Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008292.1 Hibiscus syriacus cultivar Beakdansim tig00110956_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: 1591938
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 8 of 8
Found at i:1463807 original size:19 final size:20
Alignment explanation
Indices: 1463770--1463807 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1463760 GTTTCGAGTG
* *
1463770 TAGGATTTAGGGGTTTAAAT
1 TAGGACTTAGGGGTATAAAT
1463790 TAGGACTTA-GGGTATAAA
1 TAGGACTTAGGGGTATAAA
1463808 ATGTTGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (20 bp):
TAGGACTTAGGGGTATAAAT
Found at i:1467242 original size:24 final size:24
Alignment explanation
Indices: 1467214--1467296 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
1467204 TCAGAAATGA
1467214 AACAGAATTCAGATAAGATATCAG
1 AACAGAATTCAGATAAGATATCAG
* * * *
1467238 AACAGAATCCAGATCAGAAATCAT
1 AACAGAATTCAGATAAGATATCAG
*
1467262 AACAGAATTCAGGTAATG-TATCAG
1 AACAGAATTCAGATAA-GATATCAG
*
1467286 AACAAAATTCA
1 AACAGAATTCA
1467297 AGTCGGAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 47 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.20
Consensus pattern (24 bp):
AACAGAATTCAGATAAGATATCAG
Found at i:1467306 original size:48 final size:48
Alignment explanation
Indices: 1467203--1467308 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
1467193 AAACGGAGAT
* * *
1467203 ATCAGAAATGA-AACAGAATTCAGATAAGATATCAGAACAGAATCCAG
1 ATCAGAAATCATAACAGAATTCAGATAAGATATCAGAACAAAATCAAG
*
1467250 ATCAGAAATCATAACAGAATTCAGGTAATG-TATCAGAACAAAATTCAAG
1 ATCAGAAATCATAACAGAATTCAGATAA-GATATCAGAACAAAA-TCAAG
*
1467299 -TCGGAAATCA
1 ATCAGAAATCA
1467309 AATAAAATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
47 10 0.20
48 36 0.71
49 5 0.10
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCATAACAGAATTCAGATAAGATATCAGAACAAAATCAAG
Found at i:1470214 original size:23 final size:23
Alignment explanation
Indices: 1470166--1470223 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
1470156 TATTATATGA
* **
1470166 CACTACGGTGCAATTCTACGTGG
1 CACTATGGTGCAATTCTACGCAG
1470189 CACTATGGTGCAATTCTACGCAG
1 CACTATGGTGCAATTCTACGCAG
1470212 CACT-TCGGTGCA
1 CACTAT-GGTGCA
1470224 TTTATACGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (23 bp):
CACTATGGTGCAATTCTACGCAG
Found at i:1475166 original size:25 final size:26
Alignment explanation
Indices: 1475138--1475193 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1475128 TACAACTCTT
* * *
1475138 TTAATGAATATTTAATTT-GGAATAG
1 TTAAAGAAGATTTAATTTCGGAATAA
*
1475163 TTAAAGAAGATTTTATTTCGGAATAA
1 TTAAAGAAGATTTAATTTCGGAATAA
1475189 TTAAA
1 TTAAA
1475194 ATAAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (26 bp):
TTAAAGAAGATTTAATTTCGGAATAA
Found at i:1481883 original size:16 final size:17
Alignment explanation
Indices: 1481864--1481910 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
1481854 AAATTAAAAA
1481864 TATTAAATT-TTCATTT
1 TATTAAATTATTCATTT
1481880 TATTAATTAATTATTCATTT
1 TATT-A--AATTATTCATTT
*
1481900 TAATAAATTAT
1 TATTAAATTAT
1481911 AAAAATCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.15
17 7 0.27
19 5 0.19
20 10 0.38
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTAAATTATTCATTT
Found at i:1482328 original size:37 final size:38
Alignment explanation
Indices: 1482253--1482330 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
1482243 AACTTGAACT
1482253 CGACCCGACCCGAATATCACACTTAAAAAAACCCGACC
1 CGACCCGACCCGAATATCACACTTAAAAAAACCCGACC
*
1482291 CGACTCGACCCGAATATCACACTT-AAAAAACCCGACC
1 CGACCCGACCCGAATATCACACTTAAAAAAACCCGACC
1482328 CGA
1 CGA
1482331 ACAAAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 16 0.41
38 23 0.59
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (38 bp):
CGACCCGACCCGAATATCACACTTAAAAAAACCCGACC
Found at i:1482732 original size:254 final size:251
Alignment explanation
Indices: 1482201--1483051 Score: 1205
Period size: 248 Copynumber: 3.4 Consensus size: 251
1482191 TATAAGGTAA
*
1482201 AATTATATATATTTTTCGGGTCGGTCCCG-TTTTTTCACCCTAAACTTGAACTCG-ACCCGACCC
1 AATTATATATA-TTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAAC-----C-CGAACCCGACCC
1482264 GAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAA-C-CCGAC
59 GAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCACCGAC
*
1482327 CCGAACAAAATAAAGTTTCAT-----CCGACCCTAATATATGAATTAGAAA-T----CCGACCCG
124 CCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATTCGACCCGACCCG
*
1482382 ACCCGAAATAATAAAAAATTAATTTTATTTAATAAAAACAGTGACTTAATCCAACTCGACCCGAC
189 ACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAAT----C-CGACCCGAC
1482447 CCG
249 CCG
* *
1482450 AATTATATATATTTTCGAGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCTGAATATC
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGAATATC
*
1482515 ACACTTAAAAAAACCCGACCCGACTCGATCCGAATATCACACTTAAAAAACCTGACTCGACCCGA
66 ACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACC--AC-CGACCCGA
1482580 ACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATTCGACCCGACCCGACCC
128 ACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATTCGACCCGACCCGACCC
* *
1482645 TAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
193 GAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
*
1482704 AATTATATATATTTTCGGGTCAGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGAATATC
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGAATATC
*
