Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013010.1 Kokia drynarioides strain JFW-HI SEQ_128028, 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: 507880
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 307 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:110803 original size:59 final size:58
Alignment explanation
Indices: 110724--110882 Score: 205
Period size: 56 Copynumber: 2.7 Consensus size: 58
110714 AAACAAGAGC
* *
110724 AATAACAAAAACAATAGTAACAACAACATCAATAACAATAGTAACAATAACAACAACAA
1 AATAACAACATCAATAGTAACAACAACATCAA-AACAATAGTAACAATAACAACAACAA
* *
110783 AATAACAACATCAATAGTAACAACAACATC--AACAATAATAGCAATAACAACAACAA
1 AATAACAACATCAATAGTAACAACAACATCAAAACAATAGTAACAATAACAACAACAA
* *
110839 AATAACAACATCAATAGCAATAGCAACAACATCAACAATAATAG
1 AATAACAACATCAATAG---TAACAACAACATCAA-AACAATAG
110883 CAACTGCAAT
Statistics
Matches: 87, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
56 41 0.47
59 40 0.46
62 6 0.07
ACGTcount: A:0.61, C:0.20, G:0.04, T:0.14
Consensus pattern (58 bp):
AATAACAACATCAATAGTAACAACAACATCAAAACAATAGTAACAATAACAACAACAA
Found at i:110831 original size:56 final size:56
Alignment explanation
Indices: 110724--110885 Score: 225
Period size: 59 Copynumber: 2.8 Consensus size: 56
110714 AAACAAGAGC
* * * *
110724 AATAACAAAAACAATAGTAACAACAACATCAATAACAATAGTAACAATAACAACAACAA
1 AATAACAACATCAATAGTAACAACAACATC---AACAATAATAGCAATAACAACAACAA
110783 AATAACAACATCAATAGTAACAACAACATCAACAATAATAGCAATAACAACAACAA
1 AATAACAACATCAATAGTAACAACAACATCAACAATAATAGCAATAACAACAACAA
*
110839 AATAACAACATCAATAGCAATAGCAACAACATCAACAATAATAGCAA
1 AATAACAACATCAATAG---TAACAACAACATCAACAATAATAGCAA
110886 CTGCAATAAC
Statistics
Matches: 95, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
56 41 0.43
59 54 0.57
ACGTcount: A:0.61, C:0.20, G:0.04, T:0.14
Consensus pattern (56 bp):
AATAACAACATCAATAGTAACAACAACATCAACAATAATAGCAATAACAACAACAA
Found at i:111217 original size:3 final size:3
Alignment explanation
Indices: 111200--112743 Score: 150
Period size: 3 Copynumber: 516.7 Consensus size: 3
111190 CAACAGAAAT
* * * *
111200 AAC AAC AAT AGC AAC AAC -AC AAAC AAG AAC AAC AA- AAA AAC ACAC
1 AAC AAC AAC AAC AAC AAC AAC -AAC AAC AAC AAC AAC AAC AAC A-AC
* * * ** * * * *
111245 AAT AAC AAC AAC AAA AAC AAC AAC AAT AGT AAC AAT AAC AAC AAT TAT
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * * * *
111293 AAA AAT AAC AAC AAC AAC AAT AAC AAT AAC AAC AAC AAC AAC TAT AAA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * *
111341 AAT AAC AAC AAT AAT AAC AAC AAC AAC AAT AAC AAC AAC AAC AAT AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * ** * *
111389 AAA AAC -AC AA- ACAC GAGC AAT AAT AGT AAC AAC AAC AAC AAT AGC
1 AAC AAC AAC AAC A-AC -AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * * *
111434 AGC AAC AAC AAC AA- AAT AAC AA- AACC AA- AAA AAT AAT ATC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AA-C AAC AAC AAC AAC AAC AAC
** * * * * * * **
111477 AAC AAC AGT AAC AAC AAG AAT AAT AAC AAG AGC AAC AAC AAT AAC ATG
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * * * * ** *
111525 AGC AAT AAC AAC AAG AAC ATC ATC AAC AAC AAC AAT AAT AGT ATC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* ** * ** ** ** * *
111573 AAG AA- ATTGT AA- ATGC AAC AGT AGT AGT AAC AAC ATC AAC AAG AA-
1 AAC AAC A--AC AAC A-AC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
** ** ** * * *
111618 ATTAC AGT TGC AAC AAC AGT AAC AAC AA- AAGC ATC AAC AAC AAT AGC
1 A--AC AAC AAC AAC AAC AAC AAC AAC AAC AA-C AAC AAC AAC AAC AAC
* * * * *
111665 AGC AAC AAA AAC AAC TAC AAT AAC AATC -AC AAC AAC AAC -AC CAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AA-C AAC AAC AAC AAC AAC AAC
* * * * * *
111709 TAAC AAC AAC TAC AA- AAA AAT AAT AAC AGC ATC AAC AAC AA- AA-
1 -AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * * * *
111752 AAT AAC AAT AGC AAC AAC AAC AAC AAC AAC AAA AAC AAT AAC AAT AAT
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * * * *
111800 AAT AAC AAC AAC AAC AAC TAC TAC TAC AAA AAC AAC AAC AA- AAA AAT
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* ** * * * * * *
111847 AAT AGT AAT AAC AAT AAC AAC AAT AGC AAT AAC AAT AGA- AAC -AC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A-AC AAC AAC
* * * * * * * * ** *
111891 TAAC AA- AAA AAT AAA AAT AGC AAC AAC ATC ATC ATC ATT AAC AAT
1 -AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * * * * * *
111936 AGC ATC ATC AAC AAC AAT AAT AAC AAC AAT AAC AGAGT AAC AAT AAA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A-A-C AAC AAC AAC
* * * * * * * *
111983 AAC ATC ATC AAC AAT AAC AAC AAC AGC TAC AAC AAT TAC AAA AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
** * ** * *
112031 AATC -AC ATT AAC AAT AGG AAT AAC AAC AAC ATA- AAC AAG AAC AAC
1 AA-C AAC AAC AAC AAC AAC AAC AAC AAC AAC A-AC AAC AAC AAC AAC
* ** * * * * *
112076 AAT AGT AAC AAC AAC AAC AAC AAT AGC AAA AAT AAC AAT AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * * **
112124 AAC AAC AAT AAC AAC AA- AAG AAGC GAC AAC AAT AGC -AC TAGT AAC
1 AAC AAC AAC AAC AAC AAC AAC AA-C AAC AAC AAC AAC AAC -AAC AAC
* * * *** * * * **
112169 AAC AAT AAC AAC ACC AAC AA- AA- AAT TGT AGC CAT AAC AAC AGT AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* ** * ** *
112215 AAT AAC AAC AAC AAC AAC AAC ATT AAC AAC AAT AAC AGT AGC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * * * * * *
112263 AAC AAC TAC AATG AA- AAC AAT AGC AAT AAT AAC TAC TAC AAC TAC
1 AAC AAC AAC AA-C AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * * * * *
112308 AAC TAC TAT AAT AAC AAC AAT AGC AAC AAC -AC AAAC AAT AAC AAA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC -AAC AAC AAC AAC
* * * * ** * * * * *
112353 AAT AAC AAT AAT AGC AGT AAT ATC AGC AAC AAC ATC AAC AAC AAC AAT
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
** * *** * ** * * *
112401 AGT AGC GGT AAT AAC ATT AAC AAC AAT AAC AAC AAT ATA- AAC AAA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A-AC AAC AAC
* * * * * ** * * *
112446 AAT ATC AAT AAC AAC AAC AAT AAT AGT AAC AAC AAT AAC AAT AAC AAT
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * * * * **
112494 AAC AAT AAT AGC AAC AAC AAC ATC ATC AAC AAC AGC AAT AAC AGT AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
** * * * *
112542 AAC ATT AAC AAC AAC AAC AAT AAC AGAC -AC AAC AAT ATC AAC AAT
1 AAC AAC AAC AAC AAC AAC AAC AAC A-AC AAC AAC AAC AAC AAC AAC
* * * * * * * **
112587 AAT AAC AAT AAC AAC AAC AAT AAC AAT AAC AAT AGC AAT AGT AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * ** * * *
112635 ATC AAC AA- AAT AA- AAGC AAT AGA- AGC AAC ATT AAC TAT AAT AAC
1 AAC AAC AAC AAC AAC AA-C AAC A-AC AAC AAC AAC AAC AAC AAC AAC
* * * * *
112679 AAT AAC AGAC -AC AAC AAC ACC AAC AAC AAC AGC AGC AGC AAC AAC
1 AAC AAC A-AC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* *
112724 AAC AAC AAA AAC AAT AAC AA
1 AAC AAC AAC AAC AAC AAC AA
112744 AAATAGCAAT
Statistics
Matches: 1089, Mismatches: 392, Indels: 120
0.68 0.24 0.07
Matches are distributed among these distances:
2 56 0.05
3 995 0.91
4 34 0.03
5 4 0.00
ACGTcount: A:0.61, C:0.22, G:0.05, T:0.13
Consensus pattern (3 bp):
AAC
Found at i:111764 original size:25 final size:25
Alignment explanation
Indices: 111712--111817 Score: 85
Period size: 25 Copynumber: 4.3 Consensus size: 25
111702 ACACCACTAA
* *
111712 CAACAACTACAAAAAAATAATAACAG
1 CAACAACAAC-AAAAAATAACAACAG
* *
111738 CATCAACAACAAAAAATAACAATAG
1 CAACAACAACAAAAAATAACAACAG
* *
111763 CAACAACAAC-AACAACAACAA-A-
1 CAACAACAACAAAAAATAACAACAG
* *
111785 -AACAATAACAATAATAATAACAACAA
1 CAACAACAACAA-AA-AATAACAACAG
111811 CAACAAC
1 CAACAAC
111818 TACTACTACA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
21 8 0.13
22 1 0.02
23 2 0.03
24 16 0.25
25 23 0.37
26 8 0.13
27 5 0.08
ACGTcount: A:0.66, C:0.23, G:0.02, T:0.09
Consensus pattern (25 bp):
CAACAACAACAAAAAATAACAACAG
Found at i:111995 original size:26 final size:24
Alignment explanation
Indices: 111948--112002 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 24
111938 CATCATCAAC
*
111948 AACAATAATAACAACAATAACAGAGT
1 AACAATAAAAACAACAATAACA-A-T
*
111974 AACAATAAAAACATC-ATCAACAAT
1 AACAATAAAAACAACAAT-AACAAT
111998 AACAA
1 AACAA
112003 CAACAGCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 6 0.23
25 3 0.12
26 17 0.65
ACGTcount: A:0.64, C:0.18, G:0.04, T:0.15
Consensus pattern (24 bp):
AACAATAAAAACAACAATAACAAT
Found at i:112626 original size:18 final size:18
Alignment explanation
Indices: 110765--112618 Score: 232
Period size: 18 Copynumber: 101.7 Consensus size: 18
110755 ATAACAATAG
110765 TAACAATAACAACAACAA
1 TAACAATAACAACAACAA
* * * * *
110783 -AATAACAACATCAATAG
1 TAACAATAACAACAACAA
* *
110800 TAACAACAACATCAACAA
1 TAACAATAACAACAACAA
* ** *
110818 TAATAGCAATAACAACAA
1 TAACAATAACAACAACAA
* *
110836 CAA-AATAACAACATCAA
1 TAACAATAACAACAACAA
* *
110853 TAGCAATAGCAACAAC-A
1 TAACAATAACAACAACAA
**
110870 TCAACAATAATAGCAACTGCAA
1 T-AACAAT-A-A-CAACAACAA
* *
110892 TAACAATAGCTACAAC-A
1 TAACAATAACAACAACAA
* *
110909 -AA-AATAACAACAATAG
1 TAACAATAACAACAACAA
*
110925 CAACAATAACAACAACAA
1 TAACAATAACAACAACAA
* *
110943 TAGC---AACATCAACAA
1 TAACAATAACAACAACAA
* * **
110958 CAACAACAACAACCTCAA
1 TAACAATAACAACAACAA
*
110976 TAACAATAGAAACAACAAAAA
1 TAACAAT---AACAACAACAA
* * * *
110997 TAGCTACAACAACAACTAC
1 TAACAATAACAACAAC-AA
*
111016 TACACCTATAACAACAACATAAA
1 TA-A-CAATAACAACAAC---AA
* * * *
111039 AAACAGTAGCAGCAACAA
1 TAACAATAACAACAACAA
* *
111057 AAATC-ATAGCAACAACAA
1 TAA-CAATAACAACAACAA
* * * **
111075 CAATAATAGCAGTAACAA
1 TAACAATAACAACAACAA
*
111093 TAACAACT-ACAACATCAA
1 TAACAA-TAACAACAACAA
* * * *
111111 CAATAATAA-AGCAGC-A
1 TAACAATAACAACAACAA
* *** *
111127 TAA-AA-AATAGTTACAG
1 TAACAATAACAACAACAA
*
111143 TAACAATAACAA-AAAAA
1 TAACAATAACAACAACAA
* * *
111160 TAACTATAACTACAATAA
1 TAACAATAACAACAACAA
* *
111178 TAGTGATAATAGCAACAGA-AA
1 TA---ACAATAACAACA-ACAA
*
111199 TAACAACAATAGCAACAACACA
1 T---AACAATAACAACAACA-A
*
111221 -AACAAGAACAACAA-AA
1 TAACAATAACAACAACAA
* * *
111237 AAACACACAATAACAACAA
1 TAACA-ATAACAACAACAA
* * * * *
111256 CAAAAACAACAACAATAG
1 TAACAATAACAACAACAA
**
111274 TAACAATAACAACAATTA
1 TAACAATAACAACAACAA
*
111292 TAAAAATAACAACAACAACAA
1 TAACAAT---AACAACAACAA
111313 TAACAATAACAACAACAA
1 TAACAATAACAACAACAA
* * * *
111331 CAACTATAAAAATAACAA
1 TAACAATAACAACAACAA
* *
111349 CAATAATAACAACAACAA
1 TAACAATAACAACAACAA
* * *
111367 CAATAACAACAACAACAA
1 TAACAATAACAACAACAA
*
111385 TAACAAAAAC-ACAAACACGA
1 TAACAATAACAAC-AACA--A
* * **
111405 GCAATAATAGTAACAACAA
1 -TAACAATAACAACAACAA
*
111424 CAACAATAGCAGCAACAACAA
1 TAACAATA--A-CAACAACAA
*
111445 CAA-AATAACAA-AACCAA
1 TAACAATAACAACAA-CAA
* * *
111462 -AAAAATAATATCAACAA
1 TAACAATAACAACAACAA
* * *
111479 CAACAGTAACAACAAGAATAA
1 TAACAATAACAAC---AACAA
* *
111500 TAACAAGAGCAACAACAA
1 TAACAATAACAACAACAA
* *
111518 TAACATGAGCAATAACAACAA
1 TAACA--A-TAACAACAACAA
*
111539 GAACATCATCAACAACAACAA
