Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009238.1 Hibiscus syriacus cultivar Beakdansim tig00112864_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1094141
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 5 of 5
Found at i:893265 original size:29 final size:29
Alignment explanation
Indices: 893232--893287 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
893222 GAGCGAGGGT
*
893232 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
893261 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
893288 TGTGTTGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.30, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:893388 original size:29 final size:29
Alignment explanation
Indices: 893346--893431 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
893336 GAGCAAGGGT
893346 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
893375 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
893404 AGGTCGCCCTGAAG-GCATGGCGACCTAC
1 AGGTCGCCC-GGAGTGCATGGCGACCTAC
893432 GGCCACTGTG
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 52 0.95
30 3 0.05
ACGTcount: A:0.21, C:0.31, G:0.34, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:894092 original size:24 final size:22
Alignment explanation
Indices: 894046--894093 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
894036 CCGATCTAAT
**
894046 ATAAAATAAATATTTAATTAAA
1 ATAAAATAAATATTTAAAGAAA
894068 ATAATAATAAAATATTTAAAGAAA
1 ATAA-AAT-AAATATTTAAAGAAA
894092 AT
1 AT
894094 TATGTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 3 0.14
24 15 0.68
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAAAATAAATATTTAAAGAAA
Found at i:902169 original size:22 final size:22
Alignment explanation
Indices: 902104--902172 Score: 120
Period size: 22 Copynumber: 3.1 Consensus size: 22
902094 CTTTTTTCGC
*
902104 CGGCAGTCACAGCCTCCATCGC
1 CGGCAGTCACAGCCTCCATCGT
902126 CGGCAGTCACAGCCTCCATCGT
1 CGGCAGTCACAGCCTCCATCGT
*
902148 CGGCAGTCACAGCTTCCATCGT
1 CGGCAGTCACAGCCTCCATCGT
902170 CGG
1 CGG
902173 GCGCTAACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.17, C:0.41, G:0.25, T:0.17
Consensus pattern (22 bp):
CGGCAGTCACAGCCTCCATCGT
Found at i:912532 original size:212 final size:212
Alignment explanation
Indices: 912165--912803 Score: 1260
Period size: 212 Copynumber: 3.0 Consensus size: 212
912155 TGCCAATGAC
912165 AAGGAAGAGGCTTTCCACCCCGCTAGTTTCTTGTGGAAATTATCAAGAACCGGCTCCCACAATTT
1 AAGGAAGAGGCTTTCCACCCCGCTAGTTTCTTGTGGAAATTATCAAGAACCGGCTCCCACAATTT
912230 CTCACAATTTCTTTTTGCCCCTAACGGAAGTCCCAAGTAAACGGTCGGAAATGAACCTACAGAGC
66 CTCACAATTTCTTTTTGCCCCTAACGGAAGTCCCAAGTAAACGGTCGGAAATGAACCTACAGAGC
912295 ATCCAATAGCCGCAGCCCTATCTCCCATGATATCATCCTCCACATTGATGCCAAAAAGTTTGCTT
131 ATCCAATAGCCGCAGCCCTATCTCCCATGATATCATCCTCCACATTGATGCCAAAAAGTTTGCTT
912360 TTAGCTAAATAAAGATG
196 TTAGCTAAATAAAGATG
*
912377 AAGGAAGAGGCTTTCCACCTCGCTAGTTTCTTGTGGAAATTATCAAGAACCGGCTCCCACAATTT
1 AAGGAAGAGGCTTTCCACCCCGCTAGTTTCTTGTGGAAATTATCAAGAACCGGCTCCCACAATTT
912442 CTCACAATTTCTTTTTGCCCCTAACGGAAGTCCCAAGTAAACGGTCGGAAATGAACCTACAGAGC
66 CTCACAATTTCTTTTTGCCCCTAACGGAAGTCCCAAGTAAACGGTCGGAAATGAACCTACAGAGC
912507 ATCCAATAGCCGCAGCCCTATCTCCCATGATATCATCCTCCACATTGATGCCAAAAAGTTTGCTT
131 ATCCAATAGCCGCAGCCCTATCTCCCATGATATCATCCTCCACATTGATGCCAAAAAGTTTGCTT
912572 TTAGCTAAATAAAGATG
196 TTAGCTAAATAAAGATG
912589 AAGGAAGAGGCTTTCCACCCCGCTAGTTTCTTGTGGAAATTATCAAGAACCGGCTCCCACAATTT
1 AAGGAAGAGGCTTTCCACCCCGCTAGTTTCTTGTGGAAATTATCAAGAACCGGCTCCCACAATTT
912654 CTCACAATTTCTTTTTGCCCCTAACGGAAGTCCCAAGTAAACGGTCGGAAATGAACCTACAGAGC
66 CTCACAATTTCTTTTTGCCCCTAACGGAAGTCCCAAGTAAACGGTCGGAAATGAACCTACAGAGC
912719 ATCCAATAGCCGCAGCCCTATCTCCCATGATATCATCCTCCACATTGATGCCAAAAAGTTTGCTT
131 ATCCAATAGCCGCAGCCCTATCTCCCATGATATCATCCTCCACATTGATGCCAAAAAGTTTGCTT
*
912784 TTAGTTAAATAAAGATG
196 TTAGCTAAATAAAGATG
912801 AAG
1 AAG
912804 TCCCGTCATT
Statistics
Matches: 424, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
212 424 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (212 bp):
AAGGAAGAGGCTTTCCACCCCGCTAGTTTCTTGTGGAAATTATCAAGAACCGGCTCCCACAATTT
CTCACAATTTCTTTTTGCCCCTAACGGAAGTCCCAAGTAAACGGTCGGAAATGAACCTACAGAGC
ATCCAATAGCCGCAGCCCTATCTCCCATGATATCATCCTCCACATTGATGCCAAAAAGTTTGCTT
TTAGCTAAATAAAGATG
Found at i:927767 original size:24 final size:26
