Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008610.1 Hibiscus syriacus cultivar Beakdansim tig00111566_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: 2108335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1465846 original size:16 final size:16
Alignment explanation
Indices: 1465825--1465862 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1465815 TGATTCCCAA
*
1465825 GGAGCTGAAGAGTTTG
1 GGAGCTGAAGAGCTTG
1465841 GGAGCTGAAGAGCTTG
1 GGAGCTGAAGAGCTTG
1465857 GGAGCT
1 GGAGCT
1465863 CTAGAGTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.11, G:0.45, T:0.21
Consensus pattern (16 bp):
GGAGCTGAAGAGCTTG
Found at i:1465868 original size:16 final size:16
Alignment explanation
Indices: 1465825--1465868 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1465815 TGATTCCCAA
* *
1465825 GGAGCTGAAGAGTTTG
1 GGAGCTCAAGAGCTTG
*
1465841 GGAGCTGAAGAGCTTG
1 GGAGCTCAAGAGCTTG
*
1465857 GGAGCTCTAGAG
1 GGAGCTCAAGAG
1465869 TTCCGAGGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.25, C:0.11, G:0.43, T:0.20
Consensus pattern (16 bp):
GGAGCTCAAGAGCTTG
Found at i:1467692 original size:21 final size:21
Alignment explanation
Indices: 1467666--1467707 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1467656 GAAAGGAGCA
*
1467666 TCGGTAGAAGGCATTAGAGTG
1 TCGGTAAAAGGCATTAGAGTG
1467687 TCGGTAAAAGGCATTAGAGTG
1 TCGGTAAAAGGCATTAGAGTG
1467708 GACCCCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.36, T:0.24
Consensus pattern (21 bp):
TCGGTAAAAGGCATTAGAGTG
Found at i:1470002 original size:2 final size:2
Alignment explanation
Indices: 1469995--1470020 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1469985 ATTATGATGG
1469995 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
1470021 TAGAGAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1470769 original size:22 final size:20
Alignment explanation
Indices: 1470718--1470791 Score: 94
Period size: 20 Copynumber: 3.5 Consensus size: 20
1470708 ACCTAATTTT
*
1470718 GGTATCTATACCATAGTAAG
1 GGTATCGATACCATAGTAAG
*
1470738 GGTATCGATACCATATTATAG
1 GGTATCGATACCATAGTA-AG
*
1470759 AGGTATTGATACCGATAGTAAG
1 -GGTATCGATACC-ATAGTAAG
1470781 GGTATCGATAC
1 GGTATCGATAC
1470792 TGGACCACAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.35
21 12 0.26
22 13 0.28
23 5 0.11
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:1471327 original size:79 final size:79
Alignment explanation
Indices: 1471193--1471343 Score: 232
Period size: 79 Copynumber: 1.9 Consensus size: 79
1471183 AAAACAAATG
* * * *
1471193 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATATCTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCAGATCTGAAATGCATATGG
1471258 GTACATTGTCAGCA
66 GTACATTGTCAGCA
*
1471272 TAAAAGAATAATGCATATGGGTGTATTAGTGGCATGAAAGGATGCCAGAGT-TGAAATGCATATG
1 TAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCAGA-TCTGAAATGCATATG
*
1471336 GGTGCATT
65 GGTACATT
1471344 ATGAACAGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
79 64 0.98
80 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.29
Consensus pattern (79 bp):
TAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCAGATCTGAAATGCATATGG
GTACATTGTCAGCA
Found at i:1471330 original size:45 final size:45
Alignment explanation
Indices: 1471281--1471480 Score: 181
Period size: 45 Copynumber: 4.4 Consensus size: 45
1471271 ATAAAAGAAT
* * *
1471281 AATGCATATGGGTGTATTAGTG-GCATG-AAAGGATGCCAGAGTTGA
1 AATGCATATGGGTGCATTA-TGAACA-GAAAAGGATACCAGAGTTGA
* *
1471326 AATGCATATGGGTGCATTATGAACAGAAAAGTATACTAGAGTTGA
1 AATGCATATGGGTGCATTATGAACAGAAAAGGATACCAGAGTTGA
* ** * *
1471371 AATGCATATGGGTGCATTATCAACAGAAAAATATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATGAACAGAAAAGGATACCAGAGTTGA
* * * * * *
1471416 AATGTATATGAGTACATTATCAACAGAAAAGTATACTATG-GTTGA
1 AATGCATATGGGTGCATTATGAACAGAAAAGGATACCA-GAGTTGA
* * *
1471461 GATGTATATGGGTACATTAT
1 AATGCATATGGGTGCATTAT
1471481 CAGCATAAAA
Statistics
Matches: 137, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
44 3 0.02
45 133 0.97
46 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATGAACAGAAAAGGATACCAGAGTTGA
Found at i:1471481 original size:45 final size:45
Alignment explanation
Indices: 1471318--1471536 Score: 278
Period size: 45 Copynumber: 4.9 Consensus size: 45
1471308 AAAGGATGCC
* * *
1471318 AGAGTTGAAATGCATATGGGTGCATTATGAACAGAAAAGTATACT
1 AGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
1471363 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATGCT
1 AGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
1471408 AGAGTTGAAATGTATATGAGTACATTATCAACAGAAAAGTATACT
1 AGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * *
1471453 ATG-GTTGAGATGTATATGGGTACATTATCAGCATAAAAATATAAT
1 A-GAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
1471498 ATAGTTGAAATCTATATGGGTACTTTATCAACAGAAAAG
1 AGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAG
1471537 ATGTTATAGT
Statistics
Matches: 151, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
45 150 0.99
46 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (45 bp):
AGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:1471570 original size:135 final size:134
Alignment explanation
Indices: 1471321--1471575 Score: 284
Period size: 135 Copynumber: 1.9 Consensus size: 134
1471311 GGATGCCAGA
* * * * *
1471321 GTTGAAATGCATATGGGTGCATTATGAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGC
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAATATAATAGAGTTGAAATGCATATGGGTAC
* * *
1471386 ATTATCAACAGAAAAATATGCTAGAGTTGAAATGTATATGAGTACATTATCAACAGAAAAGTATA
66 ATTATCAACAGAAAAAGATGCTAGAGTTAAAATGTATATGAGTA-ATTATAAACAGAAAAGTATA
1471451 CTATG
130 CTATG
* * * * *
1471456 GTTGAGATGTATATGGGTACATTATCAGCATAAAAATATAATATAGTTGAAAT-CTATATGGGTA
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAATATAATAGAGTTGAAATGC-ATATGGGTA
* * *
1471520 CTTTATCAACAG-AAAAGATGTTATAGTTTAAAATGCGTA-ATGATGT-ATTATAAACA
65 CATTATCAACAGAAAAAGATGCTAGAG-TTAAAAT--GTATATGA-GTAATTATAAACA
1471576 TAAATAGAGG
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
134 12 0.12
135 78 0.79
136 4 0.04
137 5 0.05
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.31
Consensus pattern (134 bp):
GTTGAAATGCATATGGGTACATTATCAACAGAAAAATATAATAGAGTTGAAATGCATATGGGTAC
ATTATCAACAGAAAAAGATGCTAGAGTTAAAATGTATATGAGTAATTATAAACAGAAAAGTATAC
TATG
Found at i:1474407 original size:12 final size:12
Alignment explanation
Indices: 1474392--1474417 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1474382 TTCAGGAATA
1474392 GGAGGAGGATTT
1 GGAGGAGGATTT
1474404 GGAGGAGGATTT
1 GGAGGAGGATTT
1474416 GG
1 GG
1474418 TTGACGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (12 bp):
GGAGGAGGATTT
Found at i:1475152 original size:21 final size:22
Alignment explanation
Indices: 1475106--1475163 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
1475096 GAACCCCAGG
1475106 GGGGTATCGATTCCCCTTCAAA
1 GGGGTATCGATTCCCCTTCAAA
*
1475128 GGGGAATCGATTCCCCTTC-AA
1 GGGGTATCGATTCCCCTTCAAA
1475149 GGGGTATCGATTCCC
1 GGGGTATCGATTCCC
1475164 TCTGCCCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 16 0.47
22 18 0.53
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.26
Consensus pattern (22 bp):
GGGGTATCGATTCCCCTTCAAA
Found at i:1479013 original size:22 final size:21
Alignment explanation
Indices: 1478971--1479010 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1478961 GAGTTTATTT
*
1478971 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1478992 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1479011 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1482311 original size:20 final size:20
Alignment explanation
Indices: 1482274--1482323 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1482264 TTGCGATTGT
* * *
1482274 TGCGAAAGTTAAATTCGCAA
1 TGCGAAAATCAAAATCGCAA
1482294 TGCGAAAATCAAAATCGCAA
1 TGCGAAAATCAAAATCGCAA
**
1482314 ACCGAAAATC
1 TGCGAAAATC
1482324 GCAATGTGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (20 bp):
TGCGAAAATCAAAATCGCAA
Found at i:1482365 original size:20 final size:21
Alignment explanation
Indices: 1482331--1482386 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
1482321 ATCGCAATGT
* *
1482331 GAATTTTACTTTCG-CGTTGC
1 GAATTTGACTATCGACGTTGC
1482351 GAATTTGACTATCGCAACGTTGC
1 GAATTTGACTATCG--ACGTTGC
*
1482374 AAATTTGACTATC
1 GAATTTGACTATC
1482387 ACAACGAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.40
23 18 0.60
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (21 bp):
GAATTTGACTATCGACGTTGC
Found at i:1482378 original size:23 final size:23
Alignment explanation
Indices: 1482345--1482392 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1482335 TTTACTTTCG
* *
1482345 CGTTGCGAATTTGACTATCGCAA
1 CGTTGCAAATTTGACTATCACAA
1482368 CGTTGCAAATTTGACTATCACAA
1 CGTTGCAAATTTGACTATCACAA
1482391 CG
1 CG
1482393 AGAAAATCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (23 bp):
CGTTGCAAATTTGACTATCACAA
Found at i:1483908 original size:21 final size:21
Alignment explanation
Indices: 1483863--1483961 Score: 87
Period size: 21 Copynumber: 4.7 Consensus size: 21
1483853 GCAGGCGGGA
* *
1483863 CCTCTTGAACGATGA-CAGGG
1 CCTCTTGAATGATGAGAAGGG
* *
1483883 CCCTCTTGAATGGTGGGAAGGG
1 -CCTCTTGAATGATGAGAAGGG
1483905 CCTCTTCG-ATGATGAGAAGGG
1 CCTCTT-GAATGATGAGAAGGG
* *
1483926 CCTCTTGAATGAT-AGGAGACG
1 CCTCTTGAATGATGAGAAG-GG
*
1483947 CCTCTTGAACGATGA
1 CCTCTTGAATGATGA
1483962 CAGGTGCATT
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.08
21 53 0.83
22 6 0.09
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.23
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAAGGG
Found at i:1483909 original size:42 final size:41
Alignment explanation
Indices: 1483863--1483965 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 41
1483853 GCAGGCGGGA
* * *
1483863 CCTCTTGAACGATGACAGGGCCCTCTTGAATGGTGGGA-AGGG
1 CCTCTTGAACGATGACAGGG-CCTCTTGAATGATAGGAGA-CG
* *
1483905 CCTCTTCG-ATGATGAGAAGGGCCTCTTGAATGATAGGAGACG
1 CCTCTT-GAACGATGA-CAGGGCCTCTTGAATGATAGGAGACG
1483947 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
1483966 TGCATTGGGC
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
41 4 0.08
42 40 0.80
43 6 0.12
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.22
Consensus pattern (41 bp):
CCTCTTGAACGATGACAGGGCCTCTTGAATGATAGGAGACG
Found at i:1486133 original size:20 final size:19
Alignment explanation
Indices: 1486105--1486151 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1486095 TTCTGAAACT
*
1486105 TAAATTCGCAACGCGAAAA
1 TAAAATCGCAACGCGAAAA
* *
1486124 TGAAAATCGCAACTCGAAAC
1 T-AAAATCGCAACGCGAAAA
1486144 TAAAATCG
1 TAAAATCG
1486152 TGTTGCGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (19 bp):
TAAAATCGCAACGCGAAAA
Found at i:1486184 original size:14 final size:14
Alignment explanation
Indices: 1486165--1486198 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1486155 TGCGATTTTC
1486165 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
*
1486179 ATTTTCGTGTTGCG
1 ATTTTCGCGTTGCG
1486193 ATTTTC
1 ATTTTC
1486199 ATTTTCGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.24, T:0.50
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1486202 original size:20 final size:20
Alignment explanation
Indices: 1486149--1486211 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
1486139 GAAACTAAAA
1486149 TCGTGTTGCGATTTTCATTT
1 TCGTGTTGCGATTTTCATTT
*
1486169 TCGCGTTGCG------ATTT
1 TCGTGTTGCGATTTTCATTT
1486183 TCGTGTTGCGATTTTCATTT
1 TCGTGTTGCGATTTTCATTT
1486203 TCGTGTTGC
1 TCGTGTTGC
1486212 AAATTTTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
14 13 0.37
20 22 0.63
ACGTcount: A:0.08, C:0.17, G:0.24, T:0.51
Consensus pattern (20 bp):
TCGTGTTGCGATTTTCATTT
Found at i:1486224 original size:20 final size:20
Alignment explanation