1482769 ACACTTAAAAAAA-CCGACCCGACTCGCCCCGAATATCACACTTAAAAAACCA--GACCCGAACA
66 ACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCACCGACCCGAACA
* * * * * *
1482831 AAATAAAATTTCATCCGACCCAAACCGAATATATGAATTAGAAATCCGACCCGACCTGACTCGAA
131 AAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATTCGACCCGACCCGACCCGAA
* *
1482896 ATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGGCCTG
196 ATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
*
1482952 AATTATATATATCTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCAACCCGA
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCG-----ACCCGA
* * *
1483017 ATATCACACTTAAAAAAACTCGATCCGACCCGACC
61 ATATCACACTTAAAAAAACCCGACCCGACTCGACC
1483052 AAAATAAACT
Statistics
Matches: 550, Mismatches: 29, Indels: 41
0.89 0.05 0.07
Matches are distributed among these distances:
243 2 0.00
244 65 0.12
245 1 0.00
248 189 0.34
249 52 0.09
251 1 0.00
253 60 0.11
254 123 0.22
255 2 0.00
259 55 0.10
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.24
Consensus pattern (251 bp):
AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGAATATC
ACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCACCGACCCGAACA
AAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATTCGACCCGACCCGACCCGAA
ATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
Found at i:1482789 original size:32 final size:33
Alignment explanation
Indices: 1482753--1482827 Score: 91
Period size: 37 Copynumber: 2.2 Consensus size: 33
1482743 CTAAACCCGA
1482753 ACCCGA-CCCGAATATCACACTTAAAAAAACC-G
1 ACCCGACCCCGAATATCACACTT-AAAAAACCAG
1482785 ACCCGACTCGCCCCGAATATCACACTTAAAAAACCAG
1 ACCCGA----CCCCGAATATCACACTTAAAAAACCAG
1482822 ACCCGA
1 ACCCGA
1482828 ACAAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
32 6 0.16
36 8 0.22
37 23 0.62
ACGTcount: A:0.40, C:0.37, G:0.11, T:0.12
Consensus pattern (33 bp):
ACCCGACCCCGAATATCACACTTAAAAAACCAG
Found at i:1484734 original size:14 final size:14
Alignment explanation
Indices: 1484715--1484744 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1484705 TTTTAATTTT
1484715 ACTCTTTAGATTCG
1 ACTCTTTAGATTCG
1484729 ACTCTTTAGATTCG
1 ACTCTTTAGATTCG
1484743 AC
1 AC
1484745 GTAATTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (14 bp):
ACTCTTTAGATTCG
Found at i:1488166 original size:2 final size:2
Alignment explanation
Indices: 1488159--1488189 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1488149 TAAATTTTAC
1488159 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1488190 TGGTATAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1488596 original size:19 final size:19
Alignment explanation
Indices: 1488572--1488608 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1488562 TATTATGTTA
*
1488572 ATTAAATTAATAAAATAAT
1 ATTAAATTAAAAAAATAAT
1488591 ATTAAATTAAAAAAATAA
1 ATTAAATTAAAAAAATAA
1488609 ATAAAGTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTAAATTAAAAAAATAAT
Found at i:1488981 original size:16 final size:16
Alignment explanation
Indices: 1488960--1488990 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1488950 AATAAATAAA
1488960 GAACATAAACGAACAC
1 GAACATAAACGAACAC
1488976 GAACATAAACGAACA
1 GAACATAAACGAACA
1488991 ATTTTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:1489081 original size:23 final size:23
Alignment explanation
Indices: 1489023--1489113 Score: 94
Period size: 23 Copynumber: 3.9 Consensus size: 23
1489013 CATTTAAATG
* *
1489023 ATAAACGAACGTAAACGAAGACA
1 ATAAACGAACATAAACGAACACA
* *
1489046 A-ACGAACGAACATAAACGGACATA
1 ATA--AACGAACATAAACGAACACA
* *
1489070 ATAAATGAACATAAATGAACACA
1 ATAAACGAACATAAACGAACACA
*
1489093 ATAAACGAACATAAACAAACA
1 ATAAACGAACATAAACGAACA
1489114 ACACAAACAC
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
22 1 0.02
23 35 0.65
24 17 0.31
25 1 0.02
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.11
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACACA
Found at i:1489413 original size:14 final size:14
Alignment explanation
Indices: 1489386--1489427 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1489376 GAACATAAAT
*
1489386 GAACATAAATGAAC
1 GAACATAAACGAAC
*
1489400 GAATATAAACGAAC
1 GAACATAAACGAAC
*
1489414 GAACCTAAACGAAC
1 GAACATAAACGAAC
1489428 ATATAATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.55, C:0.19, G:0.14, T:0.12
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:1489690 original size:14 final size:14
Alignment explanation
Indices: 1489671--1489698 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1489661 TCCCTTTAAC
1489671 TTTATTAATAATAA
1 TTTATTAATAATAA
1489685 TTTATTAATAATAA
1 TTTATTAATAATAA
1489699 AACAATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTATTAATAATAA
Found at i:1491662 original size:2 final size:2
Alignment explanation
Indices: 1491655--1491721 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
1491645 TTGTTTCTTT
1491655 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
1491697 TC TC TC TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1491722 TTTTAATTAC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1495267 original size:2 final size:2
Alignment explanation
Indices: 1495255--1495284 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1495245 AAAATTAAAA
1495255 AT AT AT A- 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 A
1495285 ATTTTCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1501513 original size:20 final size:20