Alignment explanation
Indices: 927724--927779 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
927714 GTTCATGAAC
927724 GTTCGATTATATGTTCGTTTATTTAT
1 GTTCGATTATATGTTCGTTTATTTAT
*
927750 GTTC-ATT-TATGTTTGTTTATTTAT
1 GTTCGATTATATGTTCGTTTATTTAT
*
927774 ATTCGA
1 GTTCGA
927780 ACAGAGTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 19 0.70
25 4 0.15
26 4 0.15
ACGTcount: A:0.20, C:0.07, G:0.14, T:0.59
Consensus pattern (26 bp):
GTTCGATTATATGTTCGTTTATTTAT
Found at i:939260 original size:20 final size:20
Alignment explanation
Indices: 939235--939284 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
939225 ACGATTCTAT
939235 TGGTTAAAGTGACAAACCAC
1 TGGTTAAAGTGACAAACCAC
* *
939255 TGGTTAAAGTGTCAAATCAC
1 TGGTTAAAGTGACAAACCAC
939275 TGGTTAAAGT
1 TGGTTAAAGT
939285 TCTTTGGCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (20 bp):
TGGTTAAAGTGACAAACCAC
Found at i:945248 original size:26 final size:26
Alignment explanation
Indices: 945197--945249 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
945187 AAGGTGATGG
* * *
945197 AAGATGCATTAACTTGAAACACAAGA
1 AAGATGCATTAACATGAAAAAAAAGA
945223 AAGAT-CATTAACATGAATAAAAAAGA
1 AAGATGCATTAACATGAA-AAAAAAGA
945249 A
1 A
945250 CATAAACCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.19
Consensus pattern (26 bp):
AAGATGCATTAACATGAAAAAAAAGA
Found at i:950296 original size:14 final size:15
Alignment explanation
Indices: 950277--950305 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
950267 TTACATATTA
950277 TTTAACGA-CGACTG
1 TTTAACGATCGACTG
950291 TTTAACGATCGACTG
1 TTTAACGATCGACTG
950306 ACTTAATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (15 bp):
TTTAACGATCGACTG
Found at i:955737 original size:55 final size:55
Alignment explanation
Indices: 955678--956006 Score: 529
Period size: 55 Copynumber: 6.0 Consensus size: 55
955668 AGACTTAAAA
*
955678 AATCTTCA-AATAACGGGTCTGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAAC
1 AATCTTCATAA-AACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAAC
* * *
955733 AATCTTCATAAAACGGGTCTGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAAC
*
955788 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATCGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAAC
* * *
955843 AATCTTCAACAAAACGGGTCCGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAAC
1 AATCTTC-ATAAAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAAC
955899 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAAC
955954 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGA
1 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGA
956007 TCTTCAATAA
Statistics
Matches: 255, Mismatches: 13, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
54 6 0.02
55 194 0.76
56 52 0.20
57 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (55 bp):
AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAAC
Found at i:955905 original size:111 final size:110
Alignment explanation
Indices: 955678--956006 Score: 563
Period size: 111 Copynumber: 3.0 Consensus size: 110
955668 AGACTTAAAA
*
955678 AATCTTCA-AATAACGGGTCTGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCAT
1 AATCTTCATAA-AACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCAT
*
955742 AAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
65 AAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
955788 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATCGAACTCGAACAATCTTCAAC
1 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTC-AT
955853 AAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
65 AAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
955899 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATA
1 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATA
* *
955964 AAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGA
66 AAACGGGTCCGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGA
956007 TCTTCAATAA
Statistics
Matches: 208, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
109 3 0.01
110 96 0.46
111 109 0.52
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (110 bp):
AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATA
AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
Found at i:955963 original size:166 final size:162