Indices: 1486181--1486224 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1486171 GCGTTGCGAT
* *
1486181 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCAATTTTCAG
1486201 TTTCGTGTTGCAAATTTT-AG
1 TTTCGTGTTGC-AATTTTCAG
1486221 TTTC
1 TTTC
1486225 AAAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTTCAG
Found at i:1489474 original size:20 final size:22
Alignment explanation
Indices: 1489426--1489476 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 22
1489416 ATTAGTAATG
1489426 AGATTAATAATAATAATAATAT
1 AGATTAATAATAATAATAATAT
*
1489448 AGA-TAATAA-AATACTAATAT
1 AGATTAATAATAATAATAATAT
1489468 A-ATTAATAA
1 AGATTAATAA
1489477 CGTTTTTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 17 0.63
21 6 0.22
22 3 0.11
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
AGATTAATAATAATAATAATAT
Found at i:1490926 original size:276 final size:276
Alignment explanation
Indices: 1490433--1490985 Score: 1070
Period size: 276 Copynumber: 2.0 Consensus size: 276
1490423 TGGGAAAGGT
1490433 AAGATTAGGTTAAAACTGATTTACTCAATTTAACCTTTCTTTCTCAATGATCATATTTTTGTATG
1 AAGATTAGGTTAAAACTGATTTACTCAATTTAACCTTTCTTTCTCAATGATCATATTTTTGTATG
* *
1490498 TACTCTCCGATACACACCTGTTTTGAAATCCTCATACTCTGACACTTTTTAGTGTAAAGCATAAT
66 TACTCTCCGATAAACACCTGTTTTGAAATCCCCATACTCTGACACTTTTTAGTGTAAAGCATAAT
*
1490563 AAACAATGTTGTTATTGATCACTGTTTTGGTGATTCTATATAATGAATCAATCTCAAAAAATTCA
131 AAACAATGTTGTTATTGATCACTGTTTTGGTGATTCTATATAATGAATAAATCTCAAAAAATTCA
1490628 TTTAAAAGAGGCAATGAAAAAATATAATCCTTTAGAATAAGAAACAAGTAAACATTACAGGAAGA
196 TTTAAAAGAGGCAATGAAAAAATATAATCCTTTAGAATAAGAAACAAGTAAACATTACAGGAAGA
1490693 ACAAAGGAACAAATAC
261 ACAAAGGAACAAATAC
1490709 AAGATTAGGTTAAAACTGATTTACTCAATTTAACCTTTCTTTCTCAATGATCATATTTTTGTATG
1 AAGATTAGGTTAAAACTGATTTACTCAATTTAACCTTTCTTTCTCAATGATCATATTTTTGTATG
1490774 TACTCTCCGATAAACACCTGTTTTGAAATCCCCATACTCTGACACTTTTTAGTGTAAAGCATAAT
66 TACTCTCCGATAAACACCTGTTTTGAAATCCCCATACTCTGACACTTTTTAGTGTAAAGCATAAT
*
1490839 AAACAATGTTGTTATTGATCACTGTTTTGGTGATTCTATATAATGAATAAATCTTAAAAAATTCA
131 AAACAATGTTGTTATTGATCACTGTTTTGGTGATTCTATATAATGAATAAATCTCAAAAAATTCA
1490904 TTTAAAAGAGGCAATGAAAAAATATAATCCTTTAGAATAAGAAACAAGTAAACATTACAGGAAGA
196 TTTAAAAGAGGCAATGAAAAAATATAATCCTTTAGAATAAGAAACAAGTAAACATTACAGGAAGA
1490969 ACAAAGGAACAAATAC
261 ACAAAGGAACAAATAC
1490985 A
1 A
1490986 GTGGATATCA
Statistics
Matches: 273, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
276 273 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (276 bp):
AAGATTAGGTTAAAACTGATTTACTCAATTTAACCTTTCTTTCTCAATGATCATATTTTTGTATG
TACTCTCCGATAAACACCTGTTTTGAAATCCCCATACTCTGACACTTTTTAGTGTAAAGCATAAT
AAACAATGTTGTTATTGATCACTGTTTTGGTGATTCTATATAATGAATAAATCTCAAAAAATTCA
TTTAAAAGAGGCAATGAAAAAATATAATCCTTTAGAATAAGAAACAAGTAAACATTACAGGAAGA
ACAAAGGAACAAATAC
Found at i:1491477 original size:15 final size:15
Alignment explanation
Indices: 1491457--1491486 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1491447 CTAAATCACC
1491457 TTCATGAAATTCTCG
1 TTCATGAAATTCTCG
1491472 TTCATGAAATTCTCG
1 TTCATGAAATTCTCG
1491487 AGGCCTGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
TTCATGAAATTCTCG
Found at i:1495268 original size:22 final size:20
Alignment explanation
Indices: 1495220--1495293 Score: 103
Period size: 20 Copynumber: 3.5 Consensus size: 20
1495210 ACCTAATTTT
*
1495220 GGTATCTATACCATAGTAAG
1 GGTATCGATACCATAGTAAG
1495240 GGTATCGATACCATAGTATAG
1 GGTATCGATACCATAGTA-AG
1495261 AGGTATCGATACCGATAGTAAG
1 -GGTATCGATACC-ATAGTAAG
*
1495283 GGTATTGATAC
1 GGTATCGATAC
1495294 TGGACCACAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
20 17 0.35
21 12 0.24
22 14 0.29
23 6 0.12
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:1495348 original size:96 final size:96
Alignment explanation
Indices: 1495203--1495388 Score: 245
Period size: 96 Copynumber: 1.9 Consensus size: 96
1495193 GTACCGGGTA
*
1495203 ACATCGAACCTAATTTTGGTATCTATACCATAGTAAGGGTATCGATACCATAGTATAG-AGGTAT
1 ACATCGAACCTAATTTTGGTATCTATACCATAGTAAGGGTATCGATACCATAGTAGAGTA-GTAT
*
1495267 CGATACCGATAGTAAGGGTATTGATACTGGACC
65 CGATACC-ATAGTAAGGGTATCGATACTGGACC
* * * *
1495300 ACATCGAATCTAATTTTGGTA-CTAATA-C-TGGTAGGGGGTATCGATACCATAGTAGGGTAGTA
1 ACATCGAACCTAATTTTGGTATCT-ATACCATAGTA-AGGGTATCGATACCATAGTAGAGTAGTA
*
1495362 TCGATACCATAGTAGGGGTATCGATAC
64 TCGATACCATAGTAAGGGTATCGATAC
1495389 CTGAGGGCCA
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
95 21 0.27
96 34 0.43
97 24 0.30
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (96 bp):
ACATCGAACCTAATTTTGGTATCTATACCATAGTAAGGGTATCGATACCATAGTAGAGTAGTATC
GATACCATAGTAAGGGTATCGATACTGGACC
Found at i:1495384 original size:20 final size:20
Alignment explanation
Indices: 1495334--1495389 Score: 94
Period size: 22 Copynumber: 2.7 Consensus size: 20
1495324 ATACTGGTAG
1495334 GGGGTATCGATACCATAGTA
1 GGGGTATCGATACCATAGTA
1495354 GGGTAGTATCGATACCATAGTA
1 GGG--GTATCGATACCATAGTA
1495376 GGGGTATCGATACC
1 GGGGTATCGATACC
1495390 TGAGGGCCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.41
22 20 0.59
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (20 bp):
GGGGTATCGATACCATAGTA
Found at i:1495927 original size:79 final size:79
Alignment explanation
Indices: 1495792--1495943 Score: 207
Period size: 79 Copynumber: 1.9 Consensus size: 79
1495782 TAAAATAAAT
* * *
1495792 ATAAAAGAATAATGCATATGAGTGCATTATTGGCATAAAAGGATGCCATATCTGAAATGTATATG
1 ATAAAAGAATAATGCATATGAGTGCATTAGTGGCATAAAAGGATGCCAGATCTGAAATGCATATG
1495857 GGTACATTGTCAGC
66 GGTACATTGTCAGC
* * * **
1495871 ATAAAAGTATAATGCATATGGGTGTATTAGTGGCATGGAAGGATGCCAGAGT-TGAAATGCATAT
1 ATAAAAGAATAATGCATATGAGTGCATTAGTGGCATAAAAGGATGCCAGA-TCTGAAATGCATAT
*
1495935 GGGTGCATT
65 GGGTACATT
1495944 ATGAACAGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 62 0.98
80 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGAGTGCATTAGTGGCATAAAAGGATGCCAGATCTGAAATGCATATG
GGTACATTGTCAGC
Found at i:1495956 original size:79 final size:79
Alignment explanation
Indices: 1495794--1495960 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
1495784 AAATAAATAT
* * * *
1495794 AAAAGAATAATGCATATGAGTGCATTATTGGCATAAAAGGATGCCATATCTGAAATGTATATGGG
1 AAAAGTATAATGCATATGAGTGCATTAGTGGCATAAAAGGATGCCAGATCTGAAATGCATATGGG
* * *
1495859 TACATTGTCAGCAT
66 TACATTATCAACAG
* * **
1495873 AAAAGTATAATGCATATGGGTGTATTAGTGGCATGGAAGGATGCCAGAGT-TGAAATGCATATGG
1 AAAAGTATAATGCATATGAGTGCATTAGTGGCATAAAAGGATGCCAGA-TCTGAAATGCATATGG
* *
1495937 GTGCATTATGAACAG
65 GTACATTATCAACAG
1495952 AAAAGTATA
1 AAAAGTATA
1495961 CTATAGTTGA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
79 73 0.99
80 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (79 bp):
AAAAGTATAATGCATATGAGTGCATTAGTGGCATAAAAGGATGCCAGATCTGAAATGCATATGGG
TACATTATCAACAG
Found at i:1495969 original size:45 final size:45
Alignment explanation
Indices: 1495920--1496158 Score: 264
Period size: 45 Copynumber: 5.3 Consensus size: 45
1495910 AGGATGCCAG
* *
1495920 AGTTGAAATGCATATGGGTGCATTATGAACAGAAAAGTATACTAT
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAT
* * * *
1495965 AGTTGAAATGCATATGGGTTCATTATCAACAGAAACGTATGCTAG
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAT
* * *
1496010 AGTTGAAATGTATATGAGTACATTATCAACATAAAAGTATACTAT
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAT
* * * * *
1496055 GGTTGAGATGTATATGGGTACATTATCAACATAACAGTATACTAT
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAT
* * * * * **
1496100 AGTTGAAATGTATATAGGTGCTTTATTAACAGAAAAG-ATGTTAT
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAT
*
1496144 AGTTTAAAATGCATA
1 AG-TTGAAATGCATA
1496159 ATGATGTATT
Statistics
Matches: 165, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
44 7 0.04
45 158 0.96
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.32
Consensus pattern (45 bp):
AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAT
Found at i:1496154 original size:135 final size:135
Alignment explanation
Indices: 1495921--1496179 Score: 317
Period size: 135 Copynumber: 1.9 Consensus size: 135
1495911 GGATGCCAGA
* * * *
1495921 GTTGAAATGCATATGGGTGCATTATGAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTTC
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATAGGTGC
* * * *
1495986 ATTATCAACAGAAACGTATGCTAGAGTTGAAATGTAT-ATGA-GTACATTATCAACATAAAAGTA
66 ATTATCAACAGAAAAGTATGCTAGAGTTAAAATGCATAATGATGT--ATTATAAACATAAAAGTA
1496049 TACTATG
129 TACTATG
* * * * *
1496056 GTTGAGATGTATATGGGTACATTATCAACATAACAGTATACTATAGTTGAAATGTATATAGGTGC
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATAGGTGC
* * * *
1496121 TTTATTAACAGAAAAG-ATGTTATAGTTTAAAATGCATAATGATGTATTATAAACATAAA
66 ATTATCAACAGAAAAGTATGCTAGAG-TTAAAATGCATAATGATGTATTATAAACATAAA
1496180 TGGAGGTTTC
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
134 7 0.07
135 91 0.88
136 4 0.04
137 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (135 bp):
GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATAGGTGC
ATTATCAACAGAAAAGTATGCTAGAGTTAAAATGCATAATGATGTATTATAAACATAAAAGTATA
CTATG
Found at i:1497117 original size:2 final size:2
Alignment explanation
Indices: 1497110--1497148 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1497100 GTGAAAAAGA
1497110 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
1497149 CGGTTAGAGA
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:1506723 original size:59 final size:60
Alignment explanation
Indices: 1506593--1506729 Score: 172
Period size: 59 Copynumber: 2.3 Consensus size: 60
1506583 CATAACTGCA
* **
1506593 TCCATAAGGACTTACCCTAGGCCCAAAGGGCGTAGGTGCCAACCTAAGGGAGGACCTTGGG
1 TCCATAAGGTCTTACCCTAGGCCCAAA-GGCGTAGGTGCCAACCTAAGGGAGGACCTCAGG
* * *
1506654 TCCATAAGGTCTTACCCTA-G-CCGAA-GCGTAGGTGCCCACCTGAAGGGAGTGCCCTCAGG
1 TCCATAAGGTCTTACCCTAGGCCCAAAGGCGTAGGTGCCAACCT-AAGGGAG-GACCTCAGG
1506713 TCCATAAGGTCTTACCC
1 TCCATAAGGTCTTACCC
1506730 AAAAGCACAT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
57 15 0.22
58 7 0.10
59 27 0.40
60 1 0.01
61 18 0.26
ACGTcount: A:0.24, C:0.29, G:0.28, T:0.19
Consensus pattern (60 bp):
TCCATAAGGTCTTACCCTAGGCCCAAAGGCGTAGGTGCCAACCTAAGGGAGGACCTCAGG
Found at i:1512767 original size:24 final size:24
Alignment explanation
Indices: 1512726--1512785 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1512716 ACACAGAGAA
* *
1512726 AAAG-AAGAAAATATATAGAAAA-
1 AAAGAAAGAAAAAAGATAGAAAAT
*
1512748 AAAGGAAATAAAAAAGATAGAAAAT
1 AAA-GAAAGAAAAAAGATAGAAAAT
1512773 AAAGAAAGAAAAA
1 AAAGAAAGAAAAA
1512786 CTAGAAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 3 0.10
23 1 0.03
24 24 0.77
25 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (24 bp):
AAAGAAAGAAAAAAGATAGAAAAT
Found at i:1512801 original size:8 final size:8
Alignment explanation
Indices: 1512722--1512857 Score: 60
Period size: 9 Copynumber: 15.1 Consensus size: 8
1512712 GACGACACAG
1512722 AGAAAAAGA
1 AGAAAAA-A
1512731 AGAAAATATA
1 AGAAAA-A-A
1512741 TAGAAAAAA
1 -AGAAAAAA
*
1512750 AGGAAATAA
1 A-GAAAAAA
* *
1512759 A-AAAGAT
1 AGAAAAAA
1512766 AGAAAATAA
1 AGAAAA-AA
1512775 AGAAAGAAA
1 AGAAA-AAA
1512784 A-ACTAGAAAA
1 AGA--A-AAAA
*
1512794 ACAAAAAA
1 AGAAAAAA
*
1512802 GGAAAAAA
1 AGAAAAAA
1512810 AGAAAAAAA
1 AG-AAAAAA
1512819 GAGGAAAAAA
1 -A-GAAAAAA
1512829 AGAAAAAA
1 AGAAAAAA
1512837 GAGAAGAAAGA
1 -AGAA-AAA-A
1512848 AGAAATAAA
1 AGAAA-AAA
1512857 A
1 A
1512858 TCAATCAAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 34
0.70 0.06 0.24
Matches are distributed among these distances:
7 5 0.05
8 23 0.23
9 38 0.38
10 25 0.25
11 10 0.10
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (8 bp):
AGAAAAAA
Found at i:1512823 original size:19 final size:19
Alignment explanation
Indices: 1512796--1512857 Score: 76
Period size: 18 Copynumber: 3.3 Consensus size: 19
1512786 CTAGAAAAAC
1512796 AAAAA-AGGAAAAAAAGAA
1 AAAAAGAGGAAAAAAAGAA
1512814 AAAAAGAGGAAAAAAAG-A
1 AAAAAGAGGAAAAAAAGAA