1 TAACA--AT-AACAACAACAA
* * * *
111560 TAATAGTATCAACAAGAAA
1 TAACAATAACAACAA-CAA
* * * *
111579 TTGTA-AAT-GCAACAGTAGTAG
1 -T-AACAATAACAACA--A-CAA
* * *
111600 TAACAACATCAACAAGAAA
1 TAACAATAACAACAA-CAA
* * ** *
111619 TTACAGTTGCAACAACAG
1 TAACAATAACAACAACAA
* *
111637 TAACAACAA-AAGCATCAA
1 TAACAATAACAA-CAACAA
* * *
111655 CAACAATAGCAGCAACAA
1 TAACAATAACAACAACAA
* *
111673 AAACAACT-ACAATAACAA
1 TAACAA-TAACAACAACAA
* * * *
111691 TCACAACAACAACACCAC
1 TAACAATAACAACAACAA
* *
111709 TAACAACAACTACAA-AA
1 TAACAATAACAACAACAA
* * * *
111726 AAATAATAACAGCATCAA
1 TAACAATAACAACAACAA
* *
111744 CAACAA-AA-AATAACAA
1 TAACAATAACAACAACAA
* *
111760 TAGCAACAACAACAACAA
1 TAACAATAACAACAACAA
* * *
111778 CAACAAAAACAATAACAA
1 TAACAATAACAACAACAA
*
111796 TAATAATAACAACAACAA
1 TAACAATAACAACAACAA
* * *
111814 CAAC--T-ACTACTACAA
1 TAACAATAACAACAACAA
* * *
111829 AAACAACAACAA-AAAAA
1 TAACAATAACAACAACAA
* * * *
111846 TAATAGTAATAACAATAA
1 TAACAATAACAACAACAA
* * *
111864 CAACAATAGCAATAACAA
1 TAACAATAACAACAACAA
* *
111882 TAGAAACACTAACAA-AAAAA
1 T---AACAATAACAACAACAA
* *
111902 TAAAAATAGCAACAAC-A
1 TAACAATAACAACAACAA
* **
111919 T--C-ATCATCATTAACAA
1 TAACAAT-AACAACAACAA
* *
111935 TAGC-ATCATCAACAACAA
1 TAACAAT-AACAACAACAA
* * *
111953 TAATAACAACAATAACAGA
1 TAACAATAACAACAACA-A
* *
111972 GTAACAATAAAAACATC-A
1 -TAACAATAACAACAACAA
*
111990 TCAACAATAACAACAACAGC
1 T-AACAATAACAACAACA-A
* ** *
112010 T-ACAACAATTACAAAAA
1 TAACAATAACAACAACAA
* * **
112027 CAACAATCACATTAACAA
1 TAACAATAACAACAACAA
**
112045 TAGGAATAACAACAAC-A
1 TAACAATAACAACAACAA
* * *
112062 TAAACAAGAACAACAATAG
1 T-AACAATAACAACAACAA
*
112081 TAACAACAACAACAACAA
1 TAACAATAACAACAACAA
* *
112099 TAGCAAAAATAACAATAACAA
1 T---AACAATAACAACAACAA
* * *
112120 CAACAACAACAATAACAA
1 TAACAATAACAACAACAA
* * *
112138 CAA-AAGAAGCGACAACAA
1 TAACAATAA-CAACAACAA
* * **
112156 TAGCACTAGTAACAACAA
1 TAACAATAACAACAACAA
* *
112174 TAACAACACCAACAA-AA
1 TAACAATAACAACAACAA
*** * *
112191 -AATTGTAGCCATAACAACAG
1 TAACAATA---ACAACAACAA
112211 TAACAATAACAACAACAA
1 TAACAATAACAACAACAA
* * **
112229 CAACAACATTAACAACAA
1 TAACAATAACAACAACAA
* *
112247 TAACAGTAGCAACAACAA
1 TAACAATAACAACAACAA
* * * *
112265 CAACTACAATGAA-AACAA
1 TAACAATAA-CAACAACAA
* *
112283 TAGCAATAATAACTACTACAA
1 TAACAATAACAAC-A--ACAA
* * *
112304 CT-ACAACT-ACTATAATAA
1 -TAACAA-TAACAACAACAA
* *
112322 CAACAATAGCAACAACACA
1 TAACAATAACAACAACA-A
112341 -AACAATAAC-A-AA-AA
1 TAACAATAACAACAACAA
* * **
112355 TAACAATAATAGCAGTAA
1 TAACAATAACAACAACAA
* *
112373 TATCAGCAACAACATCAACAA
1 TA--A-CAATAACAACAACAA
* ** * ***
112394 CAACAATAGTAGCGGTAA
1 TAACAATAACAACAACAA
* *
112412 TAACATTAACAACAATAA
1 TAACAATAACAACAACAA
* *
112430 CAACAATATA-AACAAAAA
1 TAACAATA-ACAACAACAA
*
112448 TATCAATAACAACAACAA
1 TAACAATAACAACAACAA
**
112466 T---AATAGTAACAACAA
1 TAACAATAACAACAACAA
*
112481 TAACAATAACAATAACAA
1 TAACAATAACAACAACAA
*
112499 T---AATAGCAACAACAA
1 TAACAATAACAACAACAA
* * *
112514 CATC-ATCAACAACAGCAA
1 TAACAAT-AACAACAACAA
*
112532 TAACAGTAACAACATTAACAA
1 TAACAATAACAAC---AACAA
* * *
112553 CAACAACAATAACAGAC-A
1 TAACAATAACAACA-ACAA
* * *
112571 CAACAATATCAACAATAA
1 TAACAATAACAACAACAA
112589 TAACAATAACAACAACAA
1 TAACAATAACAACAACAA
112607 TAACAATAACAA
1 TAACAATAACAA
112619 TAGCAATAGT
Statistics
Matches: 1278, Mismatches: 417, Indels: 282
0.65 0.21 0.14
Matches are distributed among these distances:
14 5 0.00
15 77 0.06
16 30 0.02
17 123 0.10
18 730 0.57
19 55 0.04
20 34 0.03
21 212 0.17
22 9 0.01
23 2 0.00
24 1 0.00
ACGTcount: A:0.60, C:0.21, G:0.05, T:0.13
Consensus pattern (18 bp):
TAACAATAACAACAACAA
Found at i:112911 original size:3 final size:3
Alignment explanation
Indices: 112905--112956 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
112895 AACAATAGCT
* * * * *
112905 ACA ACA ACA ATA ATA ACA ATA ACA ACA ACA TCA ACA ACA TCA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
112953 ACA A
1 ACA A
112957 AAGCAGTAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.63, C:0.27, G:0.00, T:0.10
Consensus pattern (3 bp):
ACA
Found at i:112921 original size:24 final size:24
Alignment explanation
Indices: 112889--113000 Score: 91
Period size: 24 Copynumber: 4.7 Consensus size: 24
112879 TAATAGTAGT
* *
112889 AATAATAACAATAGCTACAACAAC
1 AATAATAACAATAACAACAACAAC
*
112913 AATAATAACAATAACAACAACATC
1 AATAATAACAATAACAACAACAAC
* * * *
112937 AACAACATCAACAACAACAA-AAGC
1 AATAATAACAATAACAACAACAA-C
* * * * *
112961 AGTAACAATAATAACATCAATAAC
1 AATAATAACAATAACAACAACAAC
*
112985 AACAATAACAATAACA
1 AATAATAACAATAACA
113001 TCGTCAACAA
Statistics
Matches: 68, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
23 1 0.01
24 65 0.96
25 2 0.03
ACGTcount: A:0.62, C:0.21, G:0.03, T:0.14
Consensus pattern (24 bp):
AATAATAACAATAACAACAACAAC
Found at i:112922 original size:9 final size:9
Alignment explanation
Indices: 112907--112995 Score: 74
Period size: 9 Copynumber: 9.6 Consensus size: 9
112897 CAATAGCTAC
112907 AACAACAAT
1 AACAACAAT
*
112916 AATAACAAT
1 AACAACAAT
112925 AACAACAACAT
1 AACAAC-A-AT
112936 CAACAAC-AT
1 -AACAACAAT
*
112945 CAACAACAAC
1 -AACAACAAT
*
112955 AA-AAGCAGT
1 AACAA-CAAT
*
112964 AACAATAAT
1 AACAACAAT
*
112973 AACATCAAT
1 AACAACAAT
112982 AACAACAAT
1 AACAACAAT
112991 AACAA
1 AACAA
112996 TAACATCGTC
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
8 2 0.03
9 50 0.78
10 4 0.06
11 2 0.03
12 6 0.09
ACGTcount: A:0.63, C:0.22, G:0.02, T:0.12
Consensus pattern (9 bp):
AACAACAAT
Found at i:112934 original size:12 final size:12
Alignment explanation
Indices: 112895--112989 Score: 56
Period size: 12 Copynumber: 8.2 Consensus size: 12
112885 TAGTAATAAT
* *
112895 AACAATAGCTAC
1 AACAATAACAAC
* * *
112907 AACAACAATAAT
1 AACAATAACAAC
112919 AACAATAACAAC
1 AACAATAACAAC
112931 AAC-AT--CAAC
1 AACAATAACAAC
112940 AAC-ATCAACAAC
1 AACAAT-AACAAC
**
112952 AACAA-AAGCAGT
1 AACAATAA-CAAC
*
112964 AACAATAATAAC
1 AACAATAACAAC
*
112976 ATCAATAACAAC
1 AACAATAACAAC
112988 AA
1 AA
112990 TAACAATAAC
Statistics
Matches: 61, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
9 9 0.15
11 4 0.07
12 45 0.74
13 3 0.05
ACGTcount: A:0.61, C:0.23, G:0.03, T:0.13
Consensus pattern (12 bp):
AACAATAACAAC
Found at i:113057 original size:21 final size:21
Alignment explanation
Indices: 113033--113079 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
113023 ATAATAACAG
*
113033 TAACAATAACAAGAACAAGAA
1 TAACAACAACAAGAACAAGAA
** *
113054 TAACAACAACATTAACAATAA
1 TAACAACAACAAGAACAAGAA
113075 TAACA
1 TAACA
113080 GCGGCAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.64, C:0.17, G:0.04, T:0.15
Consensus pattern (21 bp):
TAACAACAACAAGAACAAGAA
Found at i:113123 original size:6 final size:6
Alignment explanation
Indices: 113114--113222 Score: 87
Period size: 6 Copynumber: 18.2 Consensus size: 6
113104 AAATAATATT
* * * * * *
113114 ACAACA ACAACA ACTACA ACTATA ACTACA ACAACA ACAACA ACTATA
1 ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA
* * * * *
113162 ACTACA ACAACA ACAACA ACAACC ATAGCA ATAAC- ACAAACA ACAACA
1 ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA AC-AACA ACAACA
113210 ACAA-A ATCAACA A
1 ACAACA A-CAACA A
113223 TAATAGTAGC
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
5 3 0.04
6 78 0.92
7 4 0.05
ACGTcount: A:0.61, C:0.29, G:0.01, T:0.09
Consensus pattern (6 bp):
ACAACA
Found at i:113197 original size:24 final size:24
Alignment explanation
Indices: 113117--113181 Score: 121
Period size: 24 Copynumber: 2.7 Consensus size: 24
113107 TAATATTACA
*
113117 ACAACAACAACTACAACTATAACT
1 ACAACAACAACAACAACTATAACT
113141 ACAACAACAACAACAACTATAACT
1 ACAACAACAACAACAACTATAACT
113165 ACAACAACAACAACAAC
1 ACAACAACAACAACAAC
113182 AACCATAGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.58, C:0.31, G:0.00, T:0.11
Consensus pattern (24 bp):
ACAACAACAACAACAACTATAACT
Found at i:113382 original size:3 final size:3
Alignment explanation
Indices: 113376--113486 Score: 71
Period size: 3 Copynumber: 37.0 Consensus size: 3
113366 ATAGCAATAG
* * * * * * *
113376 CAA CAA CAA CAT TAA CAA CAA CAA CAA TAA TAGA -TA CAA TAA CAT
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA-A CAA CAA CAA CAA
* * * * *
113421 CAA TAA AAA CAA CAA TAA CAA TAA CAA CAA CAA CAA CAA CAA CAA TAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
* * *
113469 TAA TAA CAA CAA TAA CAA
1 CAA CAA CAA CAA CAA CAA
113487 TAGCAATAAA
Statistics
Matches: 84, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
2 1 0.01
3 82 0.98
4 1 0.01
ACGTcount: A:0.65, C:0.22, G:0.01, T:0.13
Consensus pattern (3 bp):
CAA
Found at i:113397 original size:18 final size:18
Alignment explanation
Indices: 113376--113465 Score: 92
Period size: 18 Copynumber: 5.0 Consensus size: 18
113366 ATAGCAATAG
*
113376 CAACAACAACATTAACAA
1 CAACAACAACAATAACAA
* *
113394 CAACAACAATAATAGA-TA
1 CAACAACAACAATA-ACAA
* * *
113412 CAATAACATCAATAAAAA
1 CAACAACAACAATAACAA
*
113430 CAACAATAACAATAACAA
1 CAACAACAACAATAACAA
*
113448 CAACAACAACAACAACAA
1 CAACAACAACAATAACAA
113466 TAATAATAAC
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
17 1 0.02
18 55 0.96
19 1 0.02
ACGTcount: A:0.64, C:0.23, G:0.01, T:0.11
Consensus pattern (18 bp):
CAACAACAACAATAACAA
Found at i:113414 original size:21 final size:20
Alignment explanation
Indices: 113390--113488 Score: 80
Period size: 21 Copynumber: 5.0 Consensus size: 20
113380 AACAACATTA
113390 ACAACAACAACAATAATAGAT
1 ACAACAACAACAATAATA-AT
* *
113411 ACAATAACATCAATAA-AA-
1 ACAACAACAACAATAATAAT
* * *
113429 ACAACAATAACAATAACAACA
1 ACAACAACAACAATAATAA-T
*
113450 ACAACAACAACAACAATAAT
1 ACAACAACAACAATAATAAT
* *
113470 --AATAACAACAATAACAAT
1 ACAACAACAACAATAATAAT
113488 A
1 A
113489 GCAATAAAAG
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
18 28 0.45
19 3 0.05
20 1 0.02
21 30 0.48
ACGTcount: A:0.66, C:0.20, G:0.01, T:0.13
Consensus pattern (20 bp):
ACAACAACAACAATAATAAT
Found at i:113553 original size:21 final size:20
Alignment explanation
Indices: 113523--113584 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
113513 ACGGTAGTAG
*
113523 CAACATCAATAACTAAAACAA
1 CAACAACAATAA-TAAAACAA
*
113544 CAACAACAATAATAGTAACAA
1 CAACAACAATAATA-AAACAA
* * *
113565 CAACATCAACAATAATACAA
1 CAACAACAATAATAAAACAA
113585 TAGCAATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.61, C:0.23, G:0.02, T:0.15
Consensus pattern (20 bp):
CAACAACAATAATAAAACAA
Found at i:113557 original size:24 final size:25
Alignment explanation
Indices: 113530--113581 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
113520 TAGCAACATC
113530 AATAACTAA-AACAACAACAACAAT
1 AATAACTAACAACAACAACAACAAT
* *
113554 AAT-AGTAACAACAACATCAACAAT
1 AATAACTAACAACAACAACAACAAT
113578 AATA
1 AATA
113582 CAATAGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.63, C:0.19, G:0.02, T:0.15
Consensus pattern (25 bp):
AATAACTAACAACAACAACAACAAT
Found at i:113654 original size:21 final size:21
Alignment explanation
Indices: 113604--113656 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