Alignment explanation
Indices: 955678--956208 Score: 608
Period size: 166 Copynumber: 3.3 Consensus size: 162
955668 AGACTTAAAA
* * *
955678 AATCTTCAAATAACGGGTCTGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCAT
1 AATCTTCAAAAAACGGGTCCGCTCCCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCAT
* *
955742 AAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTC
65 AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTC
*
955807 CGCTCCCTATCCGTTCAGGGAGTATCGAACTCG
130 CGCTCCCTATCCGTTCAGGGAGTATAGAACTCG
*
955840 AACAATCTTCAACAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTT
1 ---AATCTTCAA-AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTT
*
955905 CATAAAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACG
62 CATAAAACGGGTCCGCTCCCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACG
955969 GGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCG
126 GGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCG
* **
956006 -ATCTTCAATAAACGTTTCCGCTCCCTATTCCTTCAGAGAGTATATG-ACT----CAATCTTCA-
1 AATCTTCAAAAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA-GAACTCGAACAATCTTCAT
* ** * * * **
956064 ACGAACTTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTG
65 A-AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGG
* * * *
956124 CCCGCTCCCTATTCC-TTCAGAGAATATAGGACTC-
128 TCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCG
** ** *
956158 AATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 AATCTTCAAAAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTC
956209 AATCTTCAAC
Statistics
Matches: 326, Mismatches: 29, Indels: 33
0.84 0.07 0.09
Matches are distributed among these distances:
152 2 0.01
153 82 0.25
154 3 0.01
156 1 0.00
157 39 0.12
158 3 0.01
161 35 0.11
162 9 0.03
165 12 0.04
166 137 0.42
167 3 0.01
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (162 bp):
AATCTTCAAAAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA
AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
GCTCCCTATCCGTTCAGGGAGTATAGAACTCG
Found at i:956031 original size:51 final size:52
Alignment explanation
Indices: 955678--956223 Score: 474
Period size: 51 Copynumber: 10.3 Consensus size: 52
955668 AGACTTAAAA
* *
955678 AATCTTCAA-ATAACGGGTCTGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCG
1 AATCTTCAATA-AACGGGTCCGCTCCCTATTCC-TTCAGAGAGTATAGAACTCG
* *
955730 AACAATCTTC-ATAAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCG
1 ---AATCTTCAAT-AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCG
* *
955785 AACAATCTTC-ATAAAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATCGAACTCG
1 ---AATCTTCAAT-AAACGGGTCCGCTCCCTATTCC-TTCAGAGAGTATAGAACTCG
* *
955840 AACAATCTTCAACAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCG
1 ---AATCTTCAA-TAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCG
*
955896 AACAATCTTC-ATAAAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCG
1 ---AATCTTCAAT-AAACGGGTCCGCTCCCTATTCC-TTCAGAGAGTATAGAACTCG
*
955951 AACAATCTTC-ATAAAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCG
1 ---AATCTTCAAT-AAACGGGTCCGCTCCCTATTCC-TTCAGAGAGTATAGAACTCG
**
956006 -ATCTTCAATAAACGTTTCCGCTCCCTATTCCTTCAGAGAGTATATG-ACTC-
1 AATCTTCAATAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA-GAACTCG
** ** * *
956056 AATCTTCAACGAACTTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTC-
1 AATCTTCAATAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCG
** ** * * *
956107 AATCTTCAACGAACTTGCCCGCTCCCTATTCCTTCAGAGAATATAGGACTC-
1 AATCTTCAATAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCG
** ** *
956158 AATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC-
1 AATCTTCAATAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCG
*
956209 AATCTTCAACAAACG
1 AATCTTCAATAAACG
956224 AGTTTGCTTC
Statistics
Matches: 449, Mismatches: 28, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
50 1 0.00
51 191 0.43
52 6 0.01
54 7 0.02
55 191 0.43
56 50 0.11
57 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (52 bp):
AATCTTCAATAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCG
Found at i:957602 original size:16 final size:17
Alignment explanation
Indices: 957569--957684 Score: 66
Period size: 17 Copynumber: 6.6 Consensus size: 17
957559 TGAACCCTCC
*
957569 TTTT-ATTTCTCTCTTT