1512832 AAAAAGA-GAAGAAAGAAGAA
1 AAAAAGAGGAA-AAA-AAGAA
1512852 ATAAAA
1 A-AAAA
1512858 TCAATCAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.08
18 16 0.41
19 14 0.36
20 2 0.05
21 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (19 bp):
AAAAAGAGGAAAAAAAGAA
Found at i:1512846 original size:16 final size:17
Alignment explanation
Indices: 1512790--1512852 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 17
1512780 GAAAAACTAG
*
1512790 AAAAACAAAAAAG-GAA
1 AAAAAGAAAAAAGAGAA
1512806 AAAAAGAAAAAAAGAGGAA
1 AAAAAG-AAAAAAGA-GAA
1512825 AAAAAGAAAAAAGAGAA
1 AAAAAGAAAAAAGAGAA
1512842 GAAAGAAGAAA
1 -AAA-AAGAAA
1512853 TAAAATCAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
16 5 0.12
17 10 0.24
18 11 0.27
19 15 0.37
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAGAGAA
Found at i:1514921 original size:55 final size:53
Alignment explanation
Indices: 1514795--1515548 Score: 483
Period size: 55 Copynumber: 14.1 Consensus size: 53
1514785 GTTTTTTAGG
* * * * *
1514795 AACTACGTCTGATTTTCAGAGGTTTCTTGACATAGTATTTTTAATTAGTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTG--AT-G-ATTTTCAAAT-GATTTTAAAGA
*
1514853 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGACTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGA--TTTTAAAGA
* * * *
1514908 AACTAAGTCTGATTTT-TGAAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGA
1 AACTAAGTCTGATTTTCAG-AAGTTTCTTGATGATTTTCAAATGA--TTTTAAAGA
* * * * * *
1514963 TACTAAGTCTGATTTTCAAAATTTTATTGATAATTTTTAAATGAGCTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGA--TTTTAAAGA
* * *
1515018 AACTAAGTATGATTTTTAGAAGTTTCATGATGA-TTTCAAATGAGTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGA--TTTTAAAGA
* * *
1515072 AACTAAGTCTGATTTTTAGAAGTTTCTTAACGATTTTCAAATGAGTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGA-TTTTAAAGA
* ** * *
1515126 AACTAAGTCCGATTTTTGGAAGTTTCTTGAT-TTTTCTCAAATGAACTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTT-TCAAATG-A-TTTTAAAGA
* * * * * *
1515181 AATTAAGCCTAATTTTTAG-GGATTTCTTGATG-TTTTCAAATGAATTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAG-TTTCTTGATGATTTTCAAATG-ATTTTAAAGA
* * * *
1515234 AATTAAGTATGA-TTTCAGAGGTTTCTTGACATGA--TT---A--ATTTAAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTG--ATGATTTTCAAATGATTTTAAAGA
* ** *
1515281 AACTAA-ACTTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGAATTTGAAAGA
1 AACTAAGTC-TGATTTTCAGAAGTTTCTTGATGATTTTCAAATG-ATTTTAAAGA
* * * ** *
1515334 AGCTAAGACTGATTTCCAGGGGTTTCTTGATG-TTTTCAAATGAATTTGAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATG-ATTTTAAAGA
* * * * * *
1515387 AACTAAGTCCGATTTTCGGAAGTTTCTTGATTA-TTT--GA-GCTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGATTTTAAAGA
* * ** * * *
1515436 AATTAAGTCT-AGTTTTTAGGGGTTTCTTAAT-ATTTTCAAATGAATTTGAAATA
1 AACTAAGTCTGA-TTTTCAGAAGTTTCTTGATGATTTTCAAATG-ATTTTAAAGA
* * * * ** *
1515489 AGCTAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTTCAAATGAATTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATG-ATTTTAAAGA
*
1515542 AATTAAG
1 AACTAAG
1515549 CCTAAGTTTT
Statistics
Matches: 573, Mismatches: 90, Indels: 71
0.78 0.12 0.10
Matches are distributed among these distances:
46 3 0.01
47 19 0.03
48 17 0.03
49 33 0.06
50 3 0.01
51 2 0.00
52 13 0.02
53 166 0.29
54 116 0.20
55 173 0.30
56 1 0.00
58 27 0.05
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (53 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGATTTTAAAGA
Found at i:1515072 original size:54 final size:55
Alignment explanation
Indices: 1514795--1515591 Score: 498
Period size: 53 Copynumber: 14.9 Consensus size: 55
1514785 GTTTTTTAGG
* * * * * *
1514795 AACTACGTCTGATTTTCAGAGGTTTCTTGACATAGTATTTT-TAATTAGTTTTTAAAGA
1 AACTAAGTCTGATTTTTAGAAGTTTCTTG--AT-G-ATTTTCAAATGAGCTTTTAAAGA
* *
1514853 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGA-CTTTTTAAAGA
1 AACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTCAAATGAGC-TTTTAAAGA
* * *
1514908 AACTAAGTCTGATTTTT-GAAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGA
1 AACTAAGTCTGATTTTTAG-AAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * * * * * *
1514963 TACTAAGTCTGATTTTCAAAATTTTATTGATAATTTTTAAATGAGCTTTTAAAGA
1 AACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * *
1515018 AACTAAGTATGATTTTTAGAAGTTTCATGATGA-TTTCAAATGAGTTTTTAAAGA
1 AACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* *
1515072 AACTAAGTCTGATTTTTAGAAGTTTCTTAACGATTTTCAAATGAG-TTTTAAAGA
1 AACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * * * *
1515126 AACTAAGTCCGATTTTTGGAAGTTTCTTGAT-TTTTCTCAAATGAACTTTCAAAGA
1 AACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTT-TCAAATGAGCTTTTAAAGA
* * * * * *
1515181 AATTAAGCCTAATTTTTAG-GGATTTCTTGATG-TTTTCAAATGA-ATTTCAAAGA
1 AACTAAGTCTGATTTTTAGAAG-TTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * * * *
1515234 AATTAAGTATGA-TTTCAGAGGTTTCTTGACATGA--TT---A--A--TTTAAAAGA
1 AACTAAGTCTGATTTTTAGAAGTTTCTTG--ATGATTTTCAAATGAGCTTTTAAAGA
* * ** * *
1515281 AACTAA-ACTTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAAAGA
1 AACTAAGTC-TGATTTTTAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * ** ** * *
1515334 AGCTAAGACTGATTTCCAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAAAGA
1 AACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* ** * *
1515387 AACTAAGTCCGATTTTCGGAAGTTTCTTGAT--TATT----TGAGCTTTCAAAGA
1 AACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* ** * * * *
1515436 AATTAAGTCT-AGTTTTTAGGGGTTTCTTAAT-ATTTTCAAATGA-ATTTGAAATA
1 AACTAAGTCTGA-TTTTTAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * * ** * *
1515489 AGCTAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTCAAAGA
1 AACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * * * * * * *
1515542 AATTAAGCCTAAGTTTTAG-GGATTTCTTTATG-TTTTGAAATGAGATTTTA
1 AACTAAGTCTGATTTTTAGAAG-TTTCTTGATGATTTTCAAATGAGCTTTTA
1515592 GAAGCCTGAT
Statistics
Matches: 612, Mismatches: 91, Indels: 76
0.79 0.12 0.10
Matches are distributed among these distances:
46 3 0.00
47 18 0.03
48 20 0.03
49 30 0.05
50 5 0.01
52 18 0.03
53 191 0.31
54 121 0.20
55 177 0.29
56 2 0.00
58 27 0.04
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (55 bp):
AACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
Found at i:1515115 original size:109 final size:107
Alignment explanation
Indices: 1514848--1515416 Score: 471
Period size: 109 Copynumber: 5.3 Consensus size: 107
1514838 ATTAGTTTTT
1514848 AAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGACTTTTTAAAGAAACTA
1 AAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGAC-TTTTAAAGAAACTA
* *
1514913 AGTCTGATTTTTGAAAGTTTCTTGATTATTTTTAAATGAGCTTTC
65 AGTATGATTTTTG-AAGTTTCTTGATTA-TTTCAAATGAGCTTTC
* * * * ** *
1514958 AAAGATACTAAGTCTGATTTTCAAAATTTTATTGATAATTTTTAAATGAGCTTTTAAAGAAACTA
1 AAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGA-CTTTTAAAGAAACTA
* * * *
1515023 AGTATGATTTTTAGAAGTTTCATGATGATTTCAAATGAGTTTTT
65 AGTATGATTTTT-GAAGTTTCTTGATTATTTCAAATGAGCTTTC
* * *
1515067 AAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTAACGATTTTCAAATGAGTTTTAAAGAAACTAA
1 AAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGACTTTTAAAGAAACTAA
** * *
1515132 GTCCGATTTTTGGAAGTTTCTTGATTTTTCTCAAATGAACTTTC
66 GTATGATTTTT-GAAGTTTCTTGATTATT-TCAAATGAGCTTTC
* * * * * * * * *
1515176 AAAGAAATTAAGCCTAATTTTTAG-GGATTTCTTGATG-TTTTCAAATGAATTTCAAAGAAATTA
1 AAAGAAACTAAGTCTGATTTTCAGAAG-TTTCTTGACGATTTTCAAATGACTTTTAAAGAAACTA
** * * * * * *
1515239 AGTATGATTTCAGAGGTTTCTTGA-CA--T--GATTA-ATTTA
65 AGTATGATTTTTGAAGTTTCTTGATTATTTCAAATGAGCTTTC
* ** * * * *
1515276 AAAGAAACTAA-ACTTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGAATTTGAAAGAAGCTA
1 AAAGAAACTAAGTC-TGATTTTCAGAAGTTTCTTGACGATTTTCAAATGACTTTTAAAGAAACTA
** ** * *
1515339 AG-ACTGATTTCCAGGGGTTTCTTGATGT-TTTCAAATGA-ATTTG
65 AGTA-TGATTT-TTGAAGTTTCTTGAT-TATTTCAAATGAGCTTTC
* *
1515382 AAAGAAACTAAGTCCGATTTTCGGAAGTTTCTTGA
1 AAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA
1515417 TTATTTGAGC
Statistics
Matches: 375, Mismatches: 69, Indels: 34
0.78 0.14 0.07
Matches are distributed among these distances:
99 2 0.01
100 62 0.17
101 18 0.05
103 1 0.00
104 1 0.00
106 35 0.09
107 12 0.03
108 70 0.19
109 93 0.25
110 79 0.21
111 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (107 bp):
AAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGACTTTTAAAGAAACTAA
GTATGATTTTTGAAGTTTCTTGATTATTTCAAATGAGCTTTC
Found at i:1515309 original size:155 final size:155
Alignment explanation
Indices: 1515147--1515548 Score: 499
Period size: 155 Copynumber: 2.6 Consensus size: 155
1515137 ATTTTTGGAA
* * ** *
1515147 GTTTCTTGATTTTTCTCAAATGAACTTTCAAAGAAATTAAGCCTAATTTTTAGGGATTTCTTGAT
1 GTTTCTTGATATTT-TCAAATGAA-TTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGAT
* *
1515212 GTTTTCAAATGAATTTCAAAGAAATTAAGTATGA-TTTCAGAGGTTTCTTGACATGA-TT-A-AT
64 GTTTTCAAATGAATTTCAAAGAAATTAAGTACGATTTTCAGAAGTTTCTTG--ATGATTTGAGAT
*
1515273 TTAAAAGAAACTAA-ACTTGATTTTCAGGG
127 TTAAAAGAAACTAAGACTAG-TTTTCAGGG
* * * **
1515302 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGACTGATTTCCAGGGGTTTCTTGATGT
1 GTTTCTTGATATTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGT
* * * * * * *
1515367 TTTCAAATGAATTTGAAAGAAACTAAGTCCGATTTTCGGAAGTTTCTTGATTATTTGAGCTTTCA
66 TTTCAAATGAATTTCAAAGAAATTAAGTACGATTTTCAGAAGTTTCTTGATGATTTGAGATTTAA
* * *
1515432 AAGAAATTAAGTCTAGTTTTTAGGG
131 AAGAAACTAAGACTAGTTTTCAGGG
* *
1515457 GTTTCTTAATATTTTCAAATGAATTTGAAATAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGT
1 GTTTCTTGATATTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGT
1515522 TTTCAAATGAATTTCAAAGAAATTAAG
66 TTTCAAATGAATTTCAAAGAAATTAAG
1515549 CCTAAGTTTT
Statistics
Matches: 211, Mismatches: 31, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
152 3 0.01
153 64 0.30
154 24 0.11
155 117 0.55
156 3 0.01
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (155 bp):
GTTTCTTGATATTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGT
TTTCAAATGAATTTCAAAGAAATTAAGTACGATTTTCAGAAGTTTCTTGATGATTTGAGATTTAA
AAGAAACTAAGACTAGTTTTCAGGG
Found at i:1516051 original size:84 final size:84
Alignment explanation
Indices: 1515921--1516115 Score: 237
Period size: 84 Copynumber: 2.3 Consensus size: 84
1515911 TTTACTATTG
* * * * * *
1515921 CTCGATTCACAACACTTTGAATCAACTTAAGTTATTCGGGCCATCCATAATACTTTCAGGCAGGA
1 CTCGATTCACAACAC-TTCAATCAGCTAAAGTCATTCGGGCCATCCATAAGACCTTCAGGCAGGA
* *
1515986 TGTTTTCAACATTTCTTTTG
65 TGTTTTCAACATTTCCTTTC
* * * * *
1516006 TTGGATTCACAACACTTCAATCAGCTAAAGTCCTTCGGGTCATCCATAAGACCTTCGGGCAGGAT
1 CTCGATTCACAACACTTCAATCAGCTAAAGTCATTCGGGCCATCCATAAGACCTTCAGGCAGGAT
*
1516071 GTTTTTAACATTTCCTTTC
66 GTTTTCAACATTTCCTTTC
*
1516090 CTCGATTCACAACATTTCGAATCAGC
1 CTCGATTCACAACACTTC-AATCAGC
1516116 AACGCCCCAC
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
84 72 0.78
85 20 0.22
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34
Consensus pattern (84 bp):
CTCGATTCACAACACTTCAATCAGCTAAAGTCATTCGGGCCATCCATAAGACCTTCAGGCAGGAT
GTTTTCAACATTTCCTTTC
Found at i:1516404 original size:37 final size:36
Alignment explanation
Indices: 1516291--1516404 Score: 99
Period size: 37 Copynumber: 3.2 Consensus size: 36
1516281 TTCATCTCGA
*
1516291 TTGAGACAATTTTACTCGAAACAAAATTTTATCTCAC
1 TTGAGACAA-TTTACTCGAAACAAAAATTTATCTCAC
*** * ** *
1516328 TTGAGATTGTTT-TTTTAAAC--AAATTTCGTCTCAC
1 TTGAGACAATTTACTCGAAACAAAAATTT-ATCTCAC
*
1516362 ATGAGACAATTTCACTCGAAACAAAAATTTATCTCAC
1 TTGAGACAATTT-ACTCGAAACAAAAATTTATCTCAC
1516399 TTGAGA
1 TTGAGA
1516405 TTGTTTTTCT
Statistics
Matches: 55, Mismatches: 17, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
33 5 0.09
34 14 0.25
35 5 0.09
36 8 0.15
37 17 0.31
38 6 0.11
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (36 bp):
TTGAGACAATTTACTCGAAACAAAAATTTATCTCAC