Alignment explanation
Indices: 1501488--1501528 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1501478 GTCTGATAAA
*
1501488 TATTATCCACAATCATAGGT
1 TATTATCCACAATCAAAGGT
*
1501508 TATTATCCATAATCAAAGGT
1 TATTATCCACAATCAAAGGT
1501528 T
1 T
1501529 GCCGTAGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (20 bp):
TATTATCCACAATCAAAGGT
Found at i:1505995 original size:63 final size:62
Alignment explanation
Indices: 1505904--1506063 Score: 205
Period size: 63 Copynumber: 2.5 Consensus size: 62
1505894 TTGTTTAAGG
* * *
1505904 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATA-GGAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTA
* *
1505968 TGCATCGATGCATAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAGGAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTA
*
1506031 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAG-G-AGTGCATCGATGCAT
1506064 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
63 49 0.57
64 21 0.24
65 16 0.19
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (62 bp):
TGCATCGATGCATAGGAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTA
Found at i:1506576 original size:18 final size:18
Alignment explanation
Indices: 1506553--1506587 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1506543 CTAGGAGATT
1506553 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1506571 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1506588 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1506721 original size:2 final size:2
Alignment explanation
Indices: 1506714--1506739 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1506704 CAGATTAGAT
1506714 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1506740 AAGAAATAAT
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):
TA
Found at i:1507660 original size:147 final size:144
Alignment explanation
Indices: 1507489--1507796 Score: 489
Period size: 149 Copynumber: 2.1 Consensus size: 144
1507479 GAGTCGAGGG
**
1507489 TCTACGCGGTCCTTCGGGATATATATAT-TTCT-TGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
1507552 A-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 ACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGG----T-TGGACATCATT
1507616 ATATGGCACTACGGTGCAAT
125 ATATGGCACTACGGTGCAAT
*
1507636 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
1507701 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTTGGACATTATTATATGG
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTTGGACATCATTATATGG
1507766 CACTACGGTGCAAT
131 CACTACGGTGCAAT
1507780 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1507797 TGCAATTATA
Statistics
Matches: 153, Mismatches: 4, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
143 1 0.01
144 45 0.29
145 1 0.01
147 28 0.18
148 4 0.03
149 73 0.48
150 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (144 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTTGGACATCATTATATGG
CACTACGGTGCAAT
Found at i:1507797 original size:23 final size:23
Alignment explanation
Indices: 1507764--1507808 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1507754 ATTATTATAT
*
1507764 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1507787 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1507809 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1513517 original size:23 final size:23
Alignment explanation
Indices: 1513487--1513530 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1513477 TGTACTTCTG
*
1513487 TGCTGAATCATTCAGCACTGATT
1 TGCTGAATCAGTCAGCACTGATT
1513510 TGCTGAATCAGTCAGCACTGA
1 TGCTGAATCAGTCAGCACTGA
1513531 ATCATTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (23 bp):
TGCTGAATCAGTCAGCACTGATT
Found at i:1518625 original size:14 final size:14
Alignment explanation
Indices: 1518603--1518644 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1518593 ATTAGTTATA
1518603 TTTTAATTAAAATG
1 TTTTAATTAAAATG
*
1518617 TTTTTATT-AAA--
1 TTTTAATTAAAATG
1518628 TTTTAATTAAAATG
1 TTTTAATTAAAATG
1518642 TTT
1 TTT
1518645 AAACATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
11 7 0.30
12 3 0.13
13 3 0.13
14 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (14 bp):
TTTTAATTAAAATG
Found at i:1518645 original size:13 final size:13
Alignment explanation
Indices: 1518604--1518646 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1518594 TTAGTTATAT
1518604 TTTAATTAAAATG
1 TTTAATTAAAATG
*
1518617 TTTTTATT-AAAT-
1 -TTTAATTAAAATG
1518629 TTTAATTAAAATG
1 TTTAATTAAAATG
1518642 TTTAA
1 TTTAA
1518647 ACATTCTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 9 0.36
14 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (13 bp):
TTTAATTAAAATG
Found at i:1519857 original size:64 final size:64
Alignment explanation
Indices: 1519772--1519935 Score: 188
Period size: 67 Copynumber: 2.5 Consensus size: 64
1519762 TTATTTAAGG
* * *
1519772 TGCATCGATGCACATACAGTGCATCGATGCATGAAT-TTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAAGAGTGCATCGATGCATGAATCTTAAATA-AAAACATCGAATAGGATTTA
* *
1519836 TGCATCGATGCATAAAGAGTGCATCGATG-ATGCATCCCCATTAAATACAAACATCGAATAGGAT
1 TGCATCGATGCATAAAGAGTGCATCGATGCATGAAT---C-TTAAATAAAAACATCGAATAGGAT
1519900 TTA
62 TTA
***
1519903 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAAG-AGTGCATCGATGCAT
1519936 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 5 0.06
64 26 0.31
67 33 0.39
68 19 0.22