1 TTTTCATTTTTCTCTTT
957585 TTTTCATTTTTCTC-TT
1 TTTTCATTTTTCTCTTT
957601 TTTTCATTTTTCAT-TTT
1 TTTTCATTTTTC-TCTTT
957618 TTCTTCCA-TTTTCTTCTTCT
1 TT-TT-CATTTTTC-TCTT-T
* *
957638 CTTT--TTTTTCCCGTTT
1 TTTTCATTTTTCTC-TTT
957654 TTTCCATCATTTTT-TCTTT
1 TTT---TCATTTTTCTCTTT
957673 TTTCTCATTTTT
1 TTT-TCATTTTT
957685 TTTCTCTTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 27
0.70 0.06 0.24
Matches are distributed among these distances:
16 22 0.28
17 28 0.35
18 8 0.10
19 13 0.16
20 3 0.04
21 5 0.06
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.72
Consensus pattern (17 bp):
TTTTCATTTTTCTCTTT
Found at i:957603 original size:9 final size:9
Alignment explanation
Indices: 957578--957717 Score: 53
Period size: 8 Copynumber: 15.9 Consensus size: 9
957568 CTTTTATTTC
957578 TCTCTTTTT
1 TCTCTTTTT
*
957587 T-TCATTTT
1 TCTCTTTTT
957595 TCTC-TTTT
1 TCTCTTTTT
*
957603 T-TCATTTT
1 TCTCTTTTT
*
957611 TC-ATTTTT
1 TCTCTTTTT
**
957619 TCTTCCATTT
1 TC-TCTTTTT
* *
957629 TCT-TCTTC
1 TCTCTTTTT
*
957637 TCTTTTTTT
1 TCTCTTTTT
*
957646 TCCCGTTTTT
1 TCTC-TTTTT
*
957656 TCCATCATTTT
1 T-C-TCTTTTT
957667 T-TCTTTTT
1 TCTCTTTTT
957675 TCTCATTTTT
1 TCTC-TTTTT
* *
957685 TTTCTCTTT
1 TCTCTTTTT
*
957694 T-T-TTTCT
1 TCTCTTTTT
*
957701 TCTTTTTTT
1 TCTCTTTTT
957710 TCTCTTTT
1 TCTCTTTT
957718 ATTTCTTCTT
Statistics
Matches: 96, Mismatches: 22, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
7 6 0.06
8 37 0.39
9 27 0.28
10 19 0.20
11 6 0.06
12 1 0.01
ACGTcount: A:0.05, C:0.21, G:0.01, T:0.74
Consensus pattern (9 bp):
TCTCTTTTT
Found at i:957700 original size:23 final size:23
Alignment explanation
Indices: 957569--957723 Score: 89
Period size: 23 Copynumber: 6.9 Consensus size: 23
957559 TGAACCCTCC
* *
957569 TTTTATTTCTCTCTTTTTT-TCA
1 TTTTTTTTCTCTTTTTTTTCTCA
* *
957591 -TTTTTCTCT-TTTTTCATTTTTCA
1 TTTTTTTTCTCTTTTT--TTTCTCA
957614 TTTTTTCTTC-CATTTTCTTCTTCTC-
1 TTTTTT-TTCTC-TTTT-TT-TTCTCA
**
957639 TTTTTTTTC-CCGTTTTTTC-CA
1 TTTTTTTTCTCTTTTTTTTCTCA
**
957660 TCATTTTT-TC--TTTTTTCTCA
1 TTTTTTTTCTCTTTTTTTTCTCA
957680 TTTTTTTTCTCTTTTTTTTCTTC-
1 TTTTTTTTCTCTTTTTTTTC-TCA
*
957703 TTTTTTTTCTCTTTTATTTCT
1 TTTTTTTTCTCTTTTTTTTCT
957724 TCTTCAAGCG
Statistics
Matches: 105, Mismatches: 12, Indels: 32
0.70 0.08 0.21
Matches are distributed among these distances:
19 7 0.07
20 13 0.12
21 19 0.18
22 6 0.06
23 31 0.30
24 11 0.10
25 9 0.09
26 8 0.08
27 1 0.01
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.74
Consensus pattern (23 bp):
TTTTTTTTCTCTTTTTTTTCTCA
Found at i:957707 original size:40 final size:39
Alignment explanation
Indices: 957568--957709 Score: 103
Period size: 41 Copynumber: 3.5 Consensus size: 39
957558 TTGAACCCTC
* *
957568 CTTTTATTTCTCTCTTTTTTTCATTTTTCTCTTTTTTCATT-T
1 CTTTTTTTTCT-TCATTTTTTC-TTTTTCTCTTTTTT--TTCT
* *
957610 -TTCATTTTTTCTTCCA--TTTTCTTCTTCTCTTTTTTTTCC
1 CTT--TTTTTTCTT-CATTTTTTCTTTTTCTCTTTTTTTTCT
* * *
957649 CGTTTTTTCCATCATTTTTTCTTTTTTCTCATTTTTTTTCT
1 CTTTTTTTTCTTCATTTTTTC-TTTTTCTC-TTTTTTTTCT
*
957690 CTTTTTTTTCTTCTTTTTTT
1 CTTTTTTTTCTTCATTTTTT
957710 TCTCTTTTAT
Statistics
Matches: 78, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
37 2 0.03
38 9 0.12
39 5 0.06
40 21 0.27
41 32 0.41
42 1 0.01
43 8 0.10
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (39 bp):
CTTTTTTTTCTTCATTTTTTCTTTTTCTCTTTTTTTTCT
Found at i:957715 original size:14 final size:14
Alignment explanation
Indices: 957614--957715 Score: 58
Period size: 13 Copynumber: 7.6 Consensus size: 14
957604 TCATTTTTCA
*
957614 TTTTTTCTTC-CAT
1 TTTTTTCTTCTCTT
*
957627 TTTCTTCTTCTCTT
1 TTTTTTCTTCTCTT
*
957641 TTTTTTC--C-CGT
1 TTTTTTCTTCTCTT
* *
957652 TTTTTCCATCAT-TT
1 TTTTTTCTTC-TCTT
* *
957666 TTTCTTTTTTCTC-A
1 TTT-TTTCTTCTCTT
957680 TTTTTT-TTCTCTT
1 TTTTTTCTTCTCTT
957693 TTTTTTCTTCT-TT
1 TTTTTTCTTCTCTT
957706 TTTTTCTCTT
1 TTTTT-TCTT
957716 TTATTTCTTC
Statistics
Matches: 68, Mismatches: 11, Indels: 19
0.69 0.11 0.19
Matches are distributed among these distances:
11 8 0.12
12 6 0.09
13 26 0.38
14 24 0.35
15 4 0.06
ACGTcount: A:0.04, C:0.22, G:0.01, T:0.74
Consensus pattern (14 bp):
TTTTTTCTTCTCTT
Found at i:957727 original size:12 final size:11
Alignment explanation
Indices: 957670--957723 Score: 81
Period size: 11 Copynumber: 4.7 Consensus size: 11
957660 TCATTTTTTC