Found at i:1516408 original size:71 final size:75
Alignment explanation
Indices: 1516292--1516506 Score: 285
Period size: 82 Copynumber: 2.8 Consensus size: 75
1516282 TCATCTCGAT
*
1516292 TGAGACAATTTTACTCGAAACAAAATTTTATCTCACTTGAGATTGTTTTT-TT-AAACAAA-T-T
1 TGAGACAATTTCACTCGAAACAAAATTTTATCTCACTTGAGATTGTTTTTATTAAAACAAACTAT
1516353 TCGTCTCACA
66 TCGTCTCACA
* *
1516363 TGAGACAATTTCACTCGAAACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTC
1 TGAGACAATTTCACTCGAAACAAAATTTTATCTCACTTGAGATTGTTTTTATTAAAACAAA---C
*
1516428 GTAACTTCGTCTCACT
63 -T-A-TTCGTCTCACA
* *
1516444 TGAGACGATTTTCACTCGAAACAAAATTTTATCTCACTTGAAATTGTTTTTATTAAAACAAAC
1 TGAGAC-AATTTCACTCGAAACAAAATTTTATCTCACTTGAGATTGTTTTTATTAAAACAAAC
1516507 GTCATCTCAC
Statistics
Matches: 126, Mismatches: 7, Indels: 14
0.86 0.05 0.10
Matches are distributed among these distances:
71 48 0.38
72 2 0.02
73 7 0.06
78 1 0.01
79 1 0.01
81 16 0.13
82 51 0.40
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (75 bp):
TGAGACAATTTCACTCGAAACAAAATTTTATCTCACTTGAGATTGTTTTTATTAAAACAAACTAT
TCGTCTCACA
Found at i:1518580 original size:29 final size:28
Alignment explanation
Indices: 1518503--1518579 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
1518493 TCGAATCCGA
** *
1518503 ACATGTTTTTTATTTATTTTAATTCGGCT
1 ACATG-TTTTTATTTATTTTAATTTAGCC
*
1518532 A-AGTAGTTTTAATTTATTTTAATTTAGCC
1 ACA-T-GTTTTTATTTATTTTAATTTAGCC
1518561 ACATGTTTTTATTTATTTT
1 ACATGTTTTTATTTATTTT
1518580 TCATTTCTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
28 15 0.38
29 23 0.57
30 2 0.05
ACGTcount: A:0.25, C:0.08, G:0.09, T:0.58
Consensus pattern (28 bp):
ACATGTTTTTATTTATTTTAATTTAGCC
Found at i:1522412 original size:15 final size:15
Alignment explanation
Indices: 1522392--1522426 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1522382 CAGCTGTGAA
*
1522392 AAGAAGGGTCATTTG
1 AAGAAGGATCATTTG
1522407 AAGAAGGATCATTTG
1 AAGAAGGATCATTTG
1522422 AAGAA
1 AAGAA
1522427 TGATTGTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.29, T:0.23
Consensus pattern (15 bp):
AAGAAGGATCATTTG
Found at i:1530961 original size:76 final size:77
Alignment explanation
Indices: 1530811--1531004 Score: 259
Period size: 76 Copynumber: 2.5 Consensus size: 77
1530801 AGATTGTTCA
* ** *
1530811 GAGGGAACCGATTCCCCCCTTTAGGAGGAACCGA-TCCCCCCTAAATGGTTTTGGCCCCGAGATT
1 GAGGGAACCGATTCCCCCC-ATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAAT
1530875 TCCAGAATGCTCG
65 TCCAGAATGCTCG
* * *
1530888 GAGGGAACCGATTCCCCCCATAGGAGGAACTGATTCCCCCCTAAACAGTTTT-GCTCTGAGAATT
1 GAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATT
*
1530952 CCAGTATGCTCG
66 CCAGAATGCTCG
* * *
1530964 GAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 GAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
1531005 TGTACAACGG
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
75 18 0.17
76 51 0.49
77 35 0.34
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (77 bp):
GAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATT
CCAGAATGCTCG
Found at i:1535772 original size:18 final size:18
Alignment explanation
Indices: 1535749--1535785 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1535739 AGTAGAATTT
1535749 ACTTTGACCACTTCATAA
1 ACTTTGACCACTTCATAA
1535767 ACTTTGACCACTTCATAA
1 ACTTTGACCACTTCATAA
1535785 A
1 A
1535786 ATCAATACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (18 bp):
ACTTTGACCACTTCATAA
Found at i:1538049 original size:33 final size:33
Alignment explanation
Indices: 1538012--1538091 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1538002 AGAAAACATT
*
1538012 ATGAATTTTCCAATAAGTTGGCCACCAATCAAG
1 ATGAATTTTCCAATAAGTTGGCCACCAACCAAG
*
1538045 ATGAAATTTCCAATAAGTTGGCCACCAACCAAG
1 ATGAATTTTCCAATAAGTTGGCCACCAACCAAG
1538078 ATGAATTTTCCAAT
1 ATGAATTTTCCAAT
1538092 TTGCAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGAATTTTCCAATAAGTTGGCCACCAACCAAG
Found at i:1560655 original size:58 final size:58
Alignment explanation
Indices: 1560593--1560704 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
1560583 TGGTATCTCA
*
1560593 ATTATAA-ACACTACTTTATTGAAT-TACTCAACTATTAAAAGTTATAAAATGATCTCTG
1 ATTATAATACACTACTTTATTGAATCT-C-CAACTATTAAAAGTTACAAAATGATCTCTG
* * * *
1560651 ATTATAATATATTACTTTTTTTAATCTCCAACTATTAAAAGTTACAAAATGATC
1 ATTATAATACACTACTTTATTGAATCTCCAACTATTAAAAGTTACAAAATGATC
1560705 ACCAAACTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 32 0.68
59 14 0.30
60 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.40
Consensus pattern (58 bp):
ATTATAATACACTACTTTATTGAATCTCCAACTATTAAAAGTTACAAAATGATCTCTG
Found at i:1568346 original size:25 final size:24
Alignment explanation
Indices: 1568312--1568390 Score: 81
Period size: 25 Copynumber: 3.1 Consensus size: 24
1568302 AAGGAAAAAG
1568312 AAATAAAAATATAAAGAAAAAATAA
1 AAATAAAAATATAAA-AAAAAATAA
1568337 AAATAAAAATATATTAAAAAACAATAA
1 AAATAAAAATATA--AAAAAA-AATAA
*
1568364 AAGA-AGAAAA-ATAAATAAAAATAA
1 AA-ATA-AAAATATAAAAAAAAATAA
1568388 AAA
1 AAA
1568391 AATATTAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
23 1 0.02
24 7 0.15
25 18 0.38
26 4 0.08
27 13 0.27
28 5 0.10
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (24 bp):
AAATAAAAATATAAAAAAAAATAA
Found at i:1568438 original size:53 final size:53
Alignment explanation
Indices: 1568347--1568471 Score: 159
Period size: 54 Copynumber: 2.4 Consensus size: 53
1568337 AAATAAAAAT
* *
1568347 ATATTAAAAAACAA-TAAAAGAAGAAAAATAAATAAAAA-TAAAAAAATATTAAA
1 ATATTAAAAAATAATTAAAAGAAGAAAAAGAAATAAAAATTAAAAAAA-ATT-AA
*
1568400 ATATTAAAAAATAATTAAAAGAAGGAAAAGAAAT-AAAATTAAAAAAAATTAA
1 ATATTAAAAAATAATTAAAAGAAGAAAAAGAAATAAAAATTAAAAAAAATTAA
*
1568452 ATA-GAAAAAATAAATTAAAA
1 ATATTAAAAAAT-AATTAAAA
1568472 TGTAAATTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
51 7 0.11
52 13 0.20
53 20 0.31
54 25 0.38
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.20
Consensus pattern (53 bp):
ATATTAAAAAATAATTAAAAGAAGAAAAAGAAATAAAAATTAAAAAAAATTAA
Found at i:1569855 original size:27 final size:26
Alignment explanation
Indices: 1569821--1569872 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
1569811 CGTATTCACC
1569821 ATATAATATATCATATAATATAATAG
1 ATATAATATATCATATAATATAATAG
* *
1569847 ATATGAATATATTATATAATGTAATA
1 ATAT-AATATATCATATAATATAATA
1569873 TCAAAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (26 bp):
ATATAATATATCATATAATATAATAG
Found at i:1577515 original size:40 final size:39
Alignment explanation
Indices: 1577471--1577592 Score: 192
Period size: 40 Copynumber: 3.1 Consensus size: 39
1577461 GGACACTAAA
1577471 TGTATATGGTGGGCACGACCTTATGTGTGATGCACTTCGG
1 TGTATATGGTGGGCACGACCTTATGTGT-ATGCACTTCGG
*
1577511 TGTATATGGTGGGCACGACCTTATGTGTAATGCACTTTGG
1 TGTATATGGTGGGCACGACCTTATGTGT-ATGCACTTCGG
* *
1577551 TGTATATGGTGGGCACGACCTTATATGTA-GCACTACGG
1 TGTATATGGTGGGCACGACCTTATGTGTATGCACTTCGG
1577589 TGTA
1 TGTA
1577593 GATATTACTC
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
38 11 0.14
39 1 0.01
40 65 0.84
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.33
Consensus pattern (39 bp):
TGTATATGGTGGGCACGACCTTATGTGTATGCACTTCGG
Found at i:1577653 original size:7 final size:7
Alignment explanation
Indices: 1577637--1577705 Score: 84
Period size: 7 Copynumber: 9.9 Consensus size: 7
1577627 TAAATTGGGC
*
1577637 TATGATT
1 TATGGTT
*
1577644 TATGGCT
1 TATGGTT
*
1577651 TATGGTC
1 TATGGTT
1577658 TATGGTT
1 TATGGTT
1577665 TATGGTT
1 TATGGTT
*
1577672 TATGGTC
1 TATGGTT
1577679 TATGGTT
1 TATGGTT
1577686 TATGGTT
1 TATGGTT
* *
1577693 TATAGTC
1 TATGGTT
1577700 TATGGT
1 TATGGT
1577706 ATATTGGTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.17, C:0.06, G:0.26, T:0.51
Consensus pattern (7 bp):
TATGGTT
Found at i:1577666 original size:21 final size:21
Alignment explanation
Indices: 1577636--1577714 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
1577626 TTAAATTGGG
* *
1577636 CTATGATTTATGGCTTATGGT
1 CTATGGTTTATGGTTTATGGT
1577657 CTATGGTTTATGGTTTATGGT
1 CTATGGTTTATGGTTTATGGT
*
1577678 CTATGGTTTATGGTTTATAGT
1 CTATGGTTTATGGTTTATGGT
*
1577699 CTATGGTATATTGGTT
1 CTATGGTTTA-TGGTT
1577715 AATAAATGGT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 48 0.91
22 5 0.09
ACGTcount: A:0.18, C:0.06, G:0.25, T:0.51
Consensus pattern (21 bp):
CTATGGTTTATGGTTTATGGT
Found at i:1580462 original size:27 final size:28
Alignment explanation
Indices: 1580432--1580502 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
1580422 CATAAGAGTT
* *
1580432 AAAAAAGTAGAAGAAAAAAG-GAAAAAG
1 AAAAAAGAAGAAGAAAAAAGAAAAAAAG
*
1580459 AAAAAA-AAAACAGAAAAAAGAAAAAAAG
1 AAAAAAGAAGA-AGAAAAAAGAAAAAAAG
1580487 AAAAAAGAAGAA-AAAA
1 AAAAAAGAAGAAGAAAA
1580503 GATGAGAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
26 2 0.05
27 19 0.51
28 13 0.35
29 3 0.08
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.01
Consensus pattern (28 bp):
AAAAAAGAAGAAGAAAAAAGAAAAAAAG
Found at i:1580468 original size:18 final size:17
Alignment explanation
Indices: 1580440--1580502 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
1580430 TTAAAAAAGT
* *
1580440 AGAAGAAAAAAGGAAAA
1 AGAAAAAAAAAAGAAAA
1580457 AGAAAAAAAAAACAGAAAAA
1 AG-AAAAAAAAA-AG-AAAA
1580477 AGAAAAAAAGAAA-AAAGA
1 AGAAAAAAA-AAAGAAA-A
1580495 AGAAAAAA
1 AGAAAAAA
1580503 GATGAGAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 5 0.13
18 17 0.44
19 9 0.23
20 8 0.21
ACGTcount: A:0.83, C:0.02, G:0.16, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAAGAAAA
Found at i:1580504 original size:7 final size:7
Alignment explanation
Indices: 1580442--1580500 Score: 75
Period size: 7 Copynumber: 8.3 Consensus size: 7
1580432 AAAAAAGTAG
1580442 AAGAAAA
1 AAGAAAA
*
1580449 AAGGAAA
1 AAGAAAA
1580456 AAGAAAA
1 AAGAAAA
1580463 AA-AAAA
1 AAGAAAA
*
1580469 CAGAAAA
1 AAGAAAA
1580476 AAGAAAAA
1 AAG-AAAA
1580484 AAGAAAA
1 AAGAAAA
1580491 AAGAAGAA
1 AAGAA-AA
1580499 AA
1 AA
1580501 AAGATGAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
6 5 0.11
7 29 0.64
8 11 0.24
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:1584393 original size:7 final size:7
Alignment explanation
Indices: 1584381--1584430 Score: 64
Period size: 7 Copynumber: 7.0 Consensus size: 7
1584371 TAAATTGGGC
1584381 TATGGTT
1 TATGGTT
1584388 TATGGTT
1 TATGGTT
*
1584395 TATGGTC
1 TATGGTT
1584402 TATGGTT
1 TATGGTT
* *
1584409 TATAGTC
1 TATGGTT
1584416 TATGGTT
1 TATGGTT
1584423 TATTGGTT
1 TA-TGGTT
1584431 AATAAATGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
7 31 0.86
8 5 0.14
ACGTcount: A:0.16, C:0.04, G:0.26, T:0.54
Consensus pattern (7 bp):
TATGGTT
Found at i:1584400 original size:14 final size:14
Alignment explanation
Indices: 1584381--1584425 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
1584371 TAAATTGGGC
*
1584381 TATGGTTTATGGTT
1 TATGGTCTATGGTT
1584395 TATGGTCTATGGTT
1 TATGGTCTATGGTT
*
1584409 TATAGTCTATGGTT
1 TATGGTCTATGGTT
1584423 TAT
1 TAT
1584426 TGGTTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.18, C:0.04, G:0.24, T:0.53
Consensus pattern (14 bp):
TATGGTCTATGGTT
Found at i:1592029 original size:18 final size:17
Alignment explanation
Indices: 1592006--1592040 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1591996 CAATAAGAAG
1592006 GAAAAAATAAAATATAAA
1 GAAAAAATAAAA-ATAAA
1592024 GAAAAAATAAAAATAAA
1 GAAAAAATAAAAATAAA
1592041 ATTATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (17 bp):
GAAAAAATAAAAATAAA
Found at i:1592071 original size:35 final size:35
Alignment explanation
Indices: 1592032--1592171 Score: 99
Period size: 35 Copynumber: 3.9 Consensus size: 35
1592022 AAGAAAAAAT
* *
1592032 AAAAATAAAATTATATTAAAAAATAA-TAAAAGAAA
1 AAAAAT-AAATTAAATTAAAAAACAATTAAAAGAAA
* *
1592067 AAAAATAATTTAAATTAAAAAACAATTAAAAGAAG
1 AAAAATAAATTAAATTAAAAAACAATTAAAAGAAA
* * * *
1592102 GAAAAGAAATAAAATTGAAAAAGTAAAATTAAATTA-AATTA
1 AAAAATAAATTAAATT-AAAAA--ACAATTAAA--AGAA--A