69 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAAAGAGTGCATCGATGCATGAATCTTAAATAAAAACATCGAATAGGATTTA
Found at i:1520795 original size:2 final size:2
Alignment explanation
Indices: 1520788--1520853 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1520778 GAACATGTGA
1520788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1520830 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
1520854 GTCTAAGAGA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1521653 original size:149 final size:148
Alignment explanation
Indices: 1521396--1521701 Score: 495
Period size: 149 Copynumber: 2.1 Consensus size: 148
1521386 GAGTCGAGGG
* * * * * *
1521396 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* * *
1521461 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTAGGGACATTATTAT
1521526 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* *
1521544 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
*
1521609 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTAGGGACATTATTA
1521674 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
1521693 TCTACGCGG
1 TCTACGCGG
1521702 CACTTTGGTA
Statistics
Matches: 145, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
148 48 0.33
149 97 0.67
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTAGGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:1525102 original size:45 final size:44
Alignment explanation
Indices: 1525052--1525151 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 44
1525042 GCACATGCAG
*
1525052 TGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTA
* *
1525097 TGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTA
1525142 TGCATCGATG
1 TGCATCGATG
1525152 TATGGTGTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
45 42 0.84
46 7 0.14
47 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (44 bp):
TGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTA
Found at i:1526863 original size:149 final size:148
Alignment explanation
Indices: 1526592--1526905 Score: 504
Period size: 149 Copynumber: 2.1 Consensus size: 148
1526582 GAGTCGAGGG
* * * * * *
1526592 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
1526657 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTATTAT
1526722 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* *
1526740 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
*
1526805 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTATTA
1526870 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
1526889 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1526906 TGCAATTATA
Statistics
Matches: 153, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
148 49 0.32
149 104 0.68
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:1526906 original size:23 final size:23
Alignment explanation
Indices: 1526873--1526917 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1526863 ATTATTATAT
*
1526873 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1526896 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1526918 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1529873 original size:20 final size:20
Alignment explanation
Indices: 1529829--1529874 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1529819 GTATTAAGGA
1529829 ACATTTAGGATCATATAGAT
1 ACATTTAGGATCATATAGAT
* * *
1529849 GCATTTAGGATCATGTAGTT
1 ACATTTAGGATCATATAGAT
1529869 ACATTT
1 ACATTT
1529875 GGTGAGATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (20 bp):
ACATTTAGGATCATATAGAT
Found at i:1532228 original size:103 final size:103
Alignment explanation
Indices: 1532044--1532253 Score: 366
Period size: 103 Copynumber: 2.0 Consensus size: 103
1532034 GGGTCTACGC
*
1532044 GGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCATTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
1532109 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
* *
1532147 GGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACGTACTTGAT
1 GGTCATTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
1532212 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
1532250 GGTC
1 GGTC
1532254 CTTATGGACA
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCATTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:1532300 original size:23 final size:22
Alignment explanation
Indices: 1532273--1532340 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
1532263 ATTATTATAT
1532273 GGCACTATGGTGCAATTCTACGC
1 GGCACT-TGGTGCAATTCTACGC
* **
1532296 GGCACTCCGGTGCAATTCTACAT
1 GGCACT-TGGTGCAATTCTACGC
*
1532319 GGCACTTCGGTGCAATTATACG
1 GGCACTT-GGTGCAATTCTACG
1532341 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.26
Consensus pattern (22 bp):
GGCACTTGGTGCAATTCTACGC
Found at i:1537463 original size:183 final size:185
Alignment explanation
Indices: 1537136--1537505 Score: 618
Period size: 183 Copynumber: 2.0 Consensus size: 185
1537126 CAAAGAAGAA
1537136 TCTTGGTCACCATTTTCTGGACTATTTGGTCAGCTCGAAATAAAAAAAAAACCAGGAAGGGACTC
1 TCTTGGTCACCATTTTCTGGACTATTTGGTCAGCTCGAAAT-AAAAAAAAACCAGGAAGGGACTC
1537201 ACCAATCAGTTGAAGATGTAGCGAGAGTTATTTCCATATTCCTGAAAGAATGAGAAGATTCTGGT
65 ACCAATCAGTTGAAGATGTAGCGAGAGTTATTTCCATATTCCTGAAAGAATGAGAAGATTCTGGT
1537266 ATCTGTAAGCCATCATCCACCGCTATCACTTCATATGCATGGTAGCCCTCATCCCC
130 ATCTGTAAGCCATCATCCACCGCTATCACTTCATATGCATGGTAGCCCTCATCCCC
* *
1537322 TCTTGGTCACCATTTTCTGGACTATTTGGTCAGCTCGAAAT-AAAAAAATCCATGAAGGGACTCA