957670 TTTTTTCTCATT
1 TTTTTTCTC-TT
957682 TTTTTTCTCTT
1 TTTTTTCTCTT
957693 TTTTTTCTTCTT
1 TTTTTTC-TCTT
957705 TTTTTTCTCTT
1 TTTTTTCTCTT
*
957716 TTATTTCT
1 TTTTTTCT
957724 TCTTCAAGCG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
11 20 0.50
12 20 0.50
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:972972 original size:22 final size:22
Alignment explanation
Indices: 972944--972988 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
972934 CATCTTCGAC
972944 TGATAATCGATCAAACAACCAT
1 TGATAATCGATCAAACAACCAT
972966 TGATAATCGATCAAACAACCAT
1 TGATAATCGATCAAACAACCAT
972988 T
1 T
972989 TGTTTGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.24
Consensus pattern (22 bp):
TGATAATCGATCAAACAACCAT
Found at i:982480 original size:23 final size:24
Alignment explanation
Indices: 982430--982485 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
982420 TCATTTTCTA
* *
982430 AACATATAAATAAACATGTTCACG
1 AACATATAAACAAACATGTTCAAG
* *
982454 AACAT-TAAACAAACATGTTGAAT
1 AACATATAAACAAACATGTTCAAG
982477 AACATATAA
1 AACATATAA
982486 CGGGCATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (24 bp):
AACATATAAACAAACATGTTCAAG
Found at i:983245 original size:17 final size:19
Alignment explanation
Indices: 983221--983265 Score: 67
Period size: 17 Copynumber: 2.5 Consensus size: 19
983211 ACGATGATAA
983221 AAACATTTAGGAT-ATTA-
1 AAACATTTAGGATGATTAC
*
983238 ATACATTTAGGATGATTAC
1 AAACATTTAGGATGATTAC
983257 AAACATTTA
1 AAACATTTA
983266 TCAAGACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.50
18 4 0.17
19 8 0.33
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (19 bp):
AAACATTTAGGATGATTAC
Found at i:983991 original size:24 final size:24
Alignment explanation
Indices: 983916--984028 Score: 86
Period size: 23 Copynumber: 4.8 Consensus size: 24
983906 CAGTTAAATG
* * * *
983916 ATAAACGAACATAAACGAACGGAT
1 ATAAACGAACACAAACAAACGAAC
* * * *
983940 GTAAACGAACA-TAATAAACAAAC
1 ATAAACGAACACAAACAAACGAAC
* *
983963 GTAAACGTACACAAACAAACGAAC
1 ATAAACGAACACAAACAAACGAAC
* *
983987 ATAAACGAACACAATC-AATGAAC
1 ATAAACGAACACAAACAAACGAAC
**
984010 ATAAACGAACGTAAACAAA
1 ATAAACGAACACAAACAAA
984029 TATAAATTTT
Statistics
Matches: 69, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
23 35 0.51
24 34 0.49
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (24 bp):
ATAAACGAACACAAACAAACGAAC
Found at i:984026 original size:47 final size:47
Alignment explanation
Indices: 983916--984028 Score: 118
Period size: 47 Copynumber: 2.4 Consensus size: 47
983906 CAGTTAAATG
* * ** *
983916 ATAAACGAACATAAACGAACGGATGTAAACGAACATAATAAACAAAC
1 ATAAACGAACATAAACAAACGAACATAAACGAACACAATAAACAAAC
* * * * **
983963 GTAAACGTACACAAACAAACGAACATAAACGAACACAATCAATGAAC
1 ATAAACGAACATAAACAAACGAACATAAACGAACACAATAAACAAAC
*
984010 ATAAACGAACGTAAACAAA
1 ATAAACGAACATAAACAAA
984029 TATAAATTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (47 bp):
ATAAACGAACATAAACAAACGAACATAAACGAACACAATAAACAAAC
Found at i:988200 original size:18 final size:18
Alignment explanation
Indices: 988145--988208 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
988135 TTCGCAGAAT
* *
988145 ATAAGATTACCGGCGAAA
1 ATAAGATTACCAGCGAGA
* *
988163 ATATGATTACCGGCGAGA
1 ATAAGATTACCAGCGAGA
* *
988181 ATAGGATTACCAGCGGGA
1 ATAAGATTACCAGCGAGA
988199 ATAAGATTAC
1 ATAAGATTAC
988209 TGGGAATGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (18 bp):
ATAAGATTACCAGCGAGA
Found at i:988443 original size:36 final size:36
Alignment explanation
Indices: 988371--988443 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
988361 TACTATAATT
**
988371 AATTTATATATTTTCTTTAAAAAATTAAATTCATAA
1 AATTTATATATTTTCTTTAAAAAATTAAAAACATAA
* *
988407 AATTTATATAATTTT-TTTACAAAATTAAAAAGATAA
1 AATTTATAT-ATTTTCTTTAAAAAATTAAAAACATAA
988443 A
1 A
988444 TAGGTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 27 0.84
37 5 0.16
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (36 bp):
AATTTATATATTTTCTTTAAAAAATTAAAAACATAA
Found at i:994413 original size:64 final size:64
Alignment explanation
Indices: 994340--994501 Score: 168
Period size: 64 Copynumber: 2.5 Consensus size: 64
994330 ATTGTTTGAA
* *** *
994340 GGTGTATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAATCTAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCATC-CCAGTAAT-AAACAAACATCGAATGCAAT