1592143 AAAAAT-AATTAAA-TAGAAAAACAATTAAA
1 AAAAATAAATTAAATTA-AAAAACAATTAAA
1592172 TTAAAATGTA
Statistics
Matches: 82, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
34 16 0.20
35 26 0.32
36 5 0.06
37 8 0.10
38 9 0.11
39 7 0.09
40 7 0.09
41 4 0.05
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.23
Consensus pattern (35 bp):
AAAAATAAATTAAATTAAAAAACAATTAAAAGAAA
Found at i:1592084 original size:34 final size:36
Alignment explanation
Indices: 1592032--1592100 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
1592022 AAGAAAAAAT
* *
1592032 AAAAATAAAATTATATTAAAAAATAA-TAAAAGAAA
1 AAAAATAAAATTAAATTAAAAAACAATTAAAAGAAA
*
1592067 AAAAAT-AATTTAAATTAAAAAACAATTAAAAGAA
1 AAAAATAAAATTAAATTAAAAAACAATTAAAAGAA
1592101 GGAAAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.23
Consensus pattern (36 bp):
AAAAATAAAATTAAATTAAAAAACAATTAAAAGAAA
Found at i:1592152 original size:16 final size:16
Alignment explanation
Indices: 1592133--1592177 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
1592123 AGTAAAATTA
*
1592133 AATTAAATTAAAAAAT
1 AATTAAATTAAAAAAC
1592149 AATTAAA-TAGAAAAAC
1 AATTAAATTA-AAAAAC
1592165 AATTAAATTAAAA
1 AATTAAATTAAAA
1592178 TGTAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (16 bp):
AATTAAATTAAAAAAC
Found at i:1593485 original size:27 final size:26
Alignment explanation
Indices: 1593451--1593502 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
1593441 CGTATTCACC
1593451 ATATAATATATCATATAATATAATAG
1 ATATAATATATCATATAATATAATAG
* *
1593477 ATATGAATATATTATATAATGTAATA
1 ATAT-AATATATCATATAATATAATA
1593503 TCAAAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (26 bp):
ATATAATATATCATATAATATAATAG
Found at i:1597372 original size:580 final size:577
Alignment explanation
Indices: 1596243--1597978 Score: 3100
Period size: 580 Copynumber: 3.0 Consensus size: 577
1596233 AGATAATTAC
1596243 AATAATATCACTCTCTATATTATATTTTCAATTGGATTCCTATTTTATAAAATAAAATTAAT-AT
1 AATAATATCACTCTCTATATTATATTTTCAATTGGATTCCTATTTTATAAAATAAAATTAATAAT
* *
1596307 TTATATATATATTTTTTTTTCGGGTCAAGTTCGAGTTATATCTCAAAATATGCAGTGGCGGAATA
66 TT-TATATATATATTTGTTTCGGGTCAAGTTCGAGTTATATCTCAAAATATGCAGTGGCGGAATA
1596372 CAAGCTAGGCTAGAGGGCGCCATGGCCCCATAAAATTTTAAAAATTATAATTTAGACTCTTAAAA
130 CAAGCTAGGCTAGAGGGCGCCATGGCCCCATAAAATTTTAAAAATTATAATTTAGACTCTTAAAA
*
1596437 TTAAAAAAAAAATTAATTTGGTCTCCCCAAAACTTTTAGAAATTCAAATTATATTTTAAAATTTT
195 TT-AAAAAAAAATTAATTTGGTCTCCCCAAAACTTTTAGAAATTCAGATTATATTTTAAAATTTT
1596502 CAAAATGTTTTAAATTAAACCTCCTCCCATAAATTTTAAAAATTCTCATTAAGCCACTAAAAATT
259 CAAAATGTTTTAAATTAAACCTCCTCCCATAAATTTTAAAAATTCTCATTAAGCCACTAAAAATT
* *
1596567 TCTAAAATGTTAATTAGATCATAATTTTTTGGG-AAAAATACTAAACCCATCAAAATTTTGCAAA
324 TC-AAAATGTTAATTAGATCATAATTTTTTGGGAAAAAATACTAAACCCATCAAAATTTGGAAAA
1596631 ATCTTAATTTGAACCTCTAGCTTTTTTAAAGTTTTAAGTTGCCCCACCCCTCAAACTCTATCACC
388 ATCTTAATTTGAACCTCTAGCTTTTTTAAAGTTTTAAGTTGCCCCACCCCTCAAACTCTATCACC
* *
1596696 AAGTTCGTCACTGAAAAGATGTGTAACCCCTCATACCGATTCGGGTAACCCGATCCGATCTGGAG
453 AAGTTCGTCACTGAAAAGATGTGTAACCCCTCAGAACGATTCGGGTAACCCGATCCGATCTGGAG
* * *
1596761 TGTCACATTAGGGCCACCGGAGCGACCCACTGTAAAAATAACGAAAAATTTAAAACTTTT
518 TGTCACATTAGGGCCACCGGAGCGACCCACTGTAAAAATAGCGGAAAATTTAAAACTCTT
1596821 AATAATATCACTCTCTATATTATATTTTCAATTGGATTCCTATTTTATAAAATAAAATTAATAAT
1 AATAATATCACTCTCTATATTATATTTTCAATTGGATTCCTATTTTATAAAATAAAATTAATAAT
*
1596886 TTTATATATATATTTGTTTCGGGTCAAGTTCGAGTTATATCTCAAAATATGCAGTGGTGGAATAC
66 TTTATATATATATTTGTTTCGGGTCAAGTTCGAGTTATATCTCAAAATATGCAGTGGCGGAATAC
1596951 AAGCTAGGCTAGAGGGCGCCATGGCCCCATAAAATTTTAAAAATTATAATTTAGACTCTTAAAAT
131 AAGCTAGGCTAGAGGGCGCCATGGCCCCATAAAATTTTAAAAATTATAATTTAGACTCTTAAAAT
*
1597016 TAAAAAAAAATTAATTTGGTCTCCCCAAAACTTGTAGAAATTCAGATTATATTTTAAAATTTTCA
196 TAAAAAAAAATTAATTTGGTCTCCCCAAAACTTTTAGAAATTCAGATTATATTTTAAAATTTTCA
1597081 AAATGTTTTAAATTAAACCTCCTCCCATAAATTTTAAAAATTCTCATTAAGCCACTAAAAATTTC
261 AAATGTTTTAAATTAAACCTCCTCCCATAAATTTTAAAAATTCTCATTAAGCCACTAAAAATTTC
1597146 GAAAATGTTAATTAGATCATAATTTTTTGGGAAAAAAAATACTAAACCCATCAAAATTTGGAAAA
326 -AAAATGTTAATTAGATCATAATTTTTTGGG--AAAAAATACTAAACCCATCAAAATTTGGAAAA
1597211 ATCTTAATTTGAACCTCTAGCTTTTTTAAAGTTTTAAGTTGCCCCACCCCTCAAACTCTATCACC
388 ATCTTAATTTGAACCTCTAGCTTTTTTAAAGTTTTAAGTTGCCCCACCCCTCAAACTCTATCACC
* * *
1597276 AAGTTCGTCACTGAAAAGATGTGTAACCCCTTAGAACGATTCGGGTAACCCAATCCAATCTGGAG
453 AAGTTCGTCACTGAAAAGATGTGTAACCCCTCAGAACGATTCGGGTAACCCGATCCGATCTGGAG
* *
1597341 TGTCACATTAGGGTCACCAGAGCGACCCACTGTAAAAATAGCGGAAAATTTAAAACTCTT
518 TGTCACATTAGGGCCACCGGAGCGACCCACTGTAAAAATAGCGGAAAATTTAAAACTCTT
* *
1597401 AATAATATCACTCTCTATATTATATTTTCAATTGGATTCATATTTTATAAAATAAAATTAATATT
1 AATAATATCACTCTCTATATTATATTTTCAATTGGATTCCTATTTTATAAAATAAAATTAATAAT
*
1597466 TTTATATATATATTTGTTTCGGGTCAAGTTCGAGTTATATCTCAAAATATGCAATGGCGGAATAC
66 TTTATATATATATTTGTTTCGGGTCAAGTTCGAGTTATATCTCAAAATATGCAGTGGCGGAATAC
1597531 AAGCTAGGCTAGAGGGCGCCATGGCCCCATAAAATTTTAAAAATTATAATTTAGACTCTTAAAAT
131 AAGCTAGGCTAGAGGGCGCCATGGCCCCATAAAATTTTAAAAATTATAATTTAGACTCTTAAAAT
* *
1597596 TAAAAAAAAA-AAAATTGGTCTCCCCAAAACTTTTAGAAATTCAGATTATATTTTAAAATTTTCA
196 TAAAAAAAAATTAATTTGGTCTCCCCAAAACTTTTAGAAATTCAGATTATATTTTAAAATTTTCA
1597660 AAATGTTTTAAATTAAACCTCCTCCCATAAATTTTAAAAATTCTCATTAAGCCACTAAAAATTTC
261 AAATGTTTTAAATTAAACCTCCTCCCATAAATTTTAAAAATTCTCATTAAGCCACTAAAAATTTC
* *
1597725 AAAAGCGTTAATAAGATCATAATTTTTTGGGAAAAAATACTAAACCCATCAAAATTTGGAAAAAT
326 AAAA-TGTTAATTAGATCATAATTTTTTGGGAAAAAATACTAAACCCATCAAAATTTGGAAAAAT
* *
1597790 CTTAATTTGAACCTCTAGCTTTTTTAAAGTTTTAAGTTGCCCCACCCTTCAAACTCTATCACTAA
390 CTTAATTTGAACCTCTAGCTTTTTTAAAGTTTTAAGTTGCCCCACCCCTCAAACTCTATCACCAA
* * *
1597855 GTTTGTCACTGAAAAGATGTGTAACCCCTCAGATCGATTCGGGTAACCTGATCCGATCTGGAGTG
455 GTTCGTCACTGAAAAGATGTGTAACCCCTCAGAACGATTCGGGTAACCCGATCCGATCTGGAGTG
* * *
1597920 TCACATTAGGGCCATCGGAACGACTCACTGTAAAAATAGCGGAAAATTTAAAACTCTT
520 TCACATTAGGGCCACCGGAGCGACCCACTGTAAAAATAGCGGAAAATTTAAAACTCTT
1597978 A
1 A
1597979 TTTAAAATAT
Statistics
Matches: 1113, Mismatches: 40, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
577 367 0.33
578 192 0.17
579 144 0.13
580 410 0.37
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (577 bp):
AATAATATCACTCTCTATATTATATTTTCAATTGGATTCCTATTTTATAAAATAAAATTAATAAT
TTTATATATATATTTGTTTCGGGTCAAGTTCGAGTTATATCTCAAAATATGCAGTGGCGGAATAC
AAGCTAGGCTAGAGGGCGCCATGGCCCCATAAAATTTTAAAAATTATAATTTAGACTCTTAAAAT
TAAAAAAAAATTAATTTGGTCTCCCCAAAACTTTTAGAAATTCAGATTATATTTTAAAATTTTCA
AAATGTTTTAAATTAAACCTCCTCCCATAAATTTTAAAAATTCTCATTAAGCCACTAAAAATTTC
AAAATGTTAATTAGATCATAATTTTTTGGGAAAAAATACTAAACCCATCAAAATTTGGAAAAATC
TTAATTTGAACCTCTAGCTTTTTTAAAGTTTTAAGTTGCCCCACCCCTCAAACTCTATCACCAAG
TTCGTCACTGAAAAGATGTGTAACCCCTCAGAACGATTCGGGTAACCCGATCCGATCTGGAGTGT
CACATTAGGGCCACCGGAGCGACCCACTGTAAAAATAGCGGAAAATTTAAAACTCTT
Found at i:1598568 original size:43 final size:43
Alignment explanation
Indices: 1598494--1598878 Score: 429
Period size: 44 Copynumber: 8.9 Consensus size: 43
1598484 GAGCATGCAA
* * * *
1598494 AAACTATAAGGTCTTATCCTTGCACATAGCAAAAGAGCCTCGGG
1 AAACTGTAAGG-CTTACCCTTGCACACAGCAAAAGAGCCTGGGG
* * * *
1598538 AAACTGTATGTCTTACCCTTGCACACAGCAAAAGAACCT-AGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAGCCTGGGG
* * *
1598580 AAACTGTAAGGCTTACCCTTGTACACAGCAAAGGAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAGCCTGGGG
* *
1598623 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAGCCTGGGG
* * *
1598666 AAATTGTAAGGCTTACCCTTGCACACAAC-AAAGGGACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAG-CCT-GGGG
* *
1598710 AAACTGTAAGGCTTGCCCTTGCACACAGC-AAAGGGACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAG-CCT-GGGG
1598754 AAACTGTAAGGCTTACCCTTGCACACAGC-AAAGAGACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAG-CCT-GGGG
* * *
1598798 AAACTGTAAGGCTTACCCTTGCACACAAC-AAAGGGACCTGGAGA
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAG-CCTGG-GG
* * * *
1598842 AAACTGTAAGACTTACCATTACACACAGCAAAGGAGC
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAGC
1598879 ATGCTGTAAC
Statistics
Matches: 304, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
42 40 0.13
43 101 0.33
44 159 0.52
45 4 0.01
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (43 bp):
AAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAGCCTGGGG
Found at i:1598797 original size:88 final size:86
Alignment explanation
Indices: 1598494--1598874 Score: 489
Period size: 88 Copynumber: 4.4 Consensus size: 86
1598484 GAGCATGCAA
* * * * * *
1598494 AAACTATAAGGTCTTATCCTTGCACATAGCAAA-AGAGCCTCGGGAAACTGTATGTCTTACCCTT
1 AAACTGTAAGG-CTTACCCTTGCACACAGCAAAGAGA-CCTGGGGAAACTGTAAGGCTTACCCTT
*
1598558 GCACACAGCAAAAGAACCT-AGG
64 GCACACAGCAAAGGAACCTGAGG
*
1598580 AAACTGTAAGGCTTACCCTTGTACACAGCAAAG-GAACCTGGGGAAACTGTAAGGCTTACCCTTG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGAG-ACCTGGGGAAACTGTAAGGCTTACCCTTG
*
1598644 CACACAGCAAAGGAACCTGGGG
65 CACACAGCAAAGGAACCTGAGG
* * * *
1598666 AAATTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAAACTGTAAGGCTTGCCCTTG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGAGACCT-GGGGAAACTGTAAGGCTTACCCTTG
* *
1598731 CACACAGCAAAGGGACCTGGGGG
65 CACACAGCAAAGGAACCT-GAGG
1598754 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGGAAACTGTAAGGCTTACCCTTG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGAGACCT-GGGGAAACTGTAAGGCTTACCCTTG
* * *
1598819 CACACAACAAAGGGACCTGGAGA
65 CACACAGCAAAGGAACCT-GAGG
* * *
1598842 AAACTGTAAGACTTACCATTACACACAGCAAAG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAG
1598875 GAGCATGCTG
Statistics
Matches: 265, Mismatches: 24, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
85 61 0.23
86 47 0.18
87 42 0.16
88 115 0.43
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (86 bp):
AAACTGTAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTGTAAGGCTTACCCTTGC
ACACAGCAAAGGAACCTGAGG
Found at i:1602865 original size:18 final size:19
Alignment explanation
Indices: 1602820--1602865 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1602810 CTTTCCCTCT
1602820 GAGTCATATCAATTAGGAG
1 GAGTCATATCAATTAGGAG
*
1602839 TGGGTCATATCAATTAGGA-
1 -GAGTCATATCAATTAGGAG
1602858 GAGTCATA
1 GAGTCATA
1602866 ATTTTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
20 17 0.71
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (19 bp):
GAGTCATATCAATTAGGAG
Found at i:1603645 original size:19 final size:19
Alignment explanation
Indices: 1603621--1603667 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1603611 ATTAGTCCAC
1603621 AAGCCACAATAAAATCCCA
1 AAGCCACAATAAAATCCCA
*
1603640 AAGCCACAATAAGATCCCA
1 AAGCCACAATAAAATCCCA
1603659 AAGCCACAA
1 AAGCCACAA
1603668 GAACTATTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.51, C:0.32, G:0.09, T:0.09
Consensus pattern (19 bp):
AAGCCACAATAAAATCCCA
Found at i:1604043 original size:22 final size:21
Alignment explanation
Indices: 1604000--1604043 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1603990 TTTTAAGTCG
**
1604000 TTGGGCTGAGTTGGGCTTAAT
1 TTGGGCTGAGTTGGGCCCAAT
*
1604021 TTGGGCTGTGGTTGGGCCCAAT
1 TTGGGCTG-AGTTGGGCCCAAT
1604043 T
1 T
1604044 AGCCATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.11, C:0.14, G:0.39, T:0.36
Consensus pattern (21 bp):
TTGGGCTGAGTTGGGCCCAAT
Found at i:1604675 original size:20 final size:21
Alignment explanation
Indices: 1604639--1604677 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1604629 GGGGTTTGAG
1604639 TATCGATACTGGGATAAATAA
1 TATCGATACTGGGATAAATAA
1604660 TATCGATACT-GGATAAAT
1 TATCGATACTGGGATAAAT
1604678 TGGGTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (21 bp):
TATCGATACTGGGATAAATAA
Found at i:1607372 original size:12 final size:12
Alignment explanation
Indices: 1607355--1607379 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1607345 CAAAATGTAA
1607355 TCTAGTAAAATT
1 TCTAGTAAAATT
1607367 TCTAGTAAAATT