1 TCTTGGTCACCATTTTCTGGACTATTTGGTCAGCTCGAAATAAAAAAAAACCAGGAAGGGACTCA
* * * * *
1537386 CCAATCAGTTGAAGATGTAGCTAGAG-TGTTTCCATGTTCCTGAAAGAATTAGAAGCTTCTGGTA
66 CCAATCAGTTGAAGATGTAGCGAGAGTTATTTCCATATTCCTGAAAGAATGAGAAGATTCTGGTA
* * * *
1537450 TTTGTAAGCCATCATCCATCGCTATCACTTCATATGCATGGTAGCCTTTATCCCC
131 TCTGTAAGCCATCATCCACCGCTATCACTTCATATGCATGGTAGCCCTCATCCCC
1537505 T
1 T
1537506 GATTTGATCA
Statistics
Matches: 173, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
183 86 0.50
184 46 0.27
186 41 0.24
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (185 bp):
TCTTGGTCACCATTTTCTGGACTATTTGGTCAGCTCGAAATAAAAAAAAACCAGGAAGGGACTCA
CCAATCAGTTGAAGATGTAGCGAGAGTTATTTCCATATTCCTGAAAGAATGAGAAGATTCTGGTA
TCTGTAAGCCATCATCCACCGCTATCACTTCATATGCATGGTAGCCCTCATCCCC
Found at i:1538503 original size:14 final size:14
Alignment explanation
Indices: 1538484--1538549 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
1538474 ACCTAACTTA
1538484 AAACCCTAAATCAT
1 AAACCCTAAATCAT
*
1538498 AAACCCTAAATCTT
1 AAACCCTAAATCAT
* * *
1538512 AAACCATAACT-TT
1 AAACCCTAAATCAT
1538525 ACAACCTCTAAATCAT
1 A-AACC-CTAAATCAT
*
1538541 AAACTCTAA
1 AAACCCTAA
1538550 TTTAGGGTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
13 3 0.07
14 30 0.71
15 7 0.17
16 2 0.05
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.26
Consensus pattern (14 bp):
AAACCCTAAATCAT
Found at i:1538579 original size:14 final size:14
Alignment explanation
Indices: 1538547--1538584 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1538537 TCATAAACTC
*
1538547 TAATTTAGGGTTTA
1 TAATTAAGGGTTTA
1538561 TAATTAAGGGTTCTA
1 TAATTAAGGGTT-TA
1538576 -AATTAAGGG
1 TAATTAAGGG
1538585 CAGAGTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 20 0.91
15 2 0.09
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (14 bp):
TAATTAAGGGTTTA
Found at i:1539043 original size:16 final size:16
Alignment explanation
Indices: 1539022--1539054 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1539012 ATTTAAATTA
1539022 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1539038 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1539054 A
1 A
1539055 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1539135 original size:10 final size:10
Alignment explanation
Indices: 1539120--1539194 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1539110 CATTTAATAA
1539120 ATAAACGAAC
1 ATAAACGAAC
1539130 ATAAACGAAC
1 ATAAACGAAC
1539140 ----ACGAAC
1 ATAAACGAAC
1539146 ATAAACGAAC
1 ATAAACGAAC
** *
1539156 ACGAAC-ATAA
1 ATAAACGA-AC
1539166 ATGAACACGAAC
1 AT-AA-ACGAAC
1539178 ATAAACGAAC
1 ATAAACGAAC
1539188 ATAAACG
1 ATAAACG
1539195 TTGGAGGCCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1539145 original size:16 final size:16
Alignment explanation
Indices: 1539124--1539188 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1539114 TAATAAATAA
1539124 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1539140 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1539156 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1539172 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1539188 A
1 A
1539189 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1539955 original size:14 final size:14
Alignment explanation
Indices: 1539938--1539993 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1539928 AATGAACATA
*
1539938 AACGAACATAATCG
1 AACGAACATAACCG
1539952 AACGAACAT-A---
1 AACGAACATAACCG
*
1539962 AACGAACATAACCA
1 AACGAACATAACCG
1539976 AACGAACATAACCG
1 AACGAACATAACCG
1539990 AACG
1 AACG
1539994 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1539958 original size:24 final size:24
Alignment explanation
Indices: 1539918--1539992 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
1539908 GATTGTATTA
*
1539918 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1539942 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
1539966 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
1539990 AAC
1 AAC
1539993 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1558153 original size:20 final size:20
Alignment explanation
Indices: 1558125--1558162 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1558115 CAATCAAACA
1558125 TTTTATATAAATATTTTAAT
1 TTTTATATAAATATTTTAAT
* *
1558145 TTTTTTATAAATTTTTTA
1 TTTTATATAAATATTTTA
1558163 TGTAAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATATAAATATTTTAAT
Found at i:1565928 original size:22 final size:19
Alignment explanation
Indices: 1565885--1565930 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
1565875 TATTGTTTAA
1565885 ATTTT-TTAAAATTATTAT
1 ATTTTATTAAAATTATTAT
1565903 ATTTTATTAATAATTATAATAT
1 ATTTTATTAA-AATTAT--TAT
1565925 ATTTTA
1 ATTTTA
1565931 GATATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 6 0.25
22 9 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTATTAAAATTATTAT
Found at i:1565949 original size:20 final size:19
Alignment explanation
Indices: 1565885--1565949 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
1565875 TATTGTTTAA
1565885 ATTTTTTAA-AATTATTAT
1 ATTTTTTAATAATTATTAT
*
1565903 ATTTTATTAATAATTATAAT
1 ATTTT-TTAATAATTATTAT
* * *
1565923 ATATTTTAGATATTTTTTAT
1 ATTTTTTA-ATAATTATTAT
1565943 ATTTTTT
1 ATTTTTT
1565950 TACTGATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 5 0.13
19 7 0.18
20 26 0.68
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTTTAATAATTATTAT
Found at i:1567558 original size:17 final size:17