994403 T
64 T
* * * *
994404 GGTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAAACAAACATCGAATGTATTT
1 GGTGCATCGATGCA-CAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATGCAATT
** *
994468 TATGCACCGATGCACAGGTAGTGCATCGATGCAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCAT
994502 TTCGATGCAC
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
63 6 0.08
64 69 0.86
65 5 0.06
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (64 bp):
GGTGCATCGATGCACAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATGCAATT
Found at i:995391 original size:103 final size:103
Alignment explanation
Indices: 995166--995383 Score: 355
Period size: 103 Copynumber: 2.1 Consensus size: 103
995156 GTCGAGGGTC
*
995166 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * * * *
995231 TTGATCCTTGGCATGTTTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATACGATTCTTAAGGAATGA
* *
995269 TATGTGGTTCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
995334 TTGATCCCTAGTATATGTATACGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATACGATTCTTAAGGAATGA
995372 TATGTGGTCCTT
1 TATGTGGTCCTT
995384 ATGGACATTA
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATACGATTCTTAAGGAATGA
Found at i:996133 original size:167 final size:167
Alignment explanation
Indices: 995857--996192 Score: 654
Period size: 167 Copynumber: 2.0 Consensus size: 167
995847 AGTAATTGTT
995857 TAGGTATGATTATTAGTTACCGTTTACCTTATATGTTTATATGCCTCACTAAGTCTTTGACTTAG
1 TAGGTATGATTATTAGTTACCGTTTACCTTATATGTTTATATGCCTCACTAAGTCTTTGACTTAG
*
995922 CGTGTAAGTGATTTACACGTAGGTTTCGAGAAGAGTAAAGAGCAATGTGGAGCAAGACATGTTAG
66 CGTGTAAGTGATTTACACGTAGGTTTCGAGAAGAGTAAAGAGCAATGTGGAGCAAGACATGTCAG
995987 TTCTCCTTACTAAAGGTCAGATCAGAAAAGATGTGAA
131 TTCTCCTTACTAAAGGTCAGATCAGAAAAGATGTGAA
996024 TAGGTATGATTATTAGTTACCGTTTACCTTATATGTTTATATGCCTCACTAAGTCTTTGACTTAG
1 TAGGTATGATTATTAGTTACCGTTTACCTTATATGTTTATATGCCTCACTAAGTCTTTGACTTAG
*
996089 CGTGTAAGTGATTTACATGTAGGTTTCGAGAAGAGTAAAGAGCAATGTGGAGCAAGACATGTCAG
66 CGTGTAAGTGATTTACACGTAGGTTTCGAGAAGAGTAAAGAGCAATGTGGAGCAAGACATGTCAG
996154 TTCTCCTTACTAAAGGTCAGATCAGAAAAGATGTGAA
131 TTCTCCTTACTAAAGGTCAGATCAGAAAAGATGTGAA
996191 TA
1 TA
996193 ATATGTATTT
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 167 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (167 bp):
TAGGTATGATTATTAGTTACCGTTTACCTTATATGTTTATATGCCTCACTAAGTCTTTGACTTAG
CGTGTAAGTGATTTACACGTAGGTTTCGAGAAGAGTAAAGAGCAATGTGGAGCAAGACATGTCAG
TTCTCCTTACTAAAGGTCAGATCAGAAAAGATGTGAA
Found at i:998629 original size:14 final size:14
Alignment explanation
Indices: 998612--998711 Score: 52
Period size: 14 Copynumber: 7.3 Consensus size: 14
998602 AAATATATTT
998612 TTTATAATAATATA
1 TTTATAATAATATA
*
998626 TTTATAATCATTTATTA
1 TTTATAAT-A-ATA-TA
*
998643 TTT-TTA-AAT-TA
1 TTTATAATAATATA
* *
998654 -TTAAAATAAAATA
1 TTTATAATAATATA
*
998667 TTTATAATAATTTA
1 TTTATAATAATATA
*
998681 TTATATTTATAATA-A
1 TT-TA-TAATAATATA
998696 -TTA-AATAATATA
1 TTTATAATAATATA
998708 TTTA
1 TTTA
998712 ACATTACAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 23
0.64 0.12 0.23
Matches are distributed among these distances:
10 2 0.03
11 9 0.14
12 3 0.05
13 8 0.13
14 22 0.35
15 4 0.06
16 10 0.16
17 5 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTATAATAATATA
Found at i:998668 original size:41 final size:41
Alignment explanation
Indices: 998617--998711 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
998607 TATTTTTTAT
* * *
998617 AATAATATATTTATAATCATTTATTATTTTTA-AATTATTAA
1 AATAATATATTTATAATAATTTATTATATTTATAATAATT-A
*
998658 AATAAAATATTTATAATAATTTATTATATTTATAATAATTA
1 AATAATATATTTATAATAATTTATTATATTTATAATAATTA
998699 AATAATATATTTA
1 AATAATATATTTA
998712 ACATTACAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 42 0.88
42 6 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (41 bp):
AATAATATATTTATAATAATTTATTATATTTATAATAATTA
Found at i:998751 original size:2 final size:2
Alignment explanation
Indices: 998744--998820 Score: 113
Period size: 2 Copynumber: 39.5 Consensus size: 2
998734 TAAAATCTTA
* * *
998744 AT AT AT AT AT AT AT AT AA AC AT -T AT AT TT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
998784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
998821 ATCGGGTAGG