113594 TAAAATCTAC
* * *
113604 AACAAAAATAACAACACCATT
1 AACAACAATAACAACAACATA
* *
113625 AATAGCAATAACAACAACATA
1 AACAACAATAACAACAACATA
113646 AACAACAATAA
1 AACAACAATAA
113657 TAGAAGCAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.64, C:0.21, G:0.02, T:0.13
Consensus pattern (21 bp):
AACAACAATAACAACAACATA
Found at i:117116 original size:19 final size:19
Alignment explanation
Indices: 117093--117245 Score: 153
Period size: 19 Copynumber: 8.1 Consensus size: 19
117083 CAGTACAATA
* *
117093 TATTGCTCTTACAAGCCAA
1 TATTGCTCTTACGAGCCAG
* *
117112 TATTGCACTCACGAGCCAG
1 TATTGCTCTTACGAGCCAG
* ** *
117131 TATTGCTCCTAAAAGCCTG
1 TATTGCTCTTACGAGCCAG
* * *
117150 TATTACTCTCACGAGCCAC
1 TATTGCTCTTACGAGCCAG
* *
117169 TATTGCTCTCATGAGCCAG
1 TATTGCTCTTACGAGCCAG
*
117188 TATTGTTCTTACGAGCCAG
1 TATTGCTCTTACGAGCCAG
*
117207 TATTGCTCTTACGAGCCAA
1 TATTGCTCTTACGAGCCAG
* *
117226 TATTACTCTTATGAGCCAG
1 TATTGCTCTTACGAGCCAG
117245 T
1 T
117246 TCAATATATT
Statistics
Matches: 106, Mismatches: 28, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 106 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (19 bp):
TATTGCTCTTACGAGCCAG
Found at i:117210 original size:57 final size:57
Alignment explanation
Indices: 117106--117245 Score: 172
Period size: 57 Copynumber: 2.5 Consensus size: 57
117096 TGCTCTTACA
* * *
117106 AGCCAATATTGCACTCACGAGCCAGTATTGCTCCTAAAAGCCTGTATTACTCTCACG
1 AGCCAATATTGCTCTCATGAGCCAGTATTGCTCCTAAAAGCCAGTATTACTCTCACG
* * * ** * *
117163 AGCCACTATTGCTCTCATGAGCCAGTATTGTTCTTACGAGCCAGTATTGCTCTTACG
1 AGCCAATATTGCTCTCATGAGCCAGTATTGCTCCTAAAAGCCAGTATTACTCTCACG
* *
117220 AGCCAATATTACTCTTATGAGCCAGT
1 AGCCAATATTGCTCTCATGAGCCAGT
117246 TCAATATATT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 70 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (57 bp):
AGCCAATATTGCTCTCATGAGCCAGTATTGCTCCTAAAAGCCAGTATTACTCTCACG
Found at i:122912 original size:3 final size:3
Alignment explanation
Indices: 122897--122977 Score: 144
Period size: 3 Copynumber: 27.0 Consensus size: 3
122887 TAGCCTAAAG
* *
122897 AAT AAT AAG AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
122945 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
122978 GAAAATAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:124569 original size:15 final size:15
Alignment explanation
Indices: 124518--124575 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
124508 CGAAAAATCA
*
124518 AGCAACAACAACAGT
1 AGCAACAACAACAAT
* *
124533 AGCTACAACAACAAC
1 AGCAACAACAACAAT
** *
124548 AAAAACAAAAACAAT
1 AGCAACAACAACAAT
*
124563 AGCAACATCAACA
1 AGCAACAACAACA
124576 TCAACAATAG
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.60, C:0.26, G:0.07, T:0.07
Consensus pattern (15 bp):
AGCAACAACAACAAT
Found at i:124575 original size:21 final size:21
Alignment explanation
Indices: 124551--124600 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
124541 CAACAACAAA
*
124551 AACAAAAACAATAGCAACATC
1 AACAAAAACAATAGCAACAGC
** * *
124572 AACATCAACAATAGTAGCAGC
1 AACAAAAACAATAGCAACAGC
124593 AACAAAAA
1 AACAAAAA
124601 TTACAGCAAC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.60, C:0.22, G:0.08, T:0.10
Consensus pattern (21 bp):
AACAAAAACAATAGCAACAGC
Found at i:124597 original size:15 final size:15
Alignment explanation
Indices: 124577--124630 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
124567 ACATCAACAT
124577 CAACAATAGTAGCAG
1 CAACAATAGTAGCAG
* *
124592 CAACAAAAATTA-CAG
1 CAAC-AATAGTAGCAG
* *
124607 CAACAATAGCAGTAG
1 CAACAATAGTAGCAG
124622 CAACAATAG
1 CAACAATAG
124631 CAACAACAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 4 0.13
15 22 0.71
16 5 0.16
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.13
Consensus pattern (15 bp):
CAACAATAGTAGCAG
Found at i:124685 original size:27 final size:27
Alignment explanation
Indices: 124626--124730 Score: 84
Period size: 27 Copynumber: 3.9 Consensus size: 27
124616 CAGTAGCAAC
* * * **
124626 AATAGCAACAACAACAACAGCTACATC
1 AATAGCAACAATAACAACAACAACAAA
* *
124653 ATTAGCAACAATAACAATAACAACAAA
1 AATAGCAACAATAACAACAACAACAAA
* * *
124680 AATAGCTACAACAACAACAACAATAAA
1 AATAGCAACAATAACAACAACAACAAA
* * * *
124707 AAAAACAACAATAAAAAGAACAAC
1 AATAGCAACAATAACAACAACAAC
124731 TACAAAAATA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.63, C:0.22, G:0.05, T:0.10
Consensus pattern (27 bp):
AATAGCAACAATAACAACAACAACAAA
Found at i:124687 original size:39 final size:39
Alignment explanation
Indices: 124632--124717 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
124622 CAACAATAGC
* * ** * * *
124632 AACAACAACAACAGCTACATCATTAGCAACAATAACAAT
1 AACAACAAAAACAGCTACAACAACAACAACAATAAAAAA
*
124671 AACAACAAAAATAGCTACAACAACAACAACAATAAAAAA
1 AACAACAAAAACAGCTACAACAACAACAACAATAAAAAA
124710 AACAACAA
1 AACAACAA
124718 TAAAAAGAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.63, C:0.23, G:0.03, T:0.10
Consensus pattern (39 bp):
AACAACAAAAACAGCTACAACAACAACAACAATAAAAAA
Found at i:124693 original size:3 final size:3
Alignment explanation
Indices: 124658--124916 Score: 68
Period size: 3 Copynumber: 86.0 Consensus size: 3
124648 ACATCATTAG
* * * * * * *
124658 CAA CAA TAA CAA TAA CAA CAA AAA TAG CTA CAA CAA CAA CAA CAA TAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
* * * * * * * * * * *
124706 AAA AAA CAA CAA TAA AAA GAA CAA CTA CAA AAA TAA CTA CAT CAA TAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
* * * * * * * *
124754 TAA CAA CCA CAA CAA CAA CAA CAA TAA TAG CAG CAG CAA CAA CAA TAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
* * * * * ** * *** * * *
124802 CAA TAA TAA CAG CAA TAG CAA CTT CAA AAA CAA GTTG CAG CCA TAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA -CAA CAA CAA CAA
* * * * * *
124848 CAA CAG TAA CAA TAA CAA CAG CAA CAA CAA CAA TAA CAA CAA CAA CTA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
* * *
124896 CTA CAA TAA AAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA
124917 TAATAGTAAT
Statistics
Matches: 179, Mismatches: 76, Indels: 2
0.70 0.30 0.01
Matches are distributed among these distances:
3 179 1.00
ACGTcount: A:0.61, C:0.23, G:0.05, T:0.11
Consensus pattern (3 bp):
CAA
Found at i:124793 original size:27 final size:27
Alignment explanation
Indices: 124748--124815 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
124738 ATAACTACAT
*
124748 CAATAATAACAACCA-CAACAACAACAA
1 CAATAATAAC-AGCAGCAACAACAACAA
* *
124775 CAATAATAGCAGCAGCAACAACAATAA
1 CAATAATAACAGCAGCAACAACAACAA
124802 CAATAATAACAGCA
1 CAATAATAACAGCA
124816 ATAGCAACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 3 0.08
27 33 0.92
ACGTcount: A:0.59, C:0.25, G:0.06, T:0.10
Consensus pattern (27 bp):
CAATAATAACAGCAGCAACAACAACAA
Found at i:124872 original size:21 final size:21
Alignment explanation
Indices: 124846--124981 Score: 95
Period size: 21 Copynumber: 6.7 Consensus size: 21
124836 TTGCAGCCAT
*
124846 AACAACAGTAACAATAACAAC
1 AACAACAATAACAATAACAAC
* *
124867 AGCAACAACAACAATAACAAC
1 AACAACAATAACAATAACAAC
* *
124888 AACAACTACT-ACAATAAAAAC
1 AACAAC-AATAACAATAACAAC
* * * *
124909 AACAACAATAATAGTAATATC
1 AACAACAATAACAATAACAAC
* *
124930 AACAA-AAAAAC-ACAACAAC
1 AACAACAATAACAATAACAAC
* * *
124949 TACAAC-A-AA-AATAGCAGC
1 AACAACAATAACAATAACAAC
124967 AACAACAATAACAAT
1 AACAACAATAACAAT
124982 GGTAGATCTG
Statistics
Matches: 85, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
18 12 0.14
19 10 0.12
20 8 0.09
21 54 0.64
22 1 0.01
ACGTcount: A:0.62, C:0.23, G:0.04, T:0.11
Consensus pattern (21 bp):
AACAACAATAACAATAACAAC
Found at i:124887 original size:15 final size:15
Alignment explanation
Indices: 124844--124980 Score: 61
Period size: 15 Copynumber: 9.5 Consensus size: 15
124834 AGTTGCAGCC
**
124844 ATAACAACAGTAACA
1 ATAACAACAACAACA
*
124859 ATAACAACAGCAACA
1 ATAACAACAACAACA
* *
124874 ACAACAATAACAACA
1 ATAACAACAACAACA
* * * *
124889 ACAACTACTACAATA
1 ATAACAACAACAACA
* *
124904 AAAACAACAACAATA
1 ATAACAACAACAACA
** * *
124919 ATAGTAATATCAACA
1 ATAACAACAACAACA
*
124934 A-AAAAAC-ACAACA
1 ATAACAACAACAACA
124947 ACT-ACAAC-A-AA-A
1 A-TAACAACAACAACA
* *
124959 ATAGCAGCAACAACA
1 ATAACAACAACAACA
124974 ATAACAA
1 ATAACAA
124981 TGGTAGATCT
Statistics
Matches: 90, Mismatches: 26, Indels: 12
0.70 0.20 0.09
Matches are distributed among these distances:
11 1 0.01
12 5 0.06
13 9 0.10
14 10 0.11
15 65 0.72
ACGTcount: A:0.63, C:0.23, G:0.04, T:0.11
Consensus pattern (15 bp):
ATAACAACAACAACA
Found at i:124891 original size:27 final size:27
Alignment explanation
Indices: 124846--124980 Score: 60
Period size: 27 Copynumber: 5.0 Consensus size: 27
124836 TTGCAGCCAT
* * * *
124846 AACAACAGTAACAATAACAACAGCAAC
1 AACAACAATAACAACAACAATAACAAC
*
124873 AACAACAATAACAACAACAACT-ACTAC
1 AACAACAATAACAACAACAA-TAACAAC
* * * * ** *
124900 AATAAAAACAACAACAATAATAGTAAT
1 AACAACAATAACAACAACAATAACAAC
* * * *
124927 ATCAACAA-AAAAAC-ACAACAACTAC
1 AACAACAATAACAACAACAATAACAAC
*
124952 AACAAAAATAGCAGCAACAACAATAACAA
1 AACAACAATA--A-CAACAACAATAACAA
124981 TGGTAGATCT
Statistics
Matches: 73, Mismatches: 28, Indels: 11
0.65 0.25 0.10
Matches are distributed among these distances:
25 11 0.15
26 7 0.10
27 43 0.59
28 1 0.01
29 3 0.04
30 8 0.11
ACGTcount: A:0.63, C:0.23, G:0.04, T:0.10
Consensus pattern (27 bp):
AACAACAATAACAACAACAATAACAAC
Found at i:145237 original size:79 final size:79
Alignment explanation
Indices: 145115--145260 Score: 211
Period size: 79 Copynumber: 1.8 Consensus size: 79
145105 GTTTATCCGC
* * *
145115 TAGGCACTGGGTGCCAGGATTTGATGGATATTATTGATAAATCCAACTAAAGTTGGGCTCACATT
1 TAGGCACTGGGTGCCAAGATTTGACGGACATTATTGATAAATCCAACTAAAGTTGGGCTCACATT
145180 TGTGGTTTACTCAA
66 TGTGGTTTACTCAA
* * * * * *
145194 TAGGCACTTGGTGCCAAGATTTGACGGACATTGTTGGTTAATCCAACTAGAGTTGGGCTCACTTT
1 TAGGCACTGGGTGCCAAGATTTGACGGACATTATTGATAAATCCAACTAAAGTTGGGCTCACATT
145259 TG
66 TG
145261 CGATTATCTG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 58 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (79 bp):
TAGGCACTGGGTGCCAAGATTTGACGGACATTATTGATAAATCCAACTAAAGTTGGGCTCACATT
TGTGGTTTACTCAA
Found at i:151563 original size:48 final size:48
Alignment explanation
Indices: 151492--151587 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
151482 AAACTAGTTT
151492 TCACATTTGAAGAGCTTGAAATCGAGTACTTTACCTTATATTTTTATA
1 TCACATTTGAAGAGCTTGAAATCGAGTACTTTACCTTATATTTTTATA
*
151540 TCACATTTGAAGAGCTTGAAATCGAGTACTTTACCTTATGTTTTTATA
1 TCACATTTGAAGAGCTTGAAATCGAGTACTTTACCTTATATTTTTATA
151588 GATTTTAGCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.42
Consensus pattern (48 bp):
TCACATTTGAAGAGCTTGAAATCGAGTACTTTACCTTATATTTTTATA
Found at i:174479 original size:38 final size:38
Alignment explanation
Indices: 174428--174504 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
174418 AAAATGCGTC
174428 CTCAGCATGTTGTAGACAATCCTCATAACTGTGGTTGT
1 CTCAGCATGTTGTAGACAATCCTCATAACTGTGGTTGT
174466 CTCAGCATGTTGTAGACAATCCTCATAACTGTGGTTGT
1 CTCAGCATGTTGTAGACAATCCTCATAACTGTGGTTGT
174504 C
1 C