1 TCTAGTAAAATT
1607379 T
1 T
1607380 ATAACCCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TCTAGTAAAATT
Found at i:1607796 original size:29 final size:29
Alignment explanation
Indices: 1607748--1607805 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1607738 TAAAACTTGA
*
1607748 ATTGAAATTAAATTTGTAAAATTGT-TAAG
1 ATTGAAATTAAATTTAT-AAATTGTATAAG
1607777 ATTGAGAATTAAA-TTATAAATTGTATAAG
1 ATTGA-AATTAAATTTATAAATTGTATAAG
1607806 TTGTGAGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 7 0.27
29 12 0.46
30 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.40
Consensus pattern (29 bp):
ATTGAAATTAAATTTATAAATTGTATAAG
Found at i:1608450 original size:66 final size:66
Alignment explanation
Indices: 1608367--1608606 Score: 302
Period size: 66 Copynumber: 3.6 Consensus size: 66
1608357 TACTGTACAT
* * * * * *
1608367 AATGAGACTCATGTACCTTTGTGGTGCTTGAGGTGGAGTGATAATTGAATACTGCATAGATAAAT
1 AATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGTACATATCACT
1608432 C
66 C
* *
1608433 AATGAGACTCAAGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATTGTACATATCACT
1 AATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGTACATATCACT
1608498 C
66 C
* * * * * *
1608499 AAAGAGACAT-GTGTACCTTTATGGTGCATGAGGTAGAGTGATAATTAAATACGGTACATATCAC
1 AATGAGAC-TCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGTACATATCAC
1608563 TC
65 TC
** * *
1608565 AATGAGACTTGTGTACCTTTGTGGTACATAAGGTGGAGTGAT
1 AATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGAT
1608607 TATATGATAC
Statistics
Matches: 151, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
65 1 0.01
66 149 0.99
67 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (66 bp):
AATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGTACATATCACT
C
Found at i:1610062 original size:64 final size:63
Alignment explanation
Indices: 1609994--1610172 Score: 209
Period size: 64 Copynumber: 2.8 Consensus size: 63
1609984 TAGAACACTT
* * * **
1609994 AGTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGCCTG
1 AGTGCATCGGTGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCA
* * *
1610058 AGTGCATCGGTGCAT-TGCTTGTGCATCGATGCATGAAATGCATTCAATGTTTTAATAAAACCCA
1 AGTGCATCGGTGCATAAG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
* *
1610122 AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
1610173 CAATTTATTC
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
62 1 0.01
64 94 0.96
65 2 0.02
66 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (63 bp):
AGTGCATCGGTGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:1618715 original size:64 final size:64
Alignment explanation
Indices: 1618632--1618789 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
1618622 TGCACCAAGT
* * ** * * ***
1618632 GTGCA-CGATGCATAAAATGCATTCGATGTTTGAA-AATAGCCTGAGTGCATCGGTGCATTGCTT
1 GTGCACCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCAAGTGCATCGATGCATAGAGA
* * *
1618695 GTGTATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCAAGTGCATCGATGCATAGAGA
1 GTGCACCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAAGTGCATCGATGCATAGAGA
1618759 GTGCACCGATGCATGAAATGCATTCGATGTT
1 GTGCACCGATGCATGAAATGCATTCGATGTT
1618790 CAATTTATTC
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
63 4 0.05
64 74 0.93
65 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (64 bp):
GTGCACCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAAGTGCATCGATGCATAGAGA
Found at i:1619667 original size:14 final size:14
Alignment explanation
Indices: 1619650--1619706 Score: 68
Period size: 14 Copynumber: 4.4 Consensus size: 14
1619640 GAATGAACAT
1619650 AAACGAACATAACC
1 AAACGAACATAACC
1619664 AAACGAACAT----
1 AAACGAACATAACC
1619674 AAACGAACATAACC
1 AAACGAACATAACC
*
1619688 GAACGAACATAACC
1 AAACGAACATAACC
*
1619702 GAACG
1 AAACG
1619707 TTCACGAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 10 0.26
14 28 0.74
ACGTcount: A:0.54, C:0.26, G:0.12, T:0.07
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:1619705 original size:10 final size:10
Alignment explanation
Indices: 1619644--1619691 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1619634 ATAAATGAAT
1619644 GAACATAAAC
1 GAACATAAAC
1619654 GAACATAACCAAAC
1 GAACAT----AAAC
1619668 GAACATAAAC
1 GAACATAAAC
*
1619678 GAACATAACC
1 GAACATAAAC
1619688 GAAC
1 GAAC
1619692 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 23 0.70
14 10 0.30
ACGTcount: A:0.56, C:0.25, G:0.10, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1619716 original size:24 final size:24
Alignment explanation
Indices: 1619644--1619705 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
1619634 ATAAATGAAT
*
1619644 GAACATAAACGAACATAACCAAAC
1 GAACATAAACGAACATAACCGAAC
1619668 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
1619692 GAACATAACCGAAC
1 GAACATAAACGAAC
1619706 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.55, C:0.26, G:0.11, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:1622430 original size:50 final size:50
Alignment explanation
Indices: 1622349--1622447 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
1622339 TTAGATAGGT
* *
1622349 CCCAACTCAAGTCCTCTTAACCTTTCTTAGACACTTTGTCTAAACTTGGC
1 CCCAACTCAAGTCCTCTTAACCCTTCATAGACACTTTGTCTAAACTTGGC
* * * *
1622399 CCCAACTTAGGTCCTCTTAGCCCTTCATAGACACTTTGTCTAAGCTTGG
1 CCCAACTCAAGTCCTCTTAACCCTTCATAGACACTTTGTCTAAACTTGG
1622448 TCCAATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.33
Consensus pattern (50 bp):
CCCAACTCAAGTCCTCTTAACCCTTCATAGACACTTTGTCTAAACTTGGC
Found at i:1624247 original size:2 final size:2
Alignment explanation
Indices: 1624192--1624227 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1624182 ATATTATACA
1624192 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
1624228 GTAGGTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1624261 original size:25 final size:25
Alignment explanation
Indices: 1624214--1624318 Score: 101
Period size: 25 Copynumber: 4.3 Consensus size: 25
1624204 ATATATATAT
* *
1624214 ATATATATATATATGTAGGTTTGAAA
1 ATATATATA-ATATATAGTTTTGAAA
1624240 ATATATATAATATATAGTTTTG-AA
1 ATATATATAATATATAGTTTTGAAA
* *
1624264 A-ATATAT-A-ATATGGTTTTTGAGA
1 ATATATATAATATATAG-TTTTGAAA
* *
1624287 ATATATATAATGTATATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAA
*
1624312 ACATATA
1 ATATATA
1624319 GTTTTTGGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
21 5 0.08
22 6 0.09
23 8 0.12
24 9 0.14
25 25 0.38
26 12 0.18
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (25 bp):
ATATATATAATATATAGTTTTGAAA
Found at i:1624269 original size:47 final size:46
Alignment explanation
Indices: 1624218--1624318 Score: 123
Period size: 47 Copynumber: 2.2 Consensus size: 46
1624208 ATATATATAT
1624218 ATATATATAT-GTAGGTTTGAAAATATATATAATATATAGTTTTGAAA
1 ATATATATATGGT--GTTTGAAAATATATATAATATATAGTTTTGAAA
* * * *
1624265 ATATATAATATGGTTTTTGAGAATATATATAATGTATATTTTTGAAA
1 ATATAT-ATATGGTGTTTGAAAATATATATAATATATAGTTTTGAAA
*
1624312 ACATATA
1 ATATATA
1624319 GTTTTTGGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
46 1 0.02
47 40 0.85
48 4 0.09
49 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.44
Consensus pattern (46 bp):
ATATATATATGGTGTTTGAAAATATATATAATATATAGTTTTGAAA
Found at i:1624325 original size:17 final size:16
Alignment explanation
Indices: 1624299--1624341 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1624289 ATATATAATG
1624299 TATATTTTTGAAAACA
1 TATATTTTTGAAAACA
* *
1624315 TATAGTTTTTGGAAATA
1 TATA-TTTTTGAAAACA
1624332 TATAATTTTT
1 TAT-ATTTTT
1624342 AACATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 18 0.78
18 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (16 bp):
TATATTTTTGAAAACA
Found at i:1624384 original size:14 final size:13
Alignment explanation
Indices: 1624365--1624425 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 13
1624355 TATATTATTA
1624365 CTATTTTCTATTTT
1 CTATTTTCT-TTTT
1624379 CTATTTTTTCTTTTT
1 CTA--TTTTCTTTTT
1624394 CT-TTTTCTTTTT
1 CTATTTTCTTTTT
*
1624406 -TATTTTTTATTTT
1 CTATTTTCT-TTTT
*
1624419 TTATTTT
1 CTATTTT
1624426 TTGATTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
11 1 0.02
12 15 0.37
13 4 0.10
14 9 0.22
15 6 0.15
16 6 0.15
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (13 bp):
CTATTTTCTTTTT
Found at i:1624426 original size:8 final size:7
Alignment explanation
Indices: 1624366--1624433 Score: 68
Period size: 7 Copynumber: 9.9 Consensus size: 7
1624356 ATATTATTAC
*
1624366 TATTTTC
1 TATTTTT
*
1624373 TATTTTC
1 TATTTTT
1624380 TATTTTT
1 TATTTTT
*
1624387 T-CTTTT
1 TATTTTT
*
1624393 T-CTTTT
1 TATTTTT
*
1624399 TCTTTTT
1 TATTTTT
1624406 TATTTTT
1 TATTTTT
1624413 TATTTTT
1 TATTTTT
1624420 TATTTTT
1 TATTTTT
1624427 TGATTTT
1 T-ATTTT
1624434 AATTTTAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
6 11 0.20
7 39 0.71
8 5 0.09
ACGTcount: A:0.10, C:0.07, G:0.01, T:0.81
Consensus pattern (7 bp):
TATTTTT
Found at i:1625892 original size:2 final size:2
Alignment explanation
Indices: 1625885--1625920 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1625875 AAAATTACTC
1625885 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
1625921 TAATATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1632133 original size:13 final size:13
Alignment explanation
Indices: 1632117--1632163 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
1632107 AATTATCTAA
1632117 TTATATAGATAAT
1 TTATATAGATAAT
1632130 TTATATAG---A-
1 TTATATAGATAAT
1632139 -TATATAGATAAT
1 TTATATAGATAAT
1632151 TTATATAGATAAT
1 TTATATAGATAAT
1632164 AATTTAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.24
10 1 0.03
11 1 0.03
13 20 0.69
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (13 bp):
TTATATAGATAAT
Found at i:1632142 original size:21 final size:21
Alignment explanation
Indices: 1632118--1632161 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1632108 ATTATCTAAT
1632118 TATATAGATAATTTATATAGA
1 TATATAGATAATTTATATAGA
1632139 TATATAGATAATTTATATAGA
1 TATATAGATAATTTATATAGA
1632160 TA
1 TA
1632162 ATAATTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (21 bp):
TATATAGATAATTTATATAGA
Found at i:1632156 original size:34 final size:35
Alignment explanation
Indices: 1632117--1632185 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
1632107 AATTATCTAA
*
1632117 TTATATAGATAATTTATATAG-ATA-TATAGATAAT
1 TTATATAGATAA-TAATATAGAATATTATAGATAAT
*
1632151 TTATATAGATAATAATTTAGAATATTATAGATAAT
1 TTATATAGATAATAATATAGAATATTATAGATAAT
1632186 AATCTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 6 0.19
34 15 0.48
35 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (35 bp):
TTATATAGATAATAATATAGAATATTATAGATAAT
Found at i:1632171 original size:25 final size:24
Alignment explanation
Indices: 1632122--1632188 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 24
1632112 TCTAATTATA
1632122 TAGATAATTTATATAGAT-AT-A-
1 TAGATAATTTATATAGATAATAAT
1632143 TAGATAATTTATATAGATAATAATT
1 TAGATAATTTATATAGATAATAA-T
*
1632168 TAG--AATAT-TATAGATAATAAT
1 TAGATAATTTATATAGATAATAAT
1632189 CTAATATATT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 19 0.46
22 14 0.34
23 5 0.12
25 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (24 bp):
TAGATAATTTATATAGATAATAAT
Found at i:1632182 original size:22 final size:22
Alignment explanation
Indices: 1632154--1632201 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1632144 AGATAATTTA
*
1632154 TATAGATAATAATTTAGA-ATAT
1 TATAGATAATAATCTA-ATATAT
1632176 TATAGATAATAATCTAATATAT
1 TATAGATAATAATCTAATATAT
1632198 TATA
1 TATA
1632202 ATATATAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (22 bp):
TATAGATAATAATCTAATATAT
Found at i:1632448 original size:20 final size:21
Alignment explanation
Indices: 1632425--1632469 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1632415 CCCTAAGTGG
*