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
1 2 0.03
2 66 0.97
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1010556 original size:12 final size:12
Alignment explanation
Indices: 1010539--1010564 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1010529 CCTATCTCCA
1010539 TCCTCCTCCTCT
1 TCCTCCTCCTCT
1010551 TCCTCCTCCTCT
1 TCCTCCTCCTCT
1010563 TC
1 TC
1010565 ATCATCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (12 bp):
TCCTCCTCCTCT
Found at i:1017623 original size:3 final size:3
Alignment explanation
Indices: 1017615--1017641 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1017605 CTTTTTGGGT
1017615 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1017642 CTTTCTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1017660 original size:21 final size:22
Alignment explanation
Indices: 1017636--1017688 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1017626 ATTATTATTA
1017636 TTATTACTT-TCTTTGTTTT-TT
1 TTATTA-TTATCTTTGTTTTGTT
*
1017657 TTATTATTATTTTTGTTTTGTT
1 TTATTATTATCTTTGTTTTGTT
*
1017679 TTATTCTTAT
1 TTATTATTAT
1017689 TTCTTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 15 0.54
22 11 0.39
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (22 bp):
TTATTATTATCTTTGTTTTGTT
Found at i:1017665 original size:24 final size:24
Alignment explanation
Indices: 1017633--1017694 Score: 85
Period size: 22 Copynumber: 2.7 Consensus size: 24
1017623 ATTATTATTA
1017633 TTATTATTACTTTCTTTGTTTT-TT
1 TTATTATTA-TTTCTTTGTTTTGTT
1017657 TTATTATTA-TT-TTTGTTTTGTT
1 TTATTATTATTTCTTTGTTTTGTT
*
1017679 TTATTCTTATTTCTTT
1 TTATTATTATTTCTTT
1017695 TTATTTAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 8 0.24
22 12 0.35
23 2 0.06
24 12 0.35
ACGTcount: A:0.13, C:0.06, G:0.05, T:0.76
Consensus pattern (24 bp):
TTATTATTATTTCTTTGTTTTGTT
Found at i:1018968 original size:17 final size:17
Alignment explanation
Indices: 1018946--1018987 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
1018936 ACCTCACTAA
1018946 CTCTTTTCATTT-TTGTT
1 CTCTTTT-ATTTATTGTT
*
1018963 CTCTTTTATTTATTTTT
1 CTCTTTTATTTATTGTT
1018980 CATCTTTT
1 C-TCTTTT
1018988 GCATCATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 12 0.55
18 6 0.27
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (17 bp):
CTCTTTTATTTATTGTT
Found at i:1021739 original size:100 final size:99
Alignment explanation
Indices: 1021566--1021761 Score: 329
Period size: 100 Copynumber: 2.0 Consensus size: 99
1021556 ATATTGCATA
*
1021566 TATACAATAAAGCTTGAGTTGTCCCTTTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
1 TATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
*
1021631 ATTCAGCTAAGCCTGATAAATGTGATTATAATGTC
66 ATTCAGCT-AGCCTGATAAAAGTGATTATAATGTC
* * *
1021666 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
*
1021731 ATTCAGCTAGCCTTATAAAAGTGATTATAAT
66 ATTCAGCTAGCCTGATAAAAGTGATTATAAT
1021762 ACAATGATAT
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
99 21 0.23
100 69 0.77
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (99 bp):
TATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
ATTCAGCTAGCCTGATAAAAGTGATTATAATGTC
Found at i:1022528 original size:84 final size:84
Alignment explanation
Indices: 1022363--1022972 Score: 576
Period size: 84 Copynumber: 7.3 Consensus size: 84
1022353 AAAACTATCG
* * * * * * *
1022363 GCAACATAACTTAAGTCGAGAAGGGTTATCTATCTGTCAAC-AAAGACCTTCAAGATCGATTAAA
1 GCAACATAACTCAAGGCTAGAAGGGTTATCT-TC---CAACAAAAGACCTTCGAGTTCGACTACA
* * *
1022427 CTTAGCTCAAAGGCACATGATTT
62 CTCAGCTCCAAGGCACATCATTT
*** * * * * *
1022450 GCGGTAGAGCTAAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAACATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACACTCA
*
1022515 GCTCCAAGACACATCATTT
66 GCTCCAAGGCACATCATTT
* * **
1022534 GCAACATAGCTCAAGGCAAGAAGGGTTAT-TTGCCAACAAAAGA-CTTCGAGTTCGACTACGTTC
1 GCAACATAACTCAAGGCTAGAAGGGTTATCTT-CCAACAAAAGACCTTCGAGTTCGACTACACTC
*
1022597 TGCTCCAAGGCACATCATTT
65 AGCTCCAAGGCACATCATTT
* * * * *
1022617 GCAACATAACTCAAGGCAAGAAGGGCTAT-TTGCCAAGAAAAGGCCTTCGAGTTCGACTACGCTC
1 GCAACATAACTCAAGGCTAGAAGGGTTATCTT-CCAACAAAAGACCTTCGAGTTCGACTACACTC
1022681 AGCTCCAAGGCACATCATTT
65 AGCTCCAAGGCACATCATTT
* * *
1022701 ACAACATAACTCAAGGCTAGAAGGGTTATCTGT-CAAC-AAAGACCTTCAAGTTCGATTACACTC