174505 ACTGCAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (38 bp):
CTCAGCATGTTGTAGACAATCCTCATAACTGTGGTTGT
Found at i:182832 original size:36 final size:36
Alignment explanation
Indices: 182785--182858 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
182775 CTAAATGTGG
182785 CTGCAAGGTAACAAATAAATGAATTGTGATGCAATT
1 CTGCAAGGTAACAAATAAATGAATTGTGATGCAATT
182821 CTGCAAGGTAACAAATAAATGAATTGTGATGCAATT
1 CTGCAAGGTAACAAATAAATGAATTGTGATGCAATT
182857 CT
1 CT
182859 TACTTCATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (36 bp):
CTGCAAGGTAACAAATAAATGAATTGTGATGCAATT
Found at i:188783 original size:22 final size:23
Alignment explanation
Indices: 188739--188784 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
188729 ATTAGGAATG
*
188739 CTTCTCGTCAGAAGTAGATTTGC
1 CTTCTCGTCAGAAGTAGAGTTGC
188762 CTTCTCGTCA-AAGTCAG-GTTGC
1 CTTCTCGTCAGAAGT-AGAGTTGC
188784 C
1 C
188785 CTCAAGGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.33
Consensus pattern (23 bp):
CTTCTCGTCAGAAGTAGAGTTGC
Found at i:189243 original size:20 final size:21
Alignment explanation
Indices: 189206--189244 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
189196 AAAGCAAGCA
189206 TCACTAAGTTAGAAAATGCAG
1 TCACTAAGTTAGAAAATGCAG
189227 TCACTAAGTTA-AAAATGC
1 TCACTAAGTTAGAAAATGC
189245 TAAAAATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (21 bp):
TCACTAAGTTAGAAAATGCAG
Found at i:202778 original size:3 final size:3
Alignment explanation
Indices: 202772--202803 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
202762 CAATGAAAAA
202772 AAT AAT AAT AAT AAT AAT AAT AAT AAT CAAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A
202804 TCCATATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:203272 original size:32 final size:32
Alignment explanation
Indices: 203236--203305 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
203226 TTCCAATTCC
*
203236 ACTTTTGTCAAGAAAATTCATAAATTATTGGA
1 ACTTTTGTCAAGAAAATTCATAAACTATTGGA
*
203268 ACTTTTGTCAAGAAAATTTATAAACTATTGGA
1 ACTTTTGTCAAGAAAATTCATAAACTATTGGA
203300 ACTTTT
1 ACTTTT
203306 AGCGCATTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (32 bp):
ACTTTTGTCAAGAAAATTCATAAACTATTGGA
Found at i:211480 original size:4 final size:4
Alignment explanation
Indices: 211439--211464 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
211429 GGAGAAACGT
211439 AGAA AGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AG
211465 GTAGGCCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:220516 original size:21 final size:22
Alignment explanation
Indices: 220490--220531 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
220480 ATATAAATAT
*
220490 TTTTCTT-TTTCTTTTCTTTTC
1 TTTTCTTCTTTCTTTTATTTTC
*
220511 TTTTCTTCTTTTTTTTATTTT
1 TTTTCTTCTTTCTTTTATTTT
220532 ATATATGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTCTTCTTTCTTTTATTTTC
Found at i:224229 original size:13 final size:13
Alignment explanation
Indices: 224211--224236 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
224201 AGGATTGTCC
224211 TAGCATCGTCTTT
1 TAGCATCGTCTTT
224224 TAGCATCGTCTTT
1 TAGCATCGTCTTT
224237 AGGAACAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
TAGCATCGTCTTT
Found at i:239142 original size:18 final size:18
Alignment explanation
Indices: 239119--239156 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
239109 TAATGCAAAG
239119 TTAGTGACCGTTGGTACC
1 TTAGTGACCGTTGGTACC
*
239137 TTAGTGACTGTTGGTACC
1 TTAGTGACCGTTGGTACC
239155 TT
1 TT
239157 TAAAAATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (18 bp):
TTAGTGACCGTTGGTACC
Found at i:240362 original size:20 final size:22
Alignment explanation
Indices: 240332--240373 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
240322 ATCATCATCC
240332 CCTTCCCCCTTCCCC-TCTTCT
1 CCTTCCCCCTTCCCCTTCTTCT
240353 CCTT-CCCCTTCCCCTTCTTCT
1 CCTTCCCCCTTCCCCTTCTTCT
240374 TACTTTCCNN
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (22 bp):
CCTTCCCCCTTCCCCTTCTTCT
Found at i:240436 original size:6 final size:6
Alignment explanation
Indices: 240425--240452 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
240415 NNNNNNNNCT
240425 CTTCCC CTTCCC CTTCCC CTTCCC CTTC
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTC
240453 TTCTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
CTTCCC
Found at i:241242 original size:11 final size:10
Alignment explanation
Indices: 241194--241296 Score: 69
Period size: 9 Copynumber: 10.3 Consensus size: 10
241184 ATGATGATTA
241194 AAATAATTTT
1 AAATAATTTT
241204 -AATAATTTT
1 AAATAATTTT
241213 --AT-ATTTT
1 AAATAATTTT
241220 AAAAAATAATTTT
1 ---AAATAATTTT
241233 AAATTAATTTT
1 AAA-TAATTTT
241244 AAAATAATTTT
1 -AAATAATTTT
241255 -AATAATTTT
1 AAATAATTTT
*
241264 --ATATTTTT
1 AAATAATTTT
241272 AAAAAATAATTTT
1 ---AAATAATTTT
241285 -AATAATTTT
1 AAATAATTTT
241294 AAA
1 AAA
241297 ATCATTTGCT
Statistics
Matches: 77, Mismatches: 2, Indels: 28
0.72 0.02 0.26
Matches are distributed among these distances:
7 5 0.06
8 9 0.12
9 27 0.35
10 5 0.06
11 14 0.18
12 5 0.06
13 12 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AAATAATTTT
Found at i:241250 original size:22 final size:20
Alignment explanation
Indices: 241191--241303 Score: 78
Period size: 20 Copynumber: 5.6 Consensus size: 20
241181 ATGATGATGA
241191 TTAAAATAATTTTAATAATT
1 TTAAAATAATTTTAATAATT
241211 TT---AT-ATTTTAAAAAATAATT
1 TTAAAATAATTTT----AATAATT
*
241231 TTAAATTAATTTTAAAATAATT
1 TTAAAATAATTTT--AATAATT
*
241253 TT--AATAATTTT-ATATTT
1 TTAAAATAATTTTAATAATT
241270 TTAAAAAATAATTTTAATAATT
1 TT--AAAATAATTTTAATAATT
*
241292 TTAAAATCATTT
1 TTAAAATAATTT
241304 GCTGACGTGG
Statistics
Matches: 75, Mismatches: 5, Indels: 26
0.71 0.05 0.25
Matches are distributed among these distances:
16 5 0.07
17 9 0.12
20 28 0.37
21 9 0.12
22 18 0.24
23 1 0.01
24 5 0.07
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAAATAATTTTAATAATT
Found at i:241267 original size:51 final size:50
Alignment explanation
Indices: 241191--241303 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 50
241181 ATGATGATGA
241191 TTAAAATAATTTTAATAATTTTATA-TTTTAAAAAATAATTTTAAATTAATT
1 TTAAAATAATTTTAATAATTTTATATTTTTAAAAAATAATTTT-AA-TAATT
241242 TTAAAATAATTTTAATAATTTTATATTTTTAAAAAATAATTTTAATAATT
1 TTAAAATAATTTTAATAATTTTATATTTTTAAAAAATAATTTTAATAATT
*
241292 TTAAAATCATTT
1 TTAAAATAATTT
241304 GCTGACGTGG
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
50 16 0.27
51 27 0.45
52 17 0.28
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (50 bp):
TTAAAATAATTTTAATAATTTTATATTTTTAAAAAATAATTTTAATAATT
Found at i:241281 original size:21 final size:22
Alignment explanation
Indices: 241255--241297 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
241245 AAATAATTTT
*
241255 AATAATTTT-ATATTTTTAAAA
1 AATAATTTTAATAATTTTAAAA
241276 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
241298 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:242378 original size:32 final size:32
Alignment explanation
Indices: 242332--242395 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
242322 TATGCCACCT
* * *
242332 AAAATTTTTAATTAATATCTTTCAAAATTTTTA
1 AAAATTTGTAATTAAT-CCTTTCAAAAATTTTA
242365 AAAATTTGT-ATTAATCCTTTCAAAAATTTTA
1 AAAATTTGTAATTAATCCTTTCAAAAATTTTA
242396 GCTCCCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 14 0.50
32 6 0.21
33 8 0.29
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (32 bp):
AAAATTTGTAATTAATCCTTTCAAAAATTTTA
Found at i:247945 original size:93 final size:93
Alignment explanation
Indices: 247817--248712 Score: 492
Period size: 93 Copynumber: 9.4 Consensus size: 93
247807 GGTGTTGCAA
* * * * * *
247817 CTTCACTCTATTCCACTGTAACCTCATGGACATTGAGATCTATTACTCATTTTGATTTGATTCAC
1 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTATTACTCGTTTTAATCTGATCCAC
* *
247882 TGTAACTTCAGGGATATAAGATCTGGTG
66 TGCAACTTCAGGGATATAGGATCTGGTG
* * * *
247910 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGA-ATCTGCTT-CGTTGTTTTAACCTGACCC
1 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCT-ATTAC-TCGTTTTAATCTGATCC
* * * *
247973 ACTACAAC-TCAGGGGTATGGGATTTGATGTTG
64 ACTGCAACTTCAGGGATATAGGATCTG--G-TG
* * * * * * *
248005 TAACTTCTCTCCATTCCACTTTAACCTTAAGGACATTGAGATCTGTTACTCATTTTGATATGATC
1 ---CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTATTACTCGTTTTAATCTGATC
* *
248070 CATTGCAACTTCAAGGATATAGGATCTGGTG
63 CACTGCAACTTCAGGGATATAGGATCTGGTG
* * * * * * * ** *
248101 CTTCACTCTACTCCATTGTAACCTTAGGGACATTGAGATATACTT-CGTTGTTTTAATCAAACCC
1 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTA-TTAC-TCGTTTTAATCTGATCC
* * * *
248165 ACTGCAA-GTCAAGGG-TATGGGATTTTATGTTGTAA
64 ACTGCAACTTC-AGGGATATAGGA---TCTG--GT-G
* ** * * * * * *
248200 CTTCTCTCCATTCCACACTAACCTTAGGGACATTGAGAT-TCGTTACTCATTTTTATCTGATTCA
1 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCT-ATTACTCGTTTTAATCTGATCCA
248264 CTGCAACTTCAGGGATATAGGATCTGGTG
65 CTGCAACTTCAGGGATATAGGATCTGGTG
* * * * * * * * *
248293 TTTTACTCTAGTCCACTATAACCTCAGGGACATTGAGATCT-TCA-TTGTTTTAATCTGACCCAC
1 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTATTACTCGTTTTAATCTGATCCAC
* * * *
248356 TACAAC-TCAGGGGTATGGGATTTGATGTTG
66 TGCAACTTCAGGGATATAGGATCTG--G-TG
* * * * ** * * **
248386 CAACTTCTCTCTATTCCA-TACTAACCTTC-GGGACATTGAGAT-TCGCTGCTCGTTTTGATCCA
1 ---CTTCACTCCATTCCACT-GTAACC-TCAAGGACATTGAGATCT-ATTACTCGTTTTAATCTG
* * *
248448 ATCCAGTACAACTTCAGGGATATAAGATCTGGTG
60 ATCCACTGCAACTTCAGGGATATAGGATCTGGTG
* * * *
248482 CTTCACTCCATTCAACTGTAACCTCAATGACATTGAGATCTGCTT-CGTTGTTTTAATCTGA-CC
1 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCT-ATTAC-TCGTTTTAATCTGATCC
* * * *
248545 TACTGTAAC-TCAGGGATATGGGATTTGATATTGTAA
64 -ACTGCAACTTCAGGGATATAGGATCTG-----GT-G
* * * * * * * * ** *
248581 CTTCTCTCCATTCCATTGTAACCTCTAGAACATTGAGATCCATTACTCATTTTGACCCAATCCAA
1 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTATTACTCGTTTTAATCTGATCCAC
* *
248646 TGCAACTTCAAGGATATAGGATTTGGTG
66 TGCAACTTCAGGGATATAGGATCTGGTG
*
248674 CTTCACTCCATTCCACTGTAACCTCAAGGACATTAAGAT
1 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGAT
248713 TTGCTTCGTT
Statistics
Matches: 601, Mismatches: 151, Indels: 102
0.70 0.18 0.12
Matches are distributed among these distances:
90 15 0.02
91 19 0.03
92 24 0.04
93 208 0.35
94 45 0.07
95 4 0.01
96 39 0.06
97 4 0.01
98 115 0.19
99 128 0.21
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.35
Consensus pattern (93 bp):
CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTATTACTCGTTTTAATCTGATCCAC
TGCAACTTCAGGGATATAGGATCTGGTG
Found at i:248235 original size:192 final size:192
Alignment explanation
Indices: 247714--248732 Score: 1122
Period size: 192 Copynumber: 5.3 Consensus size: 192
247704 TGGTATTGAA
* * ** *
247714 GCTTCTCTCCATTCCAACTGTAACCTCAAGGACATTGAGATAAGCTTTTTTTGTTTTAGT-TCGA
1 GCTTCACTCCATTCC-ACTGTAACCTCAAGGACATTGAGATATGC-TTCGTTGTTTTAATCT-GA
** * * * * * * * * * *
247778 CCCACTGTAACTTTAGGGGCATAGGATTTGGTGTTGCAACTTCACTCTATTCCACTGTAACCTCA
63 CCCACTACAAC-TCAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTCTAACCTTA
* * * * * *
247843 TGGACATTGAGATCTATTACTCATTTTGATTTGATTCACTGTAACTTCAGGGATATAAGATCTGG
127 GGGACATTGAGATCTGTTACTCATTTTGATCTGATCCACTGCAACTTCAGGGATATAGGATCTGG
247908 T
192 T
* *
247909 GCTTCACTCCATTCCACTGTAACCTCAAGGACATTGA-ATCTGCTTCGTTGTTTTAACCTGACCC
1 GCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATATGCTTCGTTGTTTTAATCTGACCC
* * *
247973 ACTACAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTTTAACCTTAAGGA
66 ACTACAACTCAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTCTAACCTTAGGGA
* * *
248038 CATTGAGATCTGTTACTCATTTTGATATGATCCATTGCAACTTCAAGGATATAGGATCTGGT
131 CATTGAGATCTGTTACTCATTTTGATCTGATCCACTGCAACTTCAGGGATATAGGATCTGGT
* * * * * * **
248100 GCTTCACTCTACTCCATTGTAACCTTAGGGACATTGAGATATACTTCGTTGTTTTAATCAAACCC
1 GCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATATGCTTCGTTGTTTTAATCTGACCC
* * * *
248165 ACTGCAAGTCAAGGGTATGGGATTTTATGTTGTAACTTCTCTCCATTCCACACTAACCTTAGGGA
66 ACTACAACTCAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTCTAACCTTAGGGA
* *
248230 CATTGAGAT-TCGTTACTCATTTTTATCTGATTCACTGCAACTTCAGGGATATAGGATCTGGT
131 CATTGAGATCT-GTTACTCATTTTGATCTGATCCACTGCAACTTCAGGGATATAGGATCTGGT
* * * * * * *
248292 GTTTTACTCTAGTCCACTATAACCTCAGGGACATTGAG--AT-CTTCATTGTTTTAATCTGACCC
1 GCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATATGCTTCGTTGTTTTAATCTGACCC
* * * *
248354 ACTACAACTCAGGGGTATGGGATTTGATGTTGCAACTTCTCTCTATTCCA-TACTAACCTTCGGG
66 ACTACAACTCAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACT-CTAACCTTAGGG
* * * ** * * *
248418 ACATTGAGAT-TCGCTGCTCGTTTTGATCCAATCCAGTACAACTTCAGGGATATAAGATCTGGT
130 ACATTGAGATCT-GTTACTCATTTTGATCTGATCCACTGCAACTTCAGGGATATAGGATCTGGT
* * * *
248481 GCTTCACTCCATTCAACTGTAACCTCAATGACATTGAGATCTGCTTCGTTGTTTTAATCTGACCT
1 GCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATATGCTTCGTTGTTTTAATCTGACCC
** * * *
248546 ACTGTAACTC-AGGGATATGGGATTTGATATTGTAACTTCTCTCCATTCCATTGTAACCTCTA-G
66 ACTACAACTCAAGGG-TATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTCTAACCT-TAGG
* ** * ** * * *
248609 AACATTGAGATCCATTACTCATTTTGACCCAATCCAATGCAACTTCAAGGATATAGGATTTGGT
129 GACATTGAGATCTGTTACTCATTTTGATCTGATCCACTGCAACTTCAGGGATATAGGATCTGGT
* * *
248673 GCTTCACTCCATTCCACTGTAACCTCAAGGACATTAAGATTTGCTTCGTTGTTTCAATCT
1 GCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATATGCTTCGTTGTTTTAATCT
248733 ACTTCATTAT
Statistics
Matches: 702, Mismatches: 111, Indels: 25
0.84 0.13 0.03
Matches are distributed among these distances:
189 157 0.22
190 2 0.00
191 139 0.20
192 361 0.51
193 7 0.01
194 22 0.03
195 14 0.02
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (192 bp):
GCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATATGCTTCGTTGTTTTAATCTGACCC
ACTACAACTCAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTCTAACCTTAGGGA
CATTGAGATCTGTTACTCATTTTGATCTGATCCACTGCAACTTCAGGGATATAGGATCTGGT
Found at i:248531 original size:381 final size:380
Alignment explanation
Indices: 247714--248726 Score: 1192
Period size: 381 Copynumber: 2.6 Consensus size: 380
247704 TGGTATTGAA
* * ** *
247714 GCTTCTCTCCATTCCAACTGTAACCTCAAGGACATTGAGATAAGCTTTTTTTGTTTTAGTTCGAC
1 GCTTCACTCCATT-CAACTGTAACCTCAAGGACATTGAGATATGC-TTCGTTGTTTTA-ATCGAC
* * * * * * * * *
247779 CCACTGTAACTTTAGGGGCATAGGATTTGGTGTTGCAACTTCACTCTATTCCACTGTAACCTCAT
63 CCACTGTAAC-TCAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTTA-
* * *
247844 GGACATTGAGA-TCTATTACTCATTTTGATTTGATTCACTGTAACTTCAGGGATATAAGATCTGG
126 GGACATTGAGATTC-ATTACTCATTTTGATCTGATTCACTGCAACTTCAGGGATATAGGATCTGG
*
247908 TGCTTCACTCCATTCCACTGTAACCTCAAGGACATTGA-ATCTGCTTCGTTGTTTTAACCTGACC
190 TGCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGA--TGCTTCATTGTTTTAACCTGACC
* *
247972 CACTACAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTTTAACCTTAAGG
253 CACTACAACTCAGGGGTATGGGATTTGATGTTGCAACTTCTCTCCATTCCACTCTAACCTTAAGG
* ** * * *
248037 ACATTGAGATCTGTTACTCATTTTGATATGATCCATTGCAACTTCAAGGATATAGGATCTGGT
318 ACATTGAGATCTGCTACTCATTTTGATACAATCCAGTACAACTTCAAGGATATAAGATCTGGT
* * * * * * * *
248100 GCTTCACTCTACTCCATTGTAACCTTAGGGACATTGAGATATACTTCGTTGTTTTAATCAAACCC
1 GCTTCACTCCATTCAACTGTAACCTCAAGGACATTGAGATATGCTTCGTTGTTTTAATC-GACCC
* * * **
248165 ACTGCAAGTCAAGGGTATGGGATTTTATGTTGTAACTTCTCTCCATTCCACACTAACCTTAGGGA
65 ACTGTAACTCAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTTA-GGA
* * *
248230 CATTGAGATTCGTTACTCATTTTTATCTGATTCACTGCAACTTCAGGGATATAGGATCTGGTGTT
129 CATTGAGATTCATTACTCATTTTGATCTGATTCACTGCAACTTCAGGGATATAGGATCTGGTGCT
* * * * * *
248295 TTACTCTAGTCCACTATAACCTCAGGGACATTGAGAT-CTTCATTGTTTTAATCTGACCCACTAC
194 TCACTCCATTCCACTGTAACCTCAAGGACATTGAGATGCTTCATTGTTTTAACCTGACCCACTAC
* **
248359 AACTCAGGGGTATGGGATTTGATGTTGCAACTTCTCTCTATTCCA-TACTAACCTTCGGGACATT
259 AACTCAGGGGTATGGGATTTGATGTTGCAACTTCTCTCCATTCCACT-CTAACCTTAAGGACATT
* * * *
248423 GAGAT-TCGCTGCTCGTTTTGATCCAATCCAGTACAACTTCAGGGATATAAGATCTGGT
323 GAGATCT-GCTACTCATTTTGATACAATCCAGTACAACTTCAAGGATATAAGATCTGGT
* * *
248481 GCTTCACTCCATTCAACTGTAACCTCAATGACATTGAGATCTGCTTCGTTGTTTTAATCTGACCT
1 GCTTCACTCCATTCAACTGTAACCTCAAGGACATTGAGATATGCTTCGTTGTTTTAATC-GACCC
* * *
248546 ACTGTAACTC-AGGGATATGGGATTTGATATTGTAACTTCTCTCCATTCCATTGTAACCTCTAGA
65 ACTGTAACTCAAGGG-TATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCT-TAGG
* * ** * * * *
248610 ACATTGAGATCCATTACTCATTTTGACCCAATCCAATGCAACTTCAAGGATATAGGATTTGGTGC
128 ACATTGAGATTCATTACTCATTTTGATCTGATTCACTGCAACTTCAGGGATATAGGATCTGGTGC
* *
248675 TTCACTCCATTCCACTGTAACCTCAAGGACATTAAGATTTGCTTCGTTGTTT
193 TTCACTCCATTCCACTGTAACCTCAAGGACATTGAGA--TGCTTCATTGTTT
248727 CAATCTACTT
Statistics
Matches: 523, Mismatches: 94, Indels: 22
0.82 0.15 0.03
Matches are distributed among these distances:
380 6 0.01
381 314 0.60
382 3 0.01
383 132 0.25
384 33 0.06
385 25 0.05
386 10 0.02
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (380 bp):
GCTTCACTCCATTCAACTGTAACCTCAAGGACATTGAGATATGCTTCGTTGTTTTAATCGACCCA
CTGTAACTCAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTTAGGACA
TTGAGATTCATTACTCATTTTGATCTGATTCACTGCAACTTCAGGGATATAGGATCTGGTGCTTC
ACTCCATTCCACTGTAACCTCAAGGACATTGAGATGCTTCATTGTTTTAACCTGACCCACTACAA
CTCAGGGGTATGGGATTTGATGTTGCAACTTCTCTCCATTCCACTCTAACCTTAAGGACATTGAG
ATCTGCTACTCATTTTGATACAATCCAGTACAACTTCAAGGATATAAGATCTGGT
Found at i:248973 original size:49 final size:49
Alignment explanation
Indices: 248896--249109 Score: 275
Period size: 49 Copynumber: 4.3 Consensus size: 49
248886 CAATCGTTAT
* * * *
248896 GGCTTCAATCTTTCCCTTCACATTTCTAGGGTATAAGGTTCATCATTGC
1 GGCTTCAATCTTTCCCTCCACATCTCTAGGGTATAAGATTCACCATTGC
* *
248945 GGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCACCATTGC
1 GGCTTCAATCTTTCCCTCCACATCTCTAGGGTATAAGATTCACCATTGC
* * * **
248994 GGCTTCAACCTTTCCCTCCATATCTATAGGGTATAAGATTCGTCATTGC
1 GGCTTCAATCTTTCCCTCCACATCTCTAGGGTATAAGATTCACCATTGC
* * * *
249043 AGCTTCAATCTTTCCCTCTATATTCTCTAAGGTATAAGATTCACCATTGC
1 GGCTTCAATCTTTCCCTCCACA-TCTCTAGGGTATAAGATTCACCATTGC
*
249093 GACTTCAATCTTTCCCT
1 GGCTTCAATCTTTCCCT
249110 TCATGTCTTC
Statistics
Matches: 146, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 108 0.74
50 38 0.26
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (49 bp):
GGCTTCAATCTTTCCCTCCACATCTCTAGGGTATAAGATTCACCATTGC
Found at i:249091 original size:50 final size:49
Alignment explanation
Indices: 248896--249135 Score: 259
Period size: 49 Copynumber: 4.9 Consensus size: 49
248886 CAATCGTTAT
* * * *
248896 GGCTTCAATCTTTCCCT-TCACATTTCTAGGGTATAAGGTTCATCATTGC
1 GGCTTCAATCTTTCCCTCT-ATATCTCTAGGGTATAAGATTCACCATTGC
* * * *
248945 GGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCACCATTGC
1 GGCTTCAATCTTTCCCTCTATATCTCTAGGGTATAAGATTCACCATTGC
* * * **
248994 GGCTTCAACCTTTCCCTCCATATCTATAGGGTATAAGATTCGTCATTGC
1 GGCTTCAATCTTTCCCTCTATATCTCTAGGGTATAAGATTCACCATTGC
* *
249043 AGCTTCAATCTTTCCCTCTATATTCTCTAAGGTATAAGATTCACCATTGC
1 GGCTTCAATCTTTCCCTCTATA-TCTCTAGGGTATAAGATTCACCATTGC
* * * *
249093 GACTTCAATCTTTCCCT-TCATGTCTTCTAAGGTATATGATTCA
1 GGCTTCAATCTTTCCCTCT-ATATC-TCTAGGGTATAAGATTCA
249136 ACGTTTCCTT
Statistics
Matches: 167, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
49 110 0.66
50 57 0.34
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.37
Consensus pattern (49 bp):
GGCTTCAATCTTTCCCTCTATATCTCTAGGGTATAAGATTCACCATTGC
Found at i:252831 original size:29 final size:29
Alignment explanation
Indices: 252797--252894 Score: 83
Period size: 29 Copynumber: 3.2 Consensus size: 29
252787 TGAAAATTTT
252797 AAAAAATAATAATAAAAGGATTAAATTAA
1 AAAAAATAATAATAAAAGGATTAAATTAA
* * *
252826 AGAAAAA-CATATTAAAAGG-GTACAATTTAA
1 A-AAAAATAATAATAAAAGGATTA-AA-TTAA
*
252856 AAATAAATGAAATCATAAAAGGATTAAATTAA
1 AAA-AAAT--AATAATAAAAGGATTAAATTAA
252888 AATAAAA
1 AA-AAAA
252895 ATGGAGTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
28 2 0.04
29 15 0.28
30 13 0.25
32 9 0.17
33 12 0.23
34 2 0.04
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.23
Consensus pattern (29 bp):
AAAAAATAATAATAAAAGGATTAAATTAA
Found at i:256668 original size:21 final size:21
Alignment explanation
Indices: 256620--256668 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
256610 CCCACAATTT
*
256620 TTTTATTTCCTTTACCTCCAA
1 TTTTATTTACTTTACCTCCAA
*** *
256641 AAATATTTACTTTACCTCCCA
1 TTTTATTTACTTTACCTCCAA
256662 TTTTATT
1 TTTTATT
256669 CCCAAAAATC
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTATTTACTTTACCTCCAA
Found at i:257693 original size:12 final size:12
Alignment explanation
Indices: 257676--257774 Score: 85
Period size: 12 Copynumber: 8.3 Consensus size: 12
257666 ATAACAGCCA
*
257676 AACAACCAAAAT
1 AACAACAAAAAT
*
257688 AACAACCAAAAT
1 AACAACAAAAAT
*
257700 AGCAGA-AAAAAT
1 AACA-ACAAAAAT
* * *
257712 AACAGC-AAGAC
1 AACAACAAAAAT
257723 AACAACAAAAAT
1 AACAACAAAAAT
*
257735 AACAGCAAAAAT
1 AACAACAAAAAT
* *
257747 AGCAACAAAAAC
1 AACAACAAAAAT
*
257759 AGCAACAAAAAT
1 AACAACAAAAAT
257771 AACA
1 AACA
257775 TCATCAAAAC
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
11 8 0.12
12 60 0.87
13 1 0.01
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:257712 original size:44 final size:46
Alignment explanation
Indices: 257662--257750 Score: 121
Period size: 47 Copynumber: 2.0 Consensus size: 46
257652 AAAAAAGCAT
*
257662 AAAAATAACAGCCAA-ACAAC-C-AAAATAACAACCAAAATAGCAGA
1 AAAAATAACAG-CAAGACAACACAAAAATAACAACAAAAATAGCAGA
*
257706 AAAAATAACAGCAAGACAACAACAAAAATAACAGCAAAAATAGCA
1 AAAAATAACAGCAAGACAAC-ACAAAAATAACAACAAAAATAGCA
257751 ACAAAAACAG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
43 3 0.08
44 16 0.41
46 1 0.03
47 19 0.49
ACGTcount: A:0.65, C:0.20, G:0.08, T:0.07
Consensus pattern (46 bp):
AAAAATAACAGCAAGACAACACAAAAATAACAACAAAAATAGCAGA
Found at i:257765 original size:36 final size:35
Alignment explanation
Indices: 257676--257774 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 35
257666 ATAACAGCCA
* * *
257676 AACAACCAAAATAACAACCAAAATAGCAGAAAAAAT
1 AACAA-CAAAACAACAACAAAAATAACAGAAAAAAT
* * *
257712 AACAGCAAGACAACAACAAAAATAACAGCAAAAAT
1 AACAACAAAACAACAACAAAAATAACAGAAAAAAT
* *
257747 AGCAACAAAAACAGCAACAAAAATAACA
