 1933
Period size: 106 Copynumber: 12.0 Consensus size: 106
5573997 ATATCGTGCC
* * * * *
5574007 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
5574072 AAATTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
5574113 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5574178 AATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
5574219 ACTCCAGACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATATACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
5574284 AATTTCAGAGACAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
5574325 ACTCAAGACAACGCAAGTTCAACTTCATGGCGAAGGGACCGCTGGTTGTCAATAAACAACTACCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5574390 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGACATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
5574431 ACTCCAGACAACGCAAGTTCAACTTCTCG-CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5574495 AATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
5574536 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5574601 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
5574642 AATCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCCCTAGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
5574707 AATTTCGGAGCCAATTTCAACTCCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
5574748 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * *
5574813 AATTTTGGAGCCAATTTCATCTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
5574854 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
5574919 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
5574960 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
5575025 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
5575066 AATCTAGACAACGCAAGTTCAACTTCACGACGAAAGGACTGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
5575131 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
5575172 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAATAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* * * *
5575236 CGATTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
5575278 ACTC
1 ACTC
5575282 GGAACAATGC
Statistics
Matches: 1067, Mismatches: 100, Indels: 4
0.91 0.09 0.00
Matches are distributed among these distances:
105 100 0.09
106 967 0.91
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:5576048 original size:37 final size:37
Alignment explanation
Indices: 5575997--5576101 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
5575987 CATTTTCGTC
5575997 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
5576034 TTACTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
5576071 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
5576102 CCACAAGCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Done.