Alignment explanation
Indices: 1567528--1567562 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1567518 TTAATAAAAC
1567528 ATGTAAAAATATTTAAA
1 ATGTAAAAATATTTAAA
1567545 ATGTATAAAA-ATTTAAA
1 ATGTA-AAAATATTTAAA
1567562 A
1 A
1567563 ATTTCAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
ATGTAAAAATATTTAAA
Found at i:1570793 original size:21 final size:21
Alignment explanation
Indices: 1570769--1570812 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1570759 CAAAGTTAAC
*
1570769 GGTTAACGGTCAACGA-TCAAT
1 GGTTAACAGTCAA-GAGTCAAT
1570790 GGTTAACAGTCAAGAGTCAAT
1 GGTTAACAGTCAAGAGTCAAT
1570811 GG
1 GG
1570813 GTCGGGTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (21 bp):
GGTTAACAGTCAAGAGTCAAT
Found at i:1572417 original size:181 final size:181
Alignment explanation
Indices: 1571939--1572417 Score: 735
Period size: 182 Copynumber: 2.6 Consensus size: 181
1571929 TCGATCTAAA
* * * * *
1571939 TAAAAAATGTATCAATCCATATCAATATAACAGGTAAAAATATGACAAAACCGGTCA-CGAAAAG
1 TAAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGT-ATCGAAATG
* * * * *
1572003 ACAATACCGGTAAAGCGCTATCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
65 ATAAAACCGGTAAATCACTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
* *
1572068 TTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTT
130 TTTGTGAATTTAAAAGAGAAACAGTTTTAACGCCTATAAAGTGTCGATACTT
* *
1572120 TATAAAAATGTATCGATCCACAACGATATAATAGGTAAAAATATGACAAAACCGGTATCTAAATG
1 TA-AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTATCGAAATG
* *
1572185 ATAAAACCGGTAAATTACTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
65 ATAAAACCGGTAAATCACTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
*
1572250 TTTGTGAATTTAAAAGAGAAACAGTTTTAATGCCTATAAAGTGTCGATACTT
130 TTTGTGAATTTAAAAGAGAAACAGTTTTAACGCCTATAAAGTGTCGATACTT
* *
1572302 TAAAAAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCGATATCGAAATGA
1 TAAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTATCGAAATGA
* * *
1572367 TAAAATCGGTAAATCACTACCGGATATATTTATAGTGTCGATACTTTAATA
66 TAAAACCGGTAAATCACTACCGGATATATTGAAAGTGTCGATACTTTAATA
1572418 AGTACGTGTA
Statistics
Matches: 270, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
181 108 0.40
182 162 0.60
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (181 bp):
TAAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTATCGAAATGA
TAAAACCGGTAAATCACTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
TTGTGAATTTAAAAGAGAAACAGTTTTAACGCCTATAAAGTGTCGATACTT
Found at i:1574664 original size:21 final size:21
Alignment explanation
Indices: 1574600--1574664 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
1574590 AAGACAATCA
1574600 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
1574621 AAAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
1574642 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1574663 AG
1 AG
1574665 GAATAAAGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.43, C:0.11, G:0.32, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1574702 original size:15 final size:16
Alignment explanation
Indices: 1574684--1574713 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1574674 GGAAGTGAAA
1574684 GGAAAAATAG-TGGAC
1 GGAAAAATAGATGGAC
1574699 GGAAAAATAGATGGA
1 GGAAAAATAGATGGA
1574714 GTGGTGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.03, G:0.33, T:0.13
Consensus pattern (16 bp):
GGAAAAATAGATGGAC
Found at i:1574755 original size:33 final size:33
Alignment explanation
Indices: 1574713--1574778 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1574703 AAATAGATGG
* * *
1574713 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAATAGAGATGTTAAGGGGTGA
*
1574746 AGTGGTGAAAGAAATTGAGATGTTAAGGGGTGA
1 AGTGGTGAAAGAAATAGAGATGTTAAGGGGTGA
1574779 TCTTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAATAGAGATGTTAAGGGGTGA
Found at i:1577801 original size:20 final size:20
Alignment explanation
Indices: 1577747--1577812 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
1577737 CCGTTAGACA
*
1577747 GGGGGG-ATCGGTACCCCCT
1 GGGGGGAATCGGTTCCCCCT
* **
1577766 GGGAGGAAATATGTTCCCCCT
1 GGG-GGGAATCGGTTCCCCCT
*
1577787 GGGGGGAATCGGTTCCTCCT
1 GGGGGGAATCGGTTCCCCCT
1577807 GGGGGG
1 GGGGGG
1577813 GGAATCTGTA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 3 0.08
20 21 0.57
21 13 0.35
ACGTcount: A:0.14, C:0.24, G:0.42, T:0.20
Consensus pattern (20 bp):
GGGGGGAATCGGTTCCCCCT
Found at i:1580117 original size:34 final size:32
Alignment explanation
Indices: 1580064--1580133 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1580054 CCTTACAAAC
*
1580064 TCCCTAGTTTTTCCGGGCTAAACTAGAACATT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
** *
1580096 TCCCTAGCTTTTACACGGGCTAAGTTATAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
1580130 TCCC
1 TCCC
1580134 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:1581143 original size:200 final size:198
Alignment explanation
Indices: 1580800--1581436 Score: 862
Period size: 200 Copynumber: 3.2 Consensus size: 198
1580790 AAATGTTTTC
1580800 AACAGAATCAAATCCCAAAAA-GGTGCACCCATATAGTGTCGATACATTTTTAAAAAGTATCGAT
1 AACAGAATCAAATCCCAAAAAGGGTGCACCCATA-AGTGTCGATACATTTTTAAAAAGTATCGAT
* * * *
1580864 CCCATAAACATCGAAACTCATAAGTATAATGTAATATGTAATTTTTCAATGTAACTGGTATAAAT
65 CCCATAAACATCGAAACCCATAAGTATAATGTAATAAGTAATTTTTCAATGTAACCGATATAAAT
1580929 ATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTGGAGATTGTGTCGATAC
130 ATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGT-GAGATTGTGTCGATAC
1580994 TCTTGG
194 T-TTGG
*
1581000 AACAGAATCAAATCCCAAAAA-GGTGCACCCATATAGTGTCGATACATTTTTAAAAAGTGTCGAT
1 AACAGAATCAAATCCCAAAAAGGGTGCACCCATA-AGTGTCGATACATTTTTAAAAAGTATCGAT
* *
1581064 CCCAGAAACATCGAAACCCATAAGTATAATGTAATAAGTAATTTTTTAATGTAACCGATATAAAT
65 CCCATAAACATCGAAACCCATAAGTATAATGTAATAAGTAATTTTTCAATGTAACCGATATAAAT
* * *
1581129 ATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGATACTTTTTA-ATTTTGTGTCGATA
130 ATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTGAGA--TTGTGTCGATA
**
1581193 CTTTTT
193 CTTTGG
* *** * ** * **
1581199 ATCCAGAAT-AAATGTAAAAAAGGGTGAACGAATAAGTGTCGGTACA-TTTGCAAAAGTATCGAT
1 A-ACAGAATCAAATCCCAAAAAGGGTGCACCCATAAGTGTCGATACATTTTTAAAAAGTATCGAT
* * *
1581262 -CCATTATACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGATATAAA
65 CCCA-TAAACATCGAAACCCATAAGTATAATGTAATAAGTAATTTTTCAATGTAACCGATATAAA
* *
1581326 TAT--CGGTTTTATGAGAGAATAGGTCTAC-AGATGTATCGACACTTGTG-GATCGTGTCGATAC
129 TATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTGAGATTGTGTCGATAC
1581387 TTTTGG
194 -TTTGG
*
1581393 AACATAATCAAATCCCAAAAAGGGTGGCACCCATAAGTGTCGAT
1 AACAGAATCAAATCCCAAAAAGGGT-GCACCCATAAGTGTCGAT
1581437 CCCAAGAACA
Statistics
Matches: 384, Mismatches: 44, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
193 16 0.04
194 17 0.04
195 30 0.08
196 25 0.07
197 3 0.01
198 73 0.19
199 24 0.06
200 196 0.51
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (198 bp):
AACAGAATCAAATCCCAAAAAGGGTGCACCCATAAGTGTCGATACATTTTTAAAAAGTATCGATC
CCATAAACATCGAAACCCATAAGTATAATGTAATAAGTAATTTTTCAATGTAACCGATATAAATA
TACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTGAGATTGTGTCGATACTT
TGG
Found at i:1582616 original size:21 final size:21
Alignment explanation
Indices: 1582590--1582633 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1582580 ATTCTGGGCT
* *
1582590 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
1582611 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
1582632 AG
1 AG
1582634 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:1582702 original size:22 final size:22
Alignment explanation
Indices: 1582659--1582702 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1582649 AATGTCATGG
*
1582659 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
1582681 GGGAACCGATTCCCCTAAAGGA
1 GGGAACCGATACCCCCAAAGGA
1582703 AAATTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1583878 original size:18 final size:18
Alignment explanation
Indices: 1583855--1583890 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1583845 CGAGGGTCTA
1583855 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1583873 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1583891 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:1583999 original size:18 final size:18
Alignment explanation
Indices: 1583976--1584011 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1583966 AGGAATGATA
*
1583976 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
1583994 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1584012 ATGTATTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:1584071 original size:119 final size:120
Alignment explanation
Indices: 1583853--1584101 Score: 437
Period size: 119 Copynumber: 2.1 Consensus size: 120
1583843 GTCGAGGGTC
1583853 TATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAA
1 TATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGACA-ATATGTATTCTTTGGAACATGTGTGAA
* *
1583918 GTCTGGTGAGACACATACTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65 GTCTGGTGAGACACATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
1583974 TATGTGGTCCTTTGGGACATTGTGGTCCTTCGGGAC-ATATGTATTCTTTGGAACATGTGTGAAG
1 TATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGACAATATGTATTCTTTGGAACATGTGTGAAG
* *
1584038 TCTGGTGAGACGCATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TCTGGTGAGACACATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1584093 TATGTGGTC
1 TATGTGGTC
1584102 TTTATGGACA
Statistics
Matches: 123, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
119 88 0.72
121 35 0.28
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.36
Consensus pattern (120 bp):
TATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGACAATATGTATTCTTTGGAACATGTGTGAAG
TCTGGTGAGACACATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1584177 original size:23 final size:23
Alignment explanation
Indices: 1584119--1584179 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1584109 ACATTTTATA
*
1584119 TGGCACTACGGTACAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1584142 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
*
1584165 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
1584180 TTTATATGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1584187 original size:23 final size:23
Alignment explanation
Indices: 1584119--1584187 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1584109 ACATTTTATA
* * *
1584119 TGGCACTACGGTACAATTCTACG
1 TGGCACTACGGTGCAATTATATG
* *
1584142 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTATATG
* *
1584165 TGGCACTTCGGTGCATTTATATG
1 TGGCACTACGGTGCAATTATATG
1584188 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATATG
Found at i:1587504 original size:125 final size:125
Alignment explanation
Indices: 1587279--1587509 Score: 354