1 AACAAC-AAAACAACAACAAAAATAACA
257775 TCATCAAAAC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 29 0.56
36 23 0.44
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.06
Consensus pattern (35 bp):
AACAACAAAACAACAACAAAAATAACAGAAAAAAT
Found at i:257824 original size:21 final size:21
Alignment explanation
Indices: 257800--257896 Score: 80
Period size: 22 Copynumber: 4.8 Consensus size: 21
257790 AAAAAGCATC
*
257800 AAAACAACAACCAAAACAGT-
1 AAAACAACAACCAAAATAGTA
*
257820 -AAA-AA-GACCAAAATAGTA
1 AAAACAACAACCAAAATAGTA
* *
257838 AAAA-AATAACACCAAAATAGCA
1 AAAACAA-CA-ACCAAAATAGTA
*
257860 TAAAACAACAACCAAAATAGAA
1 -AAAACAACAACCAAAATAGTA
257882 AAAACAAC-ACCAAAA
1 AAAACAACAACCAAAA
257897 CAATAATATA
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
17 10 0.16
18 2 0.03
19 8 0.12
20 7 0.11
21 8 0.12
22 22 0.34
23 5 0.08
24 2 0.03
ACGTcount: A:0.68, C:0.20, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAACAACAACCAAAATAGTA
Found at i:257831 original size:17 final size:17
Alignment explanation
Indices: 257809--257841 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
257799 CAAAACAACA
257809 ACCAAAACAGTAAAAAG
1 ACCAAAACAGTAAAAAG
*
257826 ACCAAAATAGTAAAAA
1 ACCAAAACAGTAAAAA
257842 AATAACACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.15, G:0.09, T:0.09
Consensus pattern (17 bp):
ACCAAAACAGTAAAAAG
Found at i:257852 original size:22 final size:20
Alignment explanation
Indices: 257826--257896 Score: 88
Period size: 22 Copynumber: 3.4 Consensus size: 20
257816 CAGTAAAAAG
*
257826 ACCAAAATAGTAAAAAAATAAC
1 ACCAAAATAG--AAAAAACAAC
*
257848 ACCAAAATAGCATAAAACAAC
1 ACCAAAATAG-AAAAAACAAC
257869 AACCAAAATAGAAAAAACAAC
1 -ACCAAAATAGAAAAAACAAC
257890 ACCAAAA
1 ACCAAAA
257897 CAATAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.16
21 17 0.39
22 20 0.45
ACGTcount: A:0.68, C:0.20, G:0.04, T:0.08
Consensus pattern (20 bp):
ACCAAAATAGAAAAAACAAC
Found at i:260494 original size:3 final size:3
Alignment explanation
Indices: 260486--260522 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
260476 CCTCTTCCTT
260486 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC -TC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
260523 TGGAATCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:264645 original size:3 final size:3
Alignment explanation
Indices: 264637--264661 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
264627 CATCTCTTCC
264637 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
264662 TGGAATCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:267467 original size:17 final size:17
Alignment explanation
Indices: 267436--267485 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 17
267426 AAATGCTAAT
267436 AAAAAATATTAAAAATTAG
1 AAAAAATA-TAAAAATT-G
*
267455 AAAAAATATAAAAATTT
1 AAAAAATATAAAAATTG
267472 AAAAAATATAAAAA
1 AAAAAATATAAAAA
267486 ATTGTGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 14 0.47
18 8 0.27
19 8 0.27
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAAATATAAAAATTG
Found at i:267467 original size:26 final size:26
Alignment explanation
Indices: 267436--267487 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
267426 AAATGCTAAT
*
267436 AAAAAATATTAAAAATTAGAAAAAATA
1 AAAAAAT-TTAAAAAATAGAAAAAATA
* *
267463 TAAAAATTTAAAAAATATAAAAAAT
1 AAAAAATTTAAAAAATAGAAAAAAT
267488 TGTGAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (26 bp):
AAAAAATTTAAAAAATAGAAAAAATA
Found at i:267524 original size:8 final size:9
Alignment explanation
Indices: 267513--267618 Score: 58
Period size: 10 Copynumber: 11.4 Consensus size: 9
267503 AAATCGTAAA
267513 AAAAT-TAT
1 AAAATATAT
267521 AAAATATAT
1 AAAATATAT
*
267530 AGAAATATAA
1 A-AAATATAT
267540 AAAAT-TAT
1 AAAATATAT
*
267548 AAAATCTAAT
1 AAAATAT-AT
* * *
267558 AAAGTCGTAAG
1 AAAAT-AT-AT
267569 AAAATTATAT
1 AAAA-TATAT
*
267579 AAAATATAA
1 AAAATATAT
267588 AGAAATATA-
1 A-AAATATAT
*
267597 AAAAT-TTT
1 AAAATATAT
267605 AAAAATATAT
1 -AAAATATAT
267615 AAAA
1 AAAA
267619 ATTATCATAT
Statistics
Matches: 77, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
7 1 0.01
8 16 0.21
9 24 0.31
10 28 0.36
11 7 0.09
12 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (9 bp):
AAAATATAT
Found at i:267601 original size:57 final size:58
Alignment explanation
Indices: 267455--267608 Score: 183
Period size: 57 Copynumber: 2.7 Consensus size: 58
267445 TAAAAATTAG
* * * * *
267455 AAAAAATATA-AAAATTTAAA-AAATATAAAAAATTGTGAAATTTTATAAAAATCGTA
1 AAAAAATATATAAAATATAAAGAAATATAAAAAATTATAAAATCTAATAAAAATCGTA
* *
267511 AAAAAAT-TATAAAATATATAGAAATATAAAAAATTATAAAATCTAAT-AAAGTCGTA
1 AAAAAATATATAAAATATAAAGAAATATAAAAAATTATAAAATCTAATAAAAATCGTA
* *
267567 AGAAAATTATATAAAATATAAAGAAATAT-AAAAATTTTAAAA
1 A-AAAAATATATAAAATATAAAGAAATATAAAAAATTATAAAA
267609 ATATATAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
55 2 0.02
56 24 0.29
57 39 0.46
58 19 0.23
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (58 bp):
AAAAAATATATAAAATATAAAGAAATATAAAAAATTATAAAATCTAATAAAAATCGTA
Found at i:267617 original size:10 final size:10
Alignment explanation
Indices: 267437--267620 Score: 78
Period size: 9 Copynumber: 19.6 Consensus size: 10
267427 AATGCTAATA
267437 AAAAATAT-T
1 AAAAATATAT
*
267446 AAAAAT-TAG
1 AAAAATATAT
267455 AAAAA-ATAT
1 AAAAATATAT
*
267464 AAAAATTTA-
1 AAAAATATAT
267473 AAAAATATA-
1 AAAAATATAT
*
267482 AAAAAT-TGT
1 AAAAATATAT
* * *
267491 GAAATTTTAT
1 AAAAATATAT
* *
267501 AAAAATCGTAA
1 AAAAAT-ATAT
267512 AAAAAT-TAT
1 AAAAATATAT
267521 -AAAATATAT
1 AAAAATATAT
*
267530 AGAAATATA-
1 AAAAATATAT
267539 AAAAAT-TAT
1 AAAAATATAT
*
267548 -AAAATCTA-
1 AAAAATATAT
* *
267556 ATAAAGTCGTA-
1 A-AAAAT-ATAT
267567 AGAAAAT-TAT
1 A-AAAATATAT
267577 ATAAAATATA-
1 A-AAAATATAT
*
267587 AAGAA-ATAT
1 AAAAATATAT
*
267596 AAAAAT-TTT
1 AAAAATATAT
267605 AAAAATATAT
1 AAAAATATAT
267615 AAAAAT
1 AAAAAT
267621 TATCATATCA
Statistics
Matches: 133, Mismatches: 24, Indels: 35
0.69 0.12 0.18
Matches are distributed among these distances:
8 17 0.13
9 65 0.49
10 34 0.26
11 17 0.13
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (10 bp):
AAAAATATAT
Found at i:268077 original size:88 final size:88
Alignment explanation
Indices: 267983--268285 Score: 256
Period size: 88 Copynumber: 3.3 Consensus size: 88
267973 TAAGAGCAAT
* *
267983 GGCTTAATTGCTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTT-GAAAGTTCAAGTACCT
1 GGCTTAATTGCTTTTTTGAAAAAGTTTGAGGGTATTTTT-ATGCATTTGGAAAGTTCAAGT-CCT
**
268047 -AATTGAGTGGGAAAAAAAAGTAGG
64 CAATTGAGTGCAAAAAAAAAGTAGG
* * *
268071 GGCTTAATTGTTTTTTTGAAGAAGTTTGAGGGTATTTTTATGCATTTGGAAAGTTCAAGTGCTCA
1 GGCTTAATTGCTTTTTTGAAAAAGTTTGAGGGTATTTTTATGCATTTGGAAAGTTCAAGTCCTCA
*
268136 ATTGAGTGCAAAAAAAAAAAAGAAAAGGAAG
66 ATTGAGTGC---AAAAAAAAAG--TA-G--G
* ** * * * * *
268167 GGCTTAATTGTTTTTTTTTTTTAAAGGTTTGAGGGTCTTTTTAATGCATTTTGAAACTTCAAGTA
1 GGCTTAATTG---CTTTTTTGAAAAAGTTTGAGGGTATTTTT-ATGCATTTGGAAAGTTCAAGTC
268232 CTCCAA-TGAGTGCAAAAAAAAA--AGG
62 CT-CAATTGAGTGCAAAAAAAAAGTAGG
* * *
268257 GACTTAATTACTTTTTTTGAGAAAGTTTG
1 GGCTTAATTGC-TTTTTTGAAAAAGTTTG
268286 GAGGATTTTT
Statistics
Matches: 176, Mismatches: 23, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
87 10 0.06
88 69 0.39
90 9 0.05
91 9 0.05
92 1 0.01
93 2 0.01
94 1 0.01
96 11 0.06
97 9 0.05
99 24 0.14
100 28 0.16
101 3 0.02
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (88 bp):
GGCTTAATTGCTTTTTTGAAAAAGTTTGAGGGTATTTTTATGCATTTGGAAAGTTCAAGTCCTCA
ATTGAGTGCAAAAAAAAAGTAGG
Found at i:273168 original size:18 final size:19
Alignment explanation
Indices: 273125--273174 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
273115 CTTTATTGAG
273125 ATAAAAACTTTCTTTTCCC
1 ATAAAAACTTTCTTTTCCC
273144 ATAAAAACTTTCTTTTCCC
1 ATAAAAACTTTCTTTTCCC
273163 ATAAAAACTTTC
1 ATAAAAACTTTC
273175 CTTCCATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAAACTTTCTTTTCCC
Found at i:278188 original size:15 final size:15
Alignment explanation
Indices: 278168--278219 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
278158 TTGTTTCAAG
278168 TTATATTTTAATTAT
1 TTATATTTTAATTAT
* *
278183 TTATATTTGAAATA-
1 TTATATTTTAATTAT
278197 TTATATTTTAATTAT
1 TTATATTTTAATTAT
278212 TTATATTT
1 TTATATTT
278220 GAAATGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:278201 original size:29 final size:29
Alignment explanation
Indices: 278167--278263 Score: 149
Period size: 29 Copynumber: 3.3 Consensus size: 29
278157 TTTGTTTCAA
278167 GTTATATTTTAATTATTTATATTTGAAAT
1 GTTATATTTTAATTATTTATATTTGAAAT
*
278196 ATTATATTTTAATTATTTATATTTGAAAT
1 GTTATATTTTAATTATTTATATTTGAAAT
* * *
278225 GTTATTTTTTACTTGTTTATATTTGAAAT
1 GTTATATTTTAATTATTTATATTTGAAAT
278254 GTTATGATTT
1 GTTAT-ATTT
278264 AGTCAATTGT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
29 58 0.95
30 3 0.05
ACGTcount: A:0.31, C:0.01, G:0.08, T:0.60
Consensus pattern (29 bp):
GTTATATTTTAATTATTTATATTTGAAAT
Found at i:278229 original size:14 final size:14
Alignment explanation
Indices: 278183--278263 Score: 65
Period size: 14 Copynumber: 5.6 Consensus size: 14
278173 TTTTAATTAT
*
278183 TTATATTTGAAATA
1 TTATATTTGAAATG
*
278197 TTATATTTTAATTAT-
1 TTATATTTGAA--ATG
278212 TTATATTTGAAATG
1 TTATATTTGAAATG
* * **
278226 TTATTTTTTACTTG
1 TTATATTTGAAATG
278240 TTTATATTTGAAATG
1 -TTATATTTGAAATG
278255 TTATGATTT
1 TTAT-ATTT
278264 AGTCAATTGT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
13 2 0.04
14 24 0.46
15 24 0.46
16 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.09, T:0.59
Consensus pattern (14 bp):
TTATATTTGAAATG
Found at i:278256 original size:15 final size:15
Alignment explanation
Indices: 278168--278256 Score: 65
Period size: 15 Copynumber: 6.1 Consensus size: 15
278158 TTGTTTCAAG
* * *
278168 TTATATTTTAATTAT
1 TTATATTTGAAATGT
*
278183 TTATATTTGAAAT-A
1 TTATATTTGAAATGT
* * *
278197 TTATATTTTAATTAT
1 TTATATTTGAAATGT
278212 TTATATTTGAAATG-
1 TTATATTTGAAATGT
* * **
278226 TTATTTTTTACTTGT
1 TTATATTTGAAATGT
278241 TTATATTTGAAATGT
1 TTATATTTGAAATGT
278256 T
1 T
278257 ATGATTTAGT
Statistics
Matches: 55, Mismatches: 17, Indels: 4
0.72 0.22 0.05
Matches are distributed among these distances:
14 21 0.38
15 34 0.62
ACGTcount: A:0.31, C:0.01, G:0.07, T:0.61
Consensus pattern (15 bp):
TTATATTTGAAATGT
Found at i:285611 original size:23 final size:23
Alignment explanation
Indices: 285574--285651 Score: 106
Period size: 25 Copynumber: 3.3 Consensus size: 23
285564 TATACATATA
285574 TTTTTTTTC-TT-CTTTTCCCTT
1 TTTTTTTTCTTTCCTTTTCCCTT
285595 TTTTTTTTCTTTCCTTTTCTCTCTT
1 TTTTTTTTCTTTCCTTTTC-C-CTT
*
285620 TTTTTTTTCTTTCCTTTTCTCTCT
1 TTTTTTTTCTTTCCTTTTCCCT-T
285644 TTTTTTTT
1 TTTTTTTT
285652 ATGTGACTGA
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
21 9 0.18
22 2 0.04
23 8 0.16
24 10 0.20
25 22 0.43
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTTTTCTTTCCTTTTCCCTT
Found at i:285619 original size:14 final size:14
Alignment explanation
Indices: 285602--285645 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