1632425 AGTATC-GATACTCAAGGGTC
1 AGTATCTGATACTCAAGGGCC
*
1632445 AGTA-CTGATACTTAAGGGCC
1 AGTATCTGATACTCAAGGGCC
1632465 AGTAT
1 AGTAT
1632470 TTGTACCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (21 bp):
AGTATCTGATACTCAAGGGCC
Found at i:1637604 original size:54 final size:54
Alignment explanation
Indices: 1637520--1638129 Score: 967
Period size: 54 Copynumber: 11.3 Consensus size: 54
1637510 ATCACTTCAA
* * * *
1637520 GGAGTA-GAACTTGAACAATCTTCTGTTTACGGGTTCGCCCCCTCTTTATTTAG
1 GGAGTAGGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
* *
1637573 GGAGTAGGAACTCGAACGATCTTTTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
1 GGAGTAGGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
* *
1637627 GGAGTAGGAACTCGAACAATCTTCTG-TCTACGGGTTTGATCCCTCTTTCTTTAG
1 GGAGTAGGAACTCGAACAATCTTCTGCT-TACGGGTTCGCTCCCTCTTTCTTTAG
* *
1637681 GGAGTAGGAACTCGAACGATCTTCTGCTTACTGGTTCGCTCCCTCTTTCTTTAG
1 GGAGTAGGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
*
1637735 GGAGTAGGAACTCGAACAATCTTCTGCTTACAGGTTCGCTCCCTCTTTCTTTAG
1 GGAGTAGGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
* * *
1637789 GGAGTAGGAACTCGAACGATCTTCTGCTTATGGGTTCGCTCCCTTTTTCTTTAG
1 GGAGTAGGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
* * *
1637843 GGAGTAGGAACTTGAACAATCTTCTTCTTAAGGGTTCGCTCCCTCTTTCTTTAG
1 GGAGTAGGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
*
1637897 GGAGTAGGAACTTGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
1 GGAGTAGGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
*
1637951 GGAGTAGGAACTCGAACAATCTTCTG-TCAACGGGTTCGCTCCCTCTTTCTTTAG
1 GGAGTAGGAACTCGAACAATCTTCTGCT-TACGGGTTCGCTCCCTCTTTCTTTAG
* *
1638005 GGAGTAGGAACTCGAACGATCTTTTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
1 GGAGTAGGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
*
1638059 GGAGTAGGAACTCGAACAATCTTCTG-TCAACGGGTTCGCTCCCTCTTTCTTTAG
1 GGAGTAGGAACTCGAACAATCTTCTGCT-TACGGGTTCGCTCCCTCTTTCTTTAG
1638113 GGAGTAGGAACTCGAAC
1 GGAGTAGGAACTCGAAC
1638130 GTCTTCTTCT
Statistics
Matches: 516, Mismatches: 35, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
53 9 0.02
54 505 0.98
55 2 0.00
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (54 bp):
GGAGTAGGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTTCTTTAG
Found at i:1654614 original size:14 final size:14
Alignment explanation
Indices: 1654588--1654627 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1654578 CTCTTCCTTA
*
1654588 TTTTTCCTCTTCT-
1 TTTTTCTTCTTCTC
1654601 TTTCTTCTTCTTCTC
1 TTT-TTCTTCTTCTC
1654616 TTTTTCTTCTTC
1 TTTTTCTTCTTC
1654628 CTCCTTCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 3 0.12
14 18 0.75
15 3 0.12
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTCTTCTTCTC
Found at i:1661534 original size:9 final size:9
Alignment explanation
Indices: 1661511--1661555 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
1661501 GAATTTCCAT
*
1661511 TATACAATA
1 TATATAATA
*
1661520 TTTATAATA
1 TATATAATA
1661529 TATAT-ATA
1 TATATAATA
*
1661537 TATCTAATA
1 TATATAATA
1661546 TATATAATA
1 TATATAATA
1661555 T
1 T
1661556 GAAGTTTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (9 bp):
TATATAATA
Found at i:1661544 original size:17 final size:16
Alignment explanation
Indices: 1661524--1661555 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1661514 ACAATATTTA
1661524 TAATATATATATATATC
1 TAATATATATA-ATATC
1661541 TAATATATATAATAT
1 TAATATATATAATAT
1661556 GAAGTTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATATATATAATATC
Found at i:1661571 original size:26 final size:25
Alignment explanation
Indices: 1661542--1661601 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
1661532 ATATATATCT
*
1661542 AATATATATA-ATATGAAGTTTTGAAA
1 AATATATATATATAT-AAGTTGTG-AA
*
1661568 AATATATAATATATATAGGTTGTGAA
1 AATATAT-ATATATATAAGTTGTGAA
1661594 AATATATA
1 AATATATA
1661602 GCTTTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 16 0.53
27 9 0.30
28 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (25 bp):
AATATATATATATATAAGTTGTGAA
Found at i:1661650 original size:42 final size:42
Alignment explanation
Indices: 1661560--1661660 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
1661550 TAATATGAAG
*
1661560 TTTTGAAAAATATATAATATATATAGGTTGTGAAAATATATAGC
1 TTTTGAAAAATATATAATATATAT--GTTGTGAAAACATATAGC
* * * *
1661604 TTTTGAAAACATATATAATGTATAT-TTTTGAAAACATATGGT
1 TTTTGAAAA-ATATATAATATATATGTTGTGAAAACATATAGC
1661646 TTTTG-AAAATATATA
1 TTTTGAAAAATATATA
1661661 GTTTTTAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
40 7 0.14
41 3 0.06
42 18 0.35
44 9 0.18
45 14 0.27
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.42
Consensus pattern (42 bp):
TTTTGAAAAATATATAATATATATGTTGTGAAAACATATAGC
Found at i:1661665 original size:16 final size:16
Alignment explanation
Indices: 1661624--1661675 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1661614 ATATATAATG
* *
1661624 TATATTTTTGAAAACA
1 TATAGTTTTGAAAATA
*
1661640 TATGGTTTTTGAAAATA
1 TATAG-TTTTGAAAATA
*
1661657 TATAGTTTTTAAAATA
1 TATAGTTTTGAAAATA
1661673 TAT
1 TAT
1661676 TTAGTATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (16 bp):
TATAGTTTTGAAAATA
Found at i:1661680 original size:18 final size:17
Alignment explanation
Indices: 1661578--1661675 Score: 72
Period size: 17 Copynumber: 5.4 Consensus size: 17
1661568 AATATATAAT
* *
1661578 ATATATAGGTTGTGAAA
1 ATATATAGTTTTTGAAA
*
1661595 ATATATAGCTTTTGAAAA
1 ATATATAGTTTTTG-AAA
1661613 CATATATAATGTATATTTTTGAAA
1 -ATATAT-A-G----TTTTTGAAA
* *
1661637 ACATATGGTTTTTGAAA
1 ATATATAGTTTTTGAAA
1661654 ATATATAGTTTTT-AAA
1 ATATATAGTTTTTGAAA
1661670 ATATAT
1 ATATAT
1661676 TTAGTATATA
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
16 9 0.14
17 32 0.48
18 3 0.05
19 6 0.09
20 1 0.02
21 2 0.03
23 5 0.08
24 3 0.05
25 5 0.08
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.43
Consensus pattern (17 bp):
ATATATAGTTTTTGAAA
Found at i:1669058 original size:29 final size:29
Alignment explanation
Indices: 1669014--1669073 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
1669004 AAGAAACCTA
*
1669014 GACGGTTTGGCGATGAACCACC-AGACGGC
1 GACGGTTTGGCAATGAACCACCGA-ACGGC
1669043 GACGGTTTGGCAATGAACCACCGAACGGC
1 GACGGTTTGGCAATGAACCACCGAACGGC
1669072 GA
1 GA
1669074 TGGTCTGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.13
Consensus pattern (29 bp):
GACGGTTTGGCAATGAACCACCGAACGGC
Found at i:1669483 original size:15 final size:15
Alignment explanation
Indices: 1669444--1669484 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1669434 ATATTTTGAG
1669444 TATGTGTTATTTGGA
1 TATGTGTTATTTGGA
*
1669459 TATTTGTTATTTGGA
1 TATGTGTTATTTGGA
*
1669474 TATGTATTATT
1 TATGTGTTATT
1669485 CAAATCGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.59
Consensus pattern (15 bp):
TATGTGTTATTTGGA
Found at i:1680834 original size:52 final size:52
Alignment explanation
Indices: 1680775--1680873 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
1680765 GCGAGTTCTT
* *
1680775 CTGGAAATATTGATCCAATGTTGAACAAGTTCTTCTCATTATGAACTCTCCA
1 CTGGAAATATTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTCTCCA
* *
1680827 CTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTTTCATTATGAACT
1 CTGGAAATATTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACT
1680874 TCTTCTCCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (52 bp):
CTGGAAATATTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTCTCCA
Found at i:1681191 original size:91 final size:91
Alignment explanation
Indices: 1681049--1681762 Score: 1184
Period size: 91 Copynumber: 7.9 Consensus size: 91
1681039 GAAACAAGTT
*
1681049 AAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
1681114 GAACTCTCCACTGGAAATGATGAACC
66 GAACTCTCCACTGGAAATGATGAACC
* * *
1681140 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGAATGAGTTCTCCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
* *
1681205 GAACTCTCCACTGGAAATGTTGAGCC
66 GAACTCTCCACTGGAAATGATGAACC
* * *
1681231 AAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAATTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
1681296 GAACTCTCCACTGGAAATGATGAACC
66 GAACTCTCCACTGGAAATGATGAACC
* *
1681322 AAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
*
1681387 GAACTCTCCACTGGAAATGATGAACT
66 GAACTCTCCACTGGAAATGATGAACC
*
1681413 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
* *
1681478 GAACTCTCCACTGGAAATGCTGAGCC
66 GAACTCTCCACTGGAAATGATGAACC
1681504 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
*
1681569 GAACTCTCCACTGGAAATG-TCGAGCC
66 GAACTCTCCACTGGAAATGAT-GAACC
* * *
1681595 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCATCGTTGGATGAGTTCTTCTCATTTT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
* *
1681660 GAACTCTCCACTGGAAATGTTGATCC
66 GAACTCTCCACTGGAAATGATGAACC
*
1681686 AAGGTTGAACAAGTTCTTCTCATTATGAA---CTTCTCCCTCGTTGGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
*
1681748 GAACTCTCAACTGGA
66 GAACTCTCCACTGGA
1681763 TATGTTGATC
Statistics
Matches: 585, Mismatches: 36, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
88 43 0.07
90 1 0.00
91 540 0.92
92 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (91 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGATGAACC
Found at i:1682142 original size:37 final size:36
Alignment explanation
Indices: 1682086--1682258 Score: 135
Period size: 36 Copynumber: 4.9 Consensus size: 36
1682076 CAAAGATTGA
1682086 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGAC-AAACTT
** *
1682123 TGTTTCAAGGGAATTTGTCTCAAGGGAGACAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAACTT
* **
1682159 TATTTCAAGGGAAACTGGT-TCAA---AG---ATTTT
1 TGTTTCAAGGGAAACT-GTCTCAAGGGAGACAAACTT
* * ** *
1682189 GTGTTTCAAGAGAAAATGTCTCAAGCAAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAACTT
* * * *
1682226 TGTTTTAAGTGAAACTGTTTCAAGAGAGACAAA
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAA
1682259 ACTGGTTTCG
Statistics
Matches: 109, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
30 6 0.06
31 17 0.16
33 2 0.02
34 2 0.02
36 49 0.45
37 33 0.30
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAACTT
Found at i:1682240 original size:67 final size:67
Alignment explanation
Indices: 1682123--1682248 Score: 162
Period size: 67 Copynumber: 1.9 Consensus size: 67
1682113 GACAAAACTT
* ** ** *
1682123 TGTTTCAAGGGAATTTGTCTCAAGGGAGACAAATTTTATTTCAAGGGAAACTGGTTCAAAGATTT
1 TGTTTCAAGAGAAAATGTCTCAAGCAAGACAAAATTTATTTCAAGGGAAACTGGTTCAAAGATTT
1682188 TG
66 TG
* * * *
1682190 TGTTTCAAGAGAAAATGTCTCAAGCAAGACAAAATTTGTTTTAAGTGAAACTGTTTCAA
1 TGTTTCAAGAGAAAATGTCTCAAGCAAGACAAAATTTATTTCAAGGGAAACTGGTTCAA
1682249 GAGAGACAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
67 49 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (67 bp):
TGTTTCAAGAGAAAATGTCTCAAGCAAGACAAAATTTATTTCAAGGGAAACTGGTTCAAAGATTT
TG
Found at i:1682249 original size:36 final size:36
Alignment explanation
Indices: 1682190--1682339 Score: 115
Period size: 36 Copynumber: 4.0 Consensus size: 36
1682180 AAAGATTTTG
1682190 TGTTTCAAGAGAAAATGTCTCAAGCA-AGACAAAATT
1 TGTTTCAAGAGAAAATGTCTCAAG-AGAGACAAAATT
* * * * *
1682226 TGTTTTAAGTGAAACTGTTTCAAGAGAGACAAAACT
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATT
* * *
1682262 GGTTTCGAGTA-AAAATTGTCTCAAGTGAGACAAAATT
1 TGTTTCAAG-AGAAAA-TGTCTCAAGAGAGACAAAATT
** * *
1682299 CATGTTTTTTAGAGAAAATAATCTCAAGTGAGACAAAATT
1 --TG-TTTCAAGAGAAAAT-GTCTCAAGAGAGACAAAATT
1682339 T
1 T
1682340 ATTCTTAGGA
Statistics
Matches: 89, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
35 1 0.01
36 38 0.43
37 18 0.20
38 1 0.01
39 3 0.03
40 28 0.31
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATT
Found at i:1682249 original size:103 final size:103
Alignment explanation
Indices: 1682055--1682258 Score: 259
Period size: 103 Copynumber: 2.0 Consensus size: 103