Period size: 125 Copynumber: 1.8 Consensus size: 125
1587269 CCATAAAGTG
* *
1587279 TCGATACATTTTTAAAAAGTAACGACCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
1 TCGATACATTTTCAAAAAGTAACGACCCCAAAAACATCGAAACCGATAATTATAATGTAATAGAT
* *
1587344 AAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAAAAATATCTATAACATGTA
66 AAATTTACAATATAACCAGTATAAATATACCGGTTTTATGAAAAATATCTATAACATGTA
** * *
1587404 TCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAATCGATAATTATAATGTAATAGAT
1 TCGATACATTTTCAAAAAGTAACGACCCCAAAAACATCGAAACCGATAATTATAATGTAATAGAT
* ** *
1587469 AATTTTGTAATATAACCAGTATAAATATACTGGTTTTATGA
66 AAATTTACAATATAACCAGTATAAATATACCGGTTTTATGA
1587510 GAGAATAGGT
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
125 94 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (125 bp):
TCGATACATTTTCAAAAAGTAACGACCCCAAAAACATCGAAACCGATAATTATAATGTAATAGAT
AAATTTACAATATAACCAGTATAAATATACCGGTTTTATGAAAAATATCTATAACATGTA
Found at i:1587747 original size:200 final size:200
Alignment explanation
Indices: 1587404--1588163 Score: 1119
Period size: 200 Copynumber: 3.8 Consensus size: 200
1587394 ATAACATGTA
* *
1587404 TCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAATCGATAATTATAATGTAATAGAT
1 TCGATACATTTTCAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGAT
* *
1587469 AATTTTGTAATATAACCAGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACAATATGTATC
66 AATTTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATC
* *
1587534 GACACGTTTTAATATTGTGTCGATACTTTTTGTCAAGAATGGATGCCAAAAAGGGTTAACGCACA
131 GACACTTTTTAATATTGTGTCGATACTTTTTGTCAAGAATGGATGCCAAAAAGGGTGAACGCACA
1587599 AAGTG
196 AAGTG
** * *
1587604 TCGATACATTTTTTAAAAGTATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGAT
1 TCGATACATTTTCAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGAT
* * *
1587669 AATTTTGTAATATAATCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATC
66 AATTTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATC
** * * *
1587734 GATTCTTTTTAATAATGTGTTGATACTTTTTGTCCAA-AATGGATGCCAAAAAGGGTGAATGCAC
131 GACACTTTTTAATATTGTGTCGATACTTTTTGT-CAAGAATGGATGCCAAAAAGGGTGAACGCAC
1587798 AAAGTG
195 AAAGTG
* * ** * *
1587804 TCGATACATTTTCAAAAAGTAACGATTCCAAAAACATCTTAACTGATAATTATAATGTAATAGGT
1 TCGATACATTTTCAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGAT
*
1587869 AATTTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAATATGTATC
66 AATTTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATC
* * * *
1587934 GACACTTTTTAATATTGTGTCAATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTGAACGAATA
131 GACACTTTTTAATATTGTGTCGATACTTTTTGTCAAGAATGGATGCCAAAAAGGGTGAACGCACA
1587999 AAGTG
196 AAGTG
* * * * *
1588004 TCGATACATTTTCAAAACGTGTCGATCCCAAAAATATCGAAACCCATAATTATAATGTAATAGGT
1 TCGATACATTTTCAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGAT
* * * * *
1588069 AATTTTGTAATATAACC-GATATAAATATACTGATTTTATGATATAATAGGTCTCCAACATGTAT
66 AATTTTGTAATATAACCAG-TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTAT
* *
1588133 CGATACTTTTTAATATTATGTCGATACTTTT
130 CGACACTTTTTAATATTGTGTCGATACTTTT
1588164 AAATAATGCG
Statistics
Matches: 502, Mismatches: 55, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
199 3 0.01
200 496 0.99
201 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (200 bp):
TCGATACATTTTCAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGAT
AATTTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATC
GACACTTTTTAATATTGTGTCGATACTTTTTGTCAAGAATGGATGCCAAAAAGGGTGAACGCACA
AAGTG
Found at i:1591742 original size:195 final size:193
Alignment explanation
Indices: 1591358--1591827 Score: 528
Period size: 195 Copynumber: 2.4 Consensus size: 193
1591348 ATAGCTACCT
* * * * *
1591358 AAAACATCAAAACCAATAATTATAATGTAATAGGTAAATTAACAATGT-ATCGGTATAAATATAC
1 AAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGATATAAATATAC
* * * * * * * * *
1591422 CGGTTAATTAGAAAACAAGTCAACATAATGTATCGACACTTGTGGAATTTGTCGATACTTATTGT
66 CGTTTTATGAG-AAATAGGTCAACATAAAGTAACGACACTTGTGAAATTTGTCGATAATTATTGT
** * *
1591487 CCAGAATGAAACCCAAACGGGGTGCAGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCC
130 CCAGAATGAAACCCAAACGACGTGCAGAATAAAGTGTCAATACATTTA-TAAAAGTATCGATCCC
*
1591552 AAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGATATAAATATA
1 -AAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGATATAAATATA
* *
1591617 CTTGTTTTATGAGAAATAGGTCAACATAAAGTAACGACACTTGTTAAATTTGTGTCGATAAATT-
65 C-CGTTTTATGAGAAATAGGTCAACATAAAGTAACGACACTTGTGAAA-TT-TGTCGAT-AATTA
* * **
1591681 TTGTCCATAATGAATGCCC-AACGACGTGCA-AATAAAGTGTCAATACATTTA-AATTGTATCGA
126 TTGTCCAGAATGAA-ACCCAAACGACGTGCAGAATAAAGTGTCAATACATTTATAAAAGTATCGA
1591743 TCCC
190 TCCC
* * * *
1591747 -AAACATCG-AA-CGAAAATTACAATGTGATAGGTAAATTTACAATGTACCCGAT-T-AATATAC
1 AAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGATATAAATATAC
1591807 CGATTTTATGAGAAATAGGTC
66 CG-TTTTATGAGAAATAGGTC
1591828 TAATAATGCA
Statistics
Matches: 237, Mismatches: 31, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
188 1 0.00
189 25 0.11
190 1 0.00
191 38 0.16
192 2 0.01
193 7 0.03
195 57 0.24
196 43 0.18
197 28 0.12
198 29 0.12
199 6 0.03
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.29
Consensus pattern (193 bp):
AAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGATATAAATATAC
CGTTTTATGAGAAATAGGTCAACATAAAGTAACGACACTTGTGAAATTTGTCGATAATTATTGTC
CAGAATGAAACCCAAACGACGTGCAGAATAAAGTGTCAATACATTTATAAAAGTATCGATCCC
Done.