285592 CTTTTTTTTT
285602 TCTTTCCTTTTCTC
1 TCTTTCCTTTTCTC
*
285616 TCTTT--TTTT-TT
1 TCTTTCCTTTTCTC
285627 TCTTTCCTTTTCTC
1 TCTTTCCTTTTCTC
285641 TCTTT
1 TCTTT
285646 TTTTTTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 4 0.16
14 11 0.44
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TCTTTCCTTTTCTC
Found at i:293467 original size:13 final size:14
Alignment explanation
Indices: 293449--293478 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
293439 GTCAATGCAA
293449 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
293462 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
293476 TCA
1 TCA
293479 AAGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:295018 original size:9 final size:9
Alignment explanation
Indices: 295006--295043 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
294996 CAAATATAAT
295006 TTTTTCTTC
1 TTTTTCTTC
295015 TTTTTC-T-
1 TTTTTCTTC
295022 TTTTTCTTC
1 TTTTTCTTC
295031 TTTTT-TTC
1 TTTTTCTTC
295039 TTTTT
1 TTTTT
295044 TCAAGTGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.22
8 10 0.37
9 11 0.41
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:295026 original size:16 final size:17
Alignment explanation
Indices: 295005--295045 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
294995 GCAAATATAA
295005 TTTTTTCTTC-TTTTTC
1 TTTTTTCTTCTTTTTTC
295021 TTTTTTCTTCTTTTTTTC
1 TTTTTTCTTC-TTTTTTC
295039 TTTTTTC
1 TTTTTTC
295046 AAGTGACCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.43
18 13 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTCTTCTTTTTTC
Found at i:295648 original size:18 final size:18
Alignment explanation
Indices: 295625--295665 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
295615 TAACAAAAGG
*
295625 AATGCAGTGACAA-AATAA
1 AATGCAGGGACAATAA-AA
295643 AATGCAGGGACAATAAAA
1 AATGCAGGGACAATAAAA
295661 AATGC
1 AATGC
295666 CTGAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.54, C:0.12, G:0.20, T:0.15
Consensus pattern (18 bp):
AATGCAGGGACAATAAAA
Found at i:299256 original size:13 final size:14
Alignment explanation
Indices: 299238--299267 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
299228 GTCAATGTAA
299238 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
299251 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
299265 TCA
1 TCA
299268 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:305911 original size:37 final size:37
Alignment explanation
Indices: 305868--305944 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
305858 TAATGTCGCT
*
305868 ACATGAGCACTTCTAGATTGCG-TCCAAAACTGTCGTC
1 ACATGAGCACTTCTAGATTG-GACCCAAAACTGTCGTC
*
305905 ACATGAGCACTTTTAGATTGGACCCAAAACTGTCGTC
1 ACATGAGCACTTCTAGATTGGACCCAAAACTGTCGTC
305942 ACA
1 ACA
305945 GGAATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (37 bp):
ACATGAGCACTTCTAGATTGGACCCAAAACTGTCGTC
Found at i:305967 original size:37 final size:37
Alignment explanation
Indices: 305891--305976 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
305881 TAGATTGCGT
* * * *
305891 CCAAAACTGTCGTCACATGAGCACTTTTAGATTGGAC
1 CCAAAACTGTCGTCACAGGAACACTTTTAGAATGCAC
* *
305928 CCAAAACTGTCGTCACAGGAATA-TTTTCGGAATGCAC
1 CCAAAACTGTCGTCACAGGAACACTTTT-AGAATGCAC
*
305965 CCAAGACTGTCG
1 CCAAAACTGTCG
305977 CTACATAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 4 0.10
37 37 0.90
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (37 bp):
CCAAAACTGTCGTCACAGGAACACTTTTAGAATGCAC
Found at i:306056 original size:37 final size:38
Alignment explanation
Indices: 305960--306060 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
305950 ATTTTCGGAA
* *
305960 TGCACCCAAGACTGTCGCTACATAAATATTCTTCAAAT
1 TGCACCCAAGAATGTCGCTGCATAAATATTCTTCAAAT
* * * *
305998 TGCATCC-AGAACTATCACTGCATAAGTATTCTTC-AAT
1 TGCACCCAAGAA-TGTCGCTGCATAAATATTCTTCAAAT
306035 TGCACCCAAGAATGTCGCTGCATAAA
1 TGCACCCAAGAATGTCGCTGCATAAA
306061 CATGTCTAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 23 0.45
38 28 0.55
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (38 bp):
TGCACCCAAGAATGTCGCTGCATAAATATTCTTCAAAT
Found at i:306081 original size:26 final size:26
Alignment explanation
Indices: 306043--306100 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
306033 ATTGCACCCA
306043 AGAA-TGTCGCTGCATAAACATGTCT
1 AGAATTGTCGCTGCATAAACATGTCT
* * *
306068 AGAATTGTTGCTGCATGAACGTGTCT
1 AGAATTGTCGCTGCATAAACATGTCT
306094 AGAATTG
1 AGAATTG
306101 CACCCAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (26 bp):
AGAATTGTCGCTGCATAAACATGTCT
Found at i:316561 original size:23 final size:23
Alignment explanation
Indices: 316513--316561 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
316503 ATTTTTTGGT
* * *
316513 AGATATATATTATATTAAATAGA
1 AGATATATATTATAGTAAAGAAA
316536 AGATATATAATT-TAGTAAAGAAA
1 AGATATAT-ATTATAGTAAAGAAA
316559 AGA
1 AGA
316562 AGAAGCTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (23 bp):
AGATATATATTATAGTAAAGAAA
Found at i:323251 original size:33 final size:33
Alignment explanation
Indices: 323214--323289 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
323204 GGGTTTAAAT
323214 GATAAAAATATCTTTAATATAATATTTATT-TTA
1 GATAAAAATATCTTTAA-ATAATATTTATTGTTA
* * *
323247 GATAAAAATATTTTTAAATATTATTTATTGTTT
1 GATAAAAATATCTTTAAATAATATTTATTGTTA
*
323280 GATATAAATA
1 GATAAAAATA
323290 ATAGATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 11 0.29
33 27 0.71
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (33 bp):
GATAAAAATATCTTTAAATAATATTTATTGTTA
Found at i:330819 original size:16 final size:16
Alignment explanation
Indices: 330798--330829 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
330788 GGTTATTTTA
330798 TATTAGCTGATCATAG
1 TATTAGCTGATCATAG
330814 TATTAGCTGATCATAG
1 TATTAGCTGATCATAG
330830 GCAAGTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (16 bp):
TATTAGCTGATCATAG
Found at i:333044 original size:16 final size:17
Alignment explanation
Indices: 333018--333051 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
333008 AGACAAAATG
*
333018 CAATCAACTTCATTGTA
1 CAATCAACTTCATGGTA
333035 CAAT-AACTTCATGGTA
1 CAATCAACTTCATGGTA
333051 C
1 C
333052 TTTAACCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (17 bp):
CAATCAACTTCATGGTA
Found at i:335497 original size:29 final size:30
Alignment explanation
Indices: 335434--335507 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
335424 AAATTTTAAA
335434 TTAATAAA-AATAAAATTACACTTTAACCTT
1 TTAA-AAATAATAAAATTACACTTTAACCTT
* *
335464 CTAAAAATAATAAAATTTA-A-TTTAATCTT
1 TTAAAAATAATAAAA-TTACACTTTAACCTT
*
335493 TTAAAAATTATAAAA
1 TTAAAAATAATAAAA
335508 ATATATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 24 0.63
30 11 0.29
31 3 0.08
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (30 bp):
TTAAAAATAATAAAATTACACTTTAACCTT
Found at i:337241 original size:20 final size:21
Alignment explanation
Indices: 337205--337265 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
337195 TTTTTGTTTT
*
337205 AATTA-AGTTTAGGGTTTTT-A
1 AATTAGAGTTTA-AGTTTTTAA
*
337225 AATTAGGGTTTAAGTTTTTAA
1 AATTAGAGTTTAAGTTTTTAA
* *
337246 AATTAGAGTTTTAGTATTTA
1 AATTAGAGTTTAAGTTTTTA
337266 TTTTATATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 11 0.32
21 23 0.68
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (21 bp):
AATTAGAGTTTAAGTTTTTAA
Found at i:337545 original size:6 final size:6
Alignment explanation
Indices: 337534--337559 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
337524 TTTAATCATC
337534 ATAATT ATAATT ATAATT ATAATT AT
1 ATAATT ATAATT ATAATT ATAATT AT
337560 GAACTGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:340981 original size:15 final size:15
Alignment explanation
Indices: 340958--340987 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
340948 GAGGTCATGA
*
340958 CATCTAAAGAGGTAT
1 CATCAAAAGAGGTAT
340973 CATCAAAAGAGGTAT
1 CATCAAAAGAGGTAT
340988 TGGAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.23
Consensus pattern (15 bp):
CATCAAAAGAGGTAT
Found at i:341944 original size:65 final size:64
Alignment explanation
Indices: 341835--341962 Score: 204
Period size: 65 Copynumber: 2.0 Consensus size: 64
341825 AATATAAACC
* *
341835 ATGTTCATGCTTGTTACGAATTAATATTCACGGAAACCCCATATCTTGCTAACTTTATGAACAAT
1 ATGTTCACGCTTGTTACGAATTAATATTCACGGAAACCCAATATCTTGCTAAC-TTATGAACAAT
*
341900 ATGTTCACGCTTGTTACGAATTAATATTCA-TGACAACCCAATATCTTGCTAACTTATGAACAA
1 ATGTTCACGCTTGTTACGAATTAATATTCACGGA-AACCCAATATCTTGCTAACTTATGAACAA
341963 CATCACTTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
64 12 0.20
65 47 0.80
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (64 bp):
ATGTTCACGCTTGTTACGAATTAATATTCACGGAAACCCAATATCTTGCTAACTTATGAACAAT
Found at i:347917 original size:78 final size:78
Alignment explanation
Indices: 347839--347987 Score: 255
Period size: 78 Copynumber: 1.9 Consensus size: 78
347829 TAATTTTTTA
347839 AAAAT-TTGATAACTCTTAATATTAATTATAAATTAAATATTATAATTTATATTAATTATTATCA
1 AAAATGTTGATAACTCTTAATATTAATTATAAATTAAATATTATAATTTATATTAATTATTATCA
347903 AAAGTTTTCATTT
66 AAAGTTTTCATTT
* * *
347916 AAAGTGTTGATAATTCTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATTATCA
1 AAAATGTTGATAACTCTTAATATTAATTATAAATTAAATATTATAATTTATATTAATTATTATCA
*
347981 AGAGTTT
66 AAAGTTT
347988 GAGATCATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
77 4 0.06
78 63 0.94
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (78 bp):
AAAATGTTGATAACTCTTAATATTAATTATAAATTAAATATTATAATTTATATTAATTATTATCA
AAAGTTTTCATTT
Found at i:352807 original size:24 final size:24
Alignment explanation
Indices: 352778--352845 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
352768 TCTAGCTCAC
*
352778 ACGAGCCTAGAATGGTTAGCTCTT
1 ACGAGCCTAGAATGGTTAACTCTT
*
352802 ATGAGCCTAGAATGGTTAACTCTT
1 ACGAGCCTAGAATGGTTAACTCTT
* *
352826 ACGAGCCCAAAATGGTTAAC
1 ACGAGCCTAGAATGGTTAAC
352846 CAGTATACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (24 bp):
ACGAGCCTAGAATGGTTAACTCTT
Found at i:355262 original size:32 final size:32
Alignment explanation
Indices: 355221--355284 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
355211 ATAAATATGT
355221 ACATATCTAGGATTGAACATTAAAGAGCTTGG
1 ACATATCTAGGATTGAACATTAAAGAGCTTGG
*
355253 ACATGTCTAGGATTGAACATTAAAGAGCTTGG
1 ACATATCTAGGATTGAACATTAAAGAGCTTGG
355285 TACTTAAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (32 bp):
ACATATCTAGGATTGAACATTAAAGAGCTTGG
Found at i:357599 original size:78 final size:77
Alignment explanation
Indices: 357510--357652 Score: 250
Period size: 77 Copynumber: 1.8 Consensus size: 77
357500 ATCTAATCTC
357510 AAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATATTAAGAATTATCA
1 AAACTCTTGATAATAATTAATATAAATTAT-AAATTTAATTTATAATTAATATTAAGAATTATCA
357575 ACTCCTTAAATGA
65 ACTCCTTAAATGA
* * *
357588 AAACTTTTGATAGTAATTAATATAAATTATAAATTTAATTTATAATTAATATTAAGAGTTATCAA
1 AAACTCTTGATAATAATTAATATAAATTATAAATTTAATTTATAATTAATATTAAGAATTATCAA
357653 AATTTTGGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
77 34 0.55
78 28 0.45