1682045 ATAAAATTTC
* * * **
1682055 TTATTTCGAGGGAAACAGATTCAAAGATTGATGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTATTTCAAGGGAAACAGATTCAAAGATTGATGTTTCAAGAGAAAATGTCTCAAGCAAGACAAAA
** *
1682120 CTTTGTTTCAAGGGAATTTGTCTCAAGGGAGACAAATT
66 CTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATT
* *
1682158 TTATTTCAAGGGAAACTGGTTCAAAGATTTTG-TGTTTCAAGAGAAAATGTCTCAAGCAAGACAA
1 TTATTTCAAGGGAAACAGATTCAAAGA--TTGATGTTTCAAGAGAAAATGTCTCAAGCAAGACAA
* * *
1682222 AA-TTTGTTTTAAGTGAAACTGTTTCAAGAGAGACAAA
64 AACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1682259 ACTGGTTTCG
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
103 53 0.62
104 30 0.35
105 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (103 bp):
TTATTTCAAGGGAAACAGATTCAAAGATTGATGTTTCAAGAGAAAATGTCTCAAGCAAGACAAAA
CTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATT
Found at i:1682848 original size:39 final size:39
Alignment explanation
Indices: 1682788--1683232 Score: 388
Period size: 39 Copynumber: 11.9 Consensus size: 39
1682778 TTAGTTTCTT
1682788 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* *
1682827 ATAAAATCTTCTATTTTGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
1682866 ACAAAATATTCTGTTTCTAGGGAAACTATCTCGAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * *
1682905 ATAAAATCTTCTGTTTCTAGGGAAACTATCTCGAGCGAC
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* *
1682944 ACAAAATCTTCTGTTTCGAGGGAAAATATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
1682983 ATAAAGTCTTCTGTTTCGAGTGAAACTGTCTCAAGGGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * * *
1683022 ACAAAA--TT-TGTTTCAAGGGAGACTGTCTCAAGGGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
1683058 ACAAAA-C-T-TGTTTCAAGGGAAACTGTCTCAAGAGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
1683094 ACAAAA--TT-TGTTTCAAGGGAAACTGTCTCAAGGGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
1683130 ACAAAAT-TTCT-TTT-AAGAGAAACTGTCTCAAG-G-G
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * * *
1683164 ATACAAAAC-T-TGTTTCAAGGGAAACTGTCTCAGGAGAG
1 ATA-AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * *
1683202 ACAAAA--TT-TGTTTCAAGGGAAACTGTCTCAA
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAA
1683233 AGGAGACTGT
Statistics
Matches: 358, Mismatches: 37, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
34 4 0.01
35 8 0.02
36 154 0.43
37 11 0.03
38 4 0.01
39 177 0.49
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (39 bp):
ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
Found at i:1682995 original size:117 final size:115
Alignment explanation
Indices: 1682790--1683239 Score: 478
Period size: 108 Copynumber: 4.0 Consensus size: 115
1682780 AGTTTCTTAT
* * * *
1682790 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTATTTTGAGGGAAACTA
1 AAAAT-TTCTGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* * * * *
1682855 TCTCAAGCGAGACAAAATATTCTGTTTCTAGGGAAACTATCTCGAGCGAGAT
65 TCTCAAGCGAGAC-AAATATTCTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
* * * *
1682907 AAAATCTTCTGTTTCTAGGGAAACTATCTCGAGCGACACAAAATCTTCTGTTTCGAGGGAAAATA
1 AAAAT-TTCTGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* * * *
1682972 TCTCAAGCGAGATAAAGTCTTCTGTTTCGAGTGAAACTGTCTCAAGGGAGAC
65 TCTCAAGCGAGACAAA-TATTCTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
* * * * *
1683024 AAAA-TT-TGTTTCAAGGGAGACTGTCTCAAGGGAGACAAAA-C-T-TGTTTCAAGGGAAACTGT
1 AAAATTTCTGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTAT
*
1683084 CTCAAGAGAGACAAA-ATT-TGTTTCAAGGGAAACTGTCTCAAGGGAGAC
66 CTCAAGCGAGACAAATATTCTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
* * * * * *
1683132 AAAATTTCT-TTT-AAGAGAAACTGTCTCAAGGGATACAAAA-C-T-TGTTTCAAGGGAAACTGT
1 AAAATTTCTGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTAT
* * *
1683192 CTCAGGAGAGACAAA-ATT-TGTTTCAAGGGAAACTGTCTCAAAGGAGAC
66 CTCAAGCGAGACAAATATTCTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
1683240 TGTCTCAAGG
Statistics
Matches: 296, Mismatches: 34, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
108 123 0.42
109 7 0.02
110 1 0.00
111 28 0.09
112 1 0.00
113 1 0.00
114 28 0.09
115 2 0.01
116 3 0.01
117 102 0.34
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (115 bp):
AAAATTTCTGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTAT
CTCAAGCGAGACAAATATTCTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
Found at i:1683039 original size:21 final size:20
Alignment explanation
Indices: 1683013--1683113 Score: 69
Period size: 21 Copynumber: 5.4 Consensus size: 20
1683003 TGAAACTGTC
1683013 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAA-TTGTT
*
1683034 TCAAGGGAGAC-----TGTC
1 TCAAGGGAGACAAAATTGTT
1683049 TCAAGGGAGACAAAACTTGTT
1 TCAAGGGAGACAAAA-TTGTT
* *
1683070 TCAA-GG-G---AAACTGTC
1 TCAAGGGAGACAAAATTGTT
*
1683085 TCAAGAGAGACAAAATTTGTT
1 TCAAGGGAGACAAAA-TTGTT
1683106 TCAAGGGA
1 TCAAGGGA
1683114 AACTGTCTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 24
0.65 0.09 0.26
Matches are distributed among these distances:
15 21 0.35
16 4 0.07
17 1 0.02
19 1 0.02
20 5 0.08
21 28 0.47
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.24
Consensus pattern (20 bp):
TCAAGGGAGACAAAATTGTT
Found at i:1683047 original size:36 final size:36
Alignment explanation
Indices: 1682799--1683423 Score: 430
Period size: 36 Copynumber: 17.0 Consensus size: 36
1682789 TAAAATCTTC
* * * *
1682799 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA--TT
* ** * *
1682837 CTATTTTGAGGGAAACTATCTCAAGCGAGACAAAATATT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGAC-AAA-ATT
* * * * *
1682876 CTGTTTCTAGGGAAACTATCTCGAGCGAGATAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA--TT
* * * * *
1682915 CTGTTTCTAGGGAAACTATCTCGAGCGACACAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA--TT
* * * * * *
1682954 CTGTTTCGAGGGAAAATATCTCAAGCGAGATAAAGTCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAA--ATT
* *
1682993 CTGTTTCGAGTGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* *
1683030 TGTTTCAAGGGAGACTGTCTCAAGGGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
*
1683066 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
1683102 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* * * * *
1683138 TCTTTTAAGAGAAACTGTCTCAAGGGATACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
1683174 TGTTTCAAGGGAAACTGTCTC-AGGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGG-GAGACAAAATT
*
1683210 TGTTTCAAGGGAAACTGTCTCAAAGGAGAC------
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* * * *
1683240 TGTCTCAAGGGAGACAAAATTTGTTTCAA-GG-G---AAA-C
1 TGTTTCAA-GG-G---AAA-CTGTCTCAAGGGAGACAAAATT
* * *
1683276 TGTCTCAAAGGAGACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
**
1683312 TGTTTCAAGGGAAACTGTCTCAAGGGAGACATATTTTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACA-A-AATT
* * * **
1683350 TGTTTCGAGTGAAACTATCTCAAACGAGACAAAATCTTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA---TT
* * * *
1683389 TGTTTCTAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
1683424 CTTCTTTAAA
Statistics
Matches: 492, Mismatches: 65, Indels: 61
0.80 0.11 0.10
Matches are distributed among these distances:
30 14 0.03
31 6 0.01
32 2 0.00
34 2 0.00
35 12 0.02
36 228 0.46
37 7 0.01
38 31 0.06
39 186 0.38
40 3 0.01
41 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
Found at i:1683241 original size:15 final size:15
Alignment explanation
Indices: 1683214--1683305 Score: 85
Period size: 15 Copynumber: 5.7 Consensus size: 15
1683204 AAAATTTGTT
*
1683214 TCAAGGGAAACTGTC
1 TCAAGGGAGACTGTC
*
1683229 TCAAAGGAGACTGTC
1 TCAAGGGAGACTGTC
*
1683244 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGAC------TGTC
*
1683265 TCAAGGGAAACTGTC
1 TCAAGGGAGACTGTC
*
1683280 TCAAAGGAGACTGTC
1 TCAAGGGAGACTGTC
1683295 TCAAGGGAGAC
1 TCAAGGGAGAC
1683306 AAAATTTGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
15 49 0.79
21 13 0.21
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (15 bp):
TCAAGGGAGACTGTC
Found at i:1683329 original size:87 final size:87
Alignment explanation
Indices: 1683106--1683379 Score: 247
Period size: 87 Copynumber: 3.1 Consensus size: 87
1683096 AAAATTTGTT
* * * * * *
1683106 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTCTTTTAAGAGAAACTGTCTCAAGGGATACAAA
1 TCAAAGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAA
*
1683171 ACTTGTTTCAAGGGAAACTGTC
66 ATTTGTTTCAAGGGAAACTGTC
* * * * * *
1683193 TC-AGGAGAGACAAAATTTGTTTCAA-GG-G---AAA-CTGTCTCAAAGGAGACTGTCTCAAGGG
1 TCAAAG-GAGAC------TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGG
1683251 AGACAAAATTTGTTTCAAGGGAAACTGTC
59 AGACAAAATTTGTTTCAAGGGAAACTGTC
1683280 TCAAAGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACATA
1 TCAAAGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACA-A
** * * *
1683345 TTTTTTGTTTCGAGTGAAACTATC
65 -AATTTGTTTCAAGGGAAACTGTC
*
1683369 TCAAACGAGAC
1 TCAAAGGAGAC
1683380 AAAATCTTTT
Statistics
Matches: 148, Mismatches: 23, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
81 7 0.05
82 2 0.01
83 1 0.01
86 6 0.04
87 88 0.59
88 6 0.04
89 28 0.19
91 1 0.01
92 2 0.01
93 7 0.05
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (87 bp):
TCAAAGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAA
ATTTGTTTCAAGGGAAACTGTC
Found at i:1683340 original size:51 final size:51
Alignment explanation
Indices: 1683061--1683341 Score: 289
Period size: 51 Copynumber: 5.4 Consensus size: 51
1683051 AAGGGAGACA
* * *
1683061 AAACTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
1 AAAC-TGTCTCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGG
** * ***** * * *
1683113 AAACTGTCTCAAGGGAGACAAAATTTCTTTTAAGA-GAAA-CTGTCTCAAGGG
1 AAACTGTCTCAAGGGAGAC--TGTCTCAAGGGAGACAAAATTTGTTTCAAGGG
* *
1683164 ATACAAAACTTGTTTCAAGGGAAACTGTCTC-AGGAGAGACAAAATTTGTTTCAAGGG
1 -----AAAC-TGTCTCAAGGGAGACTGTCTCAAGG-GAGACAAAATTTGTTTCAAGGG
*
1683221 AAACTGTCTCAAAGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGG
1 AAACTGTCTCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGG
*
1683272 AAACTGTCTCAAAGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGG
1 AAACTGTCTCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGG
1683323 AAACTGTCTCAAGGGAGAC
1 AAACTGTCTCAAGGGAGAC
1683342 ATATTTTTTG
Statistics
Matches: 188, Mismatches: 29, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
51 132 0.70
52 14 0.07
53 6 0.03
55 6 0.03
56 7 0.04
57 23 0.12
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (51 bp):
AAACTGTCTCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGG
Found at i:1683403 original size:39 final size:39
Alignment explanation
Indices: 1683293--1683426 Score: 150
Period size: 39 Copynumber: 3.5 Consensus size: 39
1683283 AAGGAGACTG
* *
1683293 TCTCAAGGGAGACAAAA---TTTGTTTCAAGGGAAACTG
1 TCTCAAGCGAGACAAAATCTTTTGTTTCAAGGGAAACTA
* * * * *
1683329 TCTCAAGGGAGAC-ATATTTTTTGTTTCGAGTGAAACTA
1 TCTCAAGCGAGACAAAATCTTTTGTTTCAAGGGAAACTA
* *
1683367 TCTCAAACGAGACAAAATCTTTTGTTTCTAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTTTGTTTCAAGGGAAACTA
*
1683406 TCTCAAGCGAGATAAAATCTT
1 TCTCAAGCGAGACAAAATCTT
1683427 CTTTAAAAAC
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
35 2 0.02
36 13 0.16
38 27 0.33
39 40 0.49
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (39 bp):
TCTCAAGCGAGACAAAATCTTTTGTTTCAAGGGAAACTA
Found at i:1684918 original size:9 final size:9
Alignment explanation
Indices: 1684891--1684934 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1684881 TTTACTTCAC
*
1684891 TTTTCCTTT
1 TTTTTCTTT
*
1684900 TTTCTACTTT
1 TTT-TTCTTT
1684910 TTTTTCTTT
1 TTTTTCTTT
1684919 TTTTTCTTT
1 TTTTTCTTT
*
1684928 TTATTCT
1 TTTTTCT
1684935 GATTAGACCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Done.