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (77 bp):
AAACTCTTGATAATAATTAATATAAATTATAAATTTAATTTATAATTAATATTAAGAATTATCAA
CTCCTTAAATGA
Found at i:384157 original size:10 final size:10
Alignment explanation
Indices: 384130--384236 Score: 55
Period size: 10 Copynumber: 10.8 Consensus size: 10
384120 CATTTATCAC
384130 ATCACATATTA
1 ATCACAT-TTA
384141 ATCACATTTA
1 ATCACATTTA
*
384151 GTCACATTTA
1 ATCACATTTA
*
384161 ATCATA-TTA
1 ATCACATTTA
* *
384170 GTCACATGAATA
1 ATCACAT--TTA
*
384182 TTTCAACATTT-
1 -ATC-ACATTTA
*
384193 ATCACA--TC
1 ATCACATTTA
*
384201 AT-ATA-TTA
1 ATCACATTTA
384209 ATCACATTTA
1 ATCACATTTA
*
384219 GTCACATTTA
1 ATCACATTTA
384229 ATCACATT
1 ATCACATT
384237 AATATTTCAG
Statistics
Matches: 73, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
7 3 0.04
8 5 0.07
9 12 0.16
10 37 0.51
11 7 0.10
12 3 0.04
13 2 0.03
14 4 0.05
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (10 bp):
ATCACATTTA
Found at i:384172 original size:19 final size:21
Alignment explanation
Indices: 384131--384236 Score: 85
Period size: 20 Copynumber: 4.9 Consensus size: 21
384121 ATTTATCACA
384131 TCACATATTAATCACATTTAG
1 TCACATATTAATCACATTTAG
*
384152 TCACAT-TTAATCATA-TTAG
1 TCACATATTAATCACATTTAG
* *
384171 TCACATGAATATTTCAACATTTA-
1 TCACAT-ATTA-ATC-ACATTTAG
384194 TCACATCATATATTAATCACATTTAG
1 T--CA-C--ATATTAATCACATTTAG
384220 TCACAT-TTAATCACATT
1 TCACATATTAATCACATT
384237 AATATTTCAG
Statistics
Matches: 68, Mismatches: 6, Indels: 23
0.70 0.06 0.24
Matches are distributed among these distances:
19 10 0.15
20 19 0.28
21 10 0.15
22 2 0.03
23 4 0.06
24 5 0.07
25 9 0.13
26 4 0.06
27 3 0.04
28 2 0.03
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.40
Consensus pattern (21 bp):
TCACATATTAATCACATTTAG
Found at i:384216 original size:68 final size:68
Alignment explanation
Indices: 384018--384327 Score: 318
Period size: 68 Copynumber: 4.7 Consensus size: 68
384008 CATTCTTTTA
* * * * *
384018 CACA-TTAATCATATTAATCACATGAGTACTT-AAGCATTTAACACAACACATATTAATCACATA
1 CACATTTAATCATATTAATCACATGAATATTTCAA-CATTTATCACATCACATATTAATCACATT
*
384081 TAAT
65 TAGT
* ** * *
384085 AACATAGAATCACATTAGTCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTT
1 CACATTTAATCATATTAATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTT
384150 AGT
66 AGT
* *
384153 CACATTTAATCATATTAGTCACATGAATATTTCAACATTTATCACATCATATATTAATCACATTT
1 CACATTTAATCATATTAATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTT
384218 AGT
66 AGT
* * * * *
384221 --C-----A-CAT-TTAATCACATTAATATTTCAGCGTTTATCACAACACATACTAATCACATTT
1 CACATTTAATCATATTAATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTT
384277 AGT
66 AGT
* * * * *
384280 CACATTTCATCACATTTAATCATATGAATGTTTCATCATTTATCACAT
1 CACATTTAATCATA-TTAATCACATGAATATTTCAACATTTATCACAT
384328 TAAACACATG
Statistics
Matches: 201, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
59 47 0.23
60 3 0.01
61 2 0.01
66 2 0.01
67 5 0.02
68 113 0.56
69 29 0.14
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (68 bp):
CACATTTAATCATATTAATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTT
AGT
Found at i:384241 original size:59 final size:59
Alignment explanation
Indices: 384152--384295 Score: 191
Period size: 59 Copynumber: 2.5 Consensus size: 59
384142 TCACATTTAG
* * * * * * *
384152 TCACATTTAATCATA-TTAGTCACATGAATATTTCAACATTTATCACATCATATATTAA
1 TCACATTTAGTCACATTTAATCACATTAATATTTCAACATTTATCACAACACATACTAA
* *
384210 TCACATTTAGTCACATTTAATCACATTAATATTTCAGCGTTTATCACAACACATACTAA
1 TCACATTTAGTCACATTTAATCACATTAATATTTCAACATTTATCACAACACATACTAA
*
384269 TCACATTTAGTCACATTTCATCACATT
1 TCACATTTAGTCACATTTAATCACATT
384296 TAATCATATG
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
58 13 0.17
59 62 0.83
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (59 bp):
TCACATTTAGTCACATTTAATCACATTAATATTTCAACATTTATCACAACACATACTAA
Found at i:384241 original size:127 final size:127
Alignment explanation
Indices: 384094--384327 Score: 344
Period size: 127 Copynumber: 1.8 Consensus size: 127
384084 TAACATAGAA
* * *
384094 TCACATTAGTCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTCACATT
1 TCACATTAATCACATGAATATTTCAACATTTATCACAACACATACTAATCACATTTAGTCACATT
* *
384159 TAATCATA-TTAGTCACATGAATATTTCAACATTTATCACATCATATATTAATCACATTTAG
66 TAATCACATTTAATCACATGAATATTTCAACATTTATCACATCATATATTAATCACATTTAG
* * *
384220 TCACATTTAATCACATTAATATTTCAGCGTTTATCACAACACATACTAATCACATTTAGTCACAT
1 TCACA-TTAATCACATGAATATTTCAACATTTATCACAACACATACTAATCACATTTAGTCACAT
* * * *
384285 TTCATCACATTTAATCATATGAATGTTTCATCATTTATCACAT
65 TTAATCACATTTAATCACATGAATATTTCAACATTTATCACAT
384328 TAAACACATG
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
126 5 0.05
127 60 0.64
128 29 0.31
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (127 bp):
TCACATTAATCACATGAATATTTCAACATTTATCACAACACATACTAATCACATTTAGTCACATT
TAATCACATTTAATCACATGAATATTTCAACATTTATCACATCATATATTAATCACATTTAG
Found at i:384301 original size:10 final size:10
Alignment explanation
Indices: 384266--384301 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
384256 CAACACATAC
384266 TAATCACATT
1 TAATCACATT
*
384276 TAGTCACATT
1 TAATCACATT
*
384286 TCATCACATT
1 TAATCACATT
384296 TAATCA
1 TAATCA
384302 TATGAATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (10 bp):
TAATCACATT
Found at i:384909 original size:36 final size:36
Alignment explanation
Indices: 384822--384909 Score: 131
Period size: 36 Copynumber: 2.4 Consensus size: 36
384812 CATATGACAC
* * * *
384822 GAATAACATACTCACATATTTAGTGTCTCATGGCGT
1 GAATAACATACCCACATATTTACTATCACATGGCGT
*
384858 GAATAACATAACCACATATTTACTATCACATGGCGT
1 GAATAACATACCCACATATTTACTATCACATGGCGT
384894 GAATAACATACCCACA
1 GAATAACATACCCACA
384910 CATCCACTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (36 bp):
GAATAACATACCCACATATTTACTATCACATGGCGT
Found at i:384923 original size:36 final size:36
Alignment explanation
Indices: 384850--384923 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
384840 TTTAGTGTCT
* **
384850 CATGGCGTGAATAACATAACCACATATTTACTATCA
1 CATGGCGTGAATAACATAACCACACATCCACTATCA
* *
384886 CATGGCGTGAATAACATACCCACACATCCACTTTCA
1 CATGGCGTGAATAACATAACCACACATCCACTATCA
384922 CA
1 CA
384924 ACAGTCATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.24
Consensus pattern (36 bp):
CATGGCGTGAATAACATAACCACACATCCACTATCA
Found at i:395185 original size:16 final size:16
Alignment explanation
Indices: 395164--395195 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
395154 CATGATGAAC
395164 AAAATAGTGAATTAAG
1 AAAATAGTGAATTAAG
395180 AAAATAGTGAATTAAG
1 AAAATAGTGAATTAAG
395196 GATTTAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (16 bp):
AAAATAGTGAATTAAG
Found at i:395418 original size:17 final size:18
Alignment explanation
Indices: 395396--395431 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
395386 TAAATGAGTT
395396 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
395413 AATTAGGTTATAAATTGG
1 AATTAGGATATAAATTGG
395431 A
1 A
395432 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:395751 original size:18 final size:18
Alignment explanation
Indices: 395728--395764 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
395718 TTTGTGATCA
395728 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
395746 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
395764 A
1 A
395765 TATAAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:395969 original size:37 final size:39
Alignment explanation
Indices: 395867--395970 Score: 106
Period size: 37 Copynumber: 2.7 Consensus size: 39
395857 CGACCTTGAG
* * *
395867 TCGATGAGACACTGGGTGTCTTTATTTTACTTCGGATAGAT
1 TCGATGAGATACTGGGTGTC--TACTTTACTTCGGATAGAC
* * * *
395908 TCGATGAGGTACTGGGT-ACTACTTTACTTCGGCTAGGC
1 TCGATGAGATACTGGGTGTCTACTTTACTTCGGATAGAC
395946 T-GATGAGATACTGGGTGTC-ACTTTA
1 TCGATGAGATACTGGGTGTCTACTTTA
395971 TTGCTCCGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
37 20 0.38
38 17 0.32
40 1 0.02
41 15 0.28
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (39 bp):
TCGATGAGATACTGGGTGTCTACTTTACTTCGGATAGAC
Found at i:396633 original size:2 final size:2
Alignment explanation
Indices: 396626--396654 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
396616 GGTTGTCAAA
396626 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 A
396655 CACTATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:402732 original size:17 final size:18
Alignment explanation
Indices: 402710--402745 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
402700 TAAATGAGTT
402710 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
402727 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
402745 A
1 A
402746 TAGAAAGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:406173 original size:14 final size:15
Alignment explanation
Indices: 406156--406196 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
406146 TTATTTCTTA
406156 AATTAATTTT-AATT
1 AATTAATTTTCAATT
406170 AATTAATTTTTCAATT
1 AATTAA-TTTTCAATT
*
406186 AAATAATTTTC
1 AATTAATTTTC
406197 GCAATTCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 9 0.38
16 9 0.38
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTAATTTTCAATT
Found at i:406187 original size:16 final size:15
Alignment explanation
Indices: 406156--406195 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
406146 TTATTTCTTA
406156 AATTAA-TTTTAATT
1 AATTAATTTTTAATT
406170 AATTAATTTTTCAATT
1 AATTAATTTTT-AATT
*
406186 AAATAATTTT
1 AATTAATTTT
406196 CGCAATTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.26
15 4 0.17
16 13 0.57
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTAATTTTTAATT
Found at i:410639 original size:38 final size:38
Alignment explanation
Indices: 410588--410660 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
410578 GTTTTGGTAT
*
410588 TATTATAGATGTAATCATTACATGATTAAACATTAGTA
1 TATTACAGATGTAATCATTACATGATTAAACATTAGTA
410626 TATTACAGATGTAATCATTACATGATTAAACATTA
1 TATTACAGATGTAATCATTACATGATTAAACATTA
410661 CATCATACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (38 bp):
TATTACAGATGTAATCATTACATGATTAAACATTAGTA
Found at i:413684 original size:43 final size:43
Alignment explanation
Indices: 413633--413732 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 43
413623 TGTTATTTCT
413633 TGACATGTTATTAAATTATATCACTTGACCCGTGTTAATATCG
1 TGACATGTTATTAAATTATATCACTTGACCCGTGTTAATATCG
* * * * *
413676 TGGCATGTTATTAAATTCTATTACTTGACTCTTGTTAATATCG
1 TGACATGTTATTAAATTATATCACTTGACCCGTGTTAATATCG
413719 TGACATGTTATTAA
1 TGACATGTTATTAA
413733 TTGTGCAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (43 bp):
TGACATGTTATTAAATTATATCACTTGACCCGTGTTAATATCG
Found at i:414578 original size:13 final size:13
Alignment explanation
Indices: 414560--414586 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
414550 TATATTTAAC
414560 TATTGATGACTTT
1 TATTGATGACTTT
414573 TATTGATGACTTT
1 TATTGATGACTTT
414586 T
1 T
414587 TACTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (13 bp):
TATTGATGACTTT
Done.