1 GCAACATAACTCAAGGCTAGAAGGGTTATCT-TCCAACAAAAGACCTTCGAGTTCGACTACACTC
* *
1022764 AGCTCAAAGACACATCATTT
65 AGCTCCAAGGCACATCATTT
** * * * *
1022784 GCGGCATAACTCAAGGCTAGAAGGGTTACCTACCAACAAAAGACCTTTGAGTTCGATTACACTCA
1 GCAACATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACACTCA
*
1022849 GCT-AAAGGGCACATCATTT
66 GCTCCAA-GGCACATCATTT
* * * * * * * *
1022868 GCAACATAACTCAAGGCTATAAAGGCTATC-T---ACCAAATACCTTTGAGTTCAATTACACTCA
1 GCAACATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACACTCA
* *
1022929 ACTCAAAGGCACATCATTT
66 GCTCCAAGGCACATCATTT
* * * *
1022948 ACAGCATAGCTCAAGGCAAGAAGGG
1 GCAACATAACTCAAGGCTAGAAGGG
1022973 CTATTTGTCA
Statistics
Matches: 446, Mismatches: 68, Indels: 25
0.83 0.13 0.05
Matches are distributed among these distances:
80 60 0.13
81 3 0.01
83 156 0.35
84 200 0.45
85 1 0.00
86 3 0.01
87 23 0.05
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (84 bp):
GCAACATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACACTCA
GCTCCAAGGCACATCATTT
Found at i:1022666 original size:167 final size:166
Alignment explanation
Indices: 1022393--1022978 Score: 588
Period size: 167 Copynumber: 3.5 Consensus size: 166
1022383 AAGGGTTATC
* * * * * * * *** *
1022393 TATCTGTCAACAAAGACCTTCAAGATCGATTAAACTTAGCTCAAAGGCACATGATTTGCGGTAGA
1 TATCTGCCAACAAAGACCTTCAAGTTCGACTACACTCAGCTCAAAGACACATCATTTGCAACATA
* * *
1022458 GCTAAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
66 ACTCAAGGCTAGAAGGGTTAT-TTCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
* *
1022523 ACACATCATTTGCAACATAGCTCAAGGCAAGAAGGGT
130 GCACATCATTTGCAACATAACTCAAGGCAAGAAGGGT
* * ** * * *
1022560 TATTTGCCAACAAAAGA-CTTCGAGTTCGACTACGTTCTGCTCCAAGGCACATCATTTGCAACAT
1 TATCTGCCAAC-AAAGACCTTCAAGTTCGACTACACTCAGCTCAAAGACACATCATTTGCAACAT
* * * *
1022624 AACTCAAGGCAAGAAGGGCTATTTGCCAAGAAAAGGCCTTCGAGTTCGACTACGCTCAGCTCCAA
65 AACTCAAGGCTAGAAGGGTTATTT-CCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
* *
1022689 GGCACATCATTTACAACATAACTCAAGGCTAGAAGGGT
129 GGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGT
* * **
1022727 TATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGACACATCATTTGCGGCATA
1 TATCTGCCAACAAAGACCTTCAAGTTCGACTACACTCAGCTCAAAGACACATCATTTGCAACATA
* * * * * *
1022792 ACTCAAGGCTAGAAGGGTTACCTACCAACAAAAGACCTTTGAGTTCGATTACACTCAGCT-AAAG
66 ACTCAAGGCTAGAAGGGTTA-TTTCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-
* * * *
1022856 GGCACATCATTTGCAACATAACTCAAGGCTATAAAGGC
129 GGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGT
* * ** * * * * * *
1022894 TATCT---ACCAAATACCTTTGAGTTCAATTACACTCAACTCAAAGGCACATCATTTACAGCATA
1 TATCTGCCAACAAAGACCTTCAAGTTCGACTACACTCAGCTCAAAGACACATCATTTGCAACATA
* * *
1022956 GCTCAAGGCAAGAAGGGCTATTT
66 ACTCAAGGCTAGAAGGGTTATTT
1022979 GTCAATAAAA
Statistics
Matches: 348, Mismatches: 66, Indels: 14
0.81 0.15 0.03
Matches are distributed among these distances:
163 1 0.00
164 65 0.19
166 9 0.03
167 267 0.77
168 6 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (166 bp):
TATCTGCCAACAAAGACCTTCAAGTTCGACTACACTCAGCTCAAAGACACATCATTTGCAACATA
ACTCAAGGCTAGAAGGGTTATTTCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
CACATCATTTGCAACATAACTCAAGGCAAGAAGGGT
Found at i:1024712 original size:10 final size:10
Alignment explanation
Indices: 1024675--1024713 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
1024665 TATATATCTA
*
1024675 ATTATCTTTT
1 ATTATTTTTT
*
1024685 ATTATTTATT
1 ATTATTTTTT
1024695 ATTATTTTTT
1 ATTATTTTTT
1024705 ATTATTTTT
1 ATTATTTTT
1024714 CCTTTTCGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTATTTTTT
Found at i:1024763 original size:27 final size:22
Alignment explanation
Indices: 1024727--1024790 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 22
1024717 TTTCGTGTTT
1024727 TTTTA-TTATTATTACTTTCTTTGTA
1 TTTTATTTATTA-TA-TTT-TTT-TA
1024752 TTTTATTCTATTATATTTTTTTA
1 TTTTATT-TATTATATTTTTTTA
*
1024775 TTTTATTTATTTTATT
1 TTTTATTTATTATATT
1024791 ATTATATTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 8 0.22
23 9 0.25
24 3 0.08
25 8 0.22
26 3 0.08
27 5 0.14
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTATTTATTATATTTTTTTA
Found at i:1024855 original size:5 final size:5
Alignment explanation
Indices: 1024750--1024907 Score: 74
Period size: 5 Copynumber: 31.0 Consensus size: 5
1024740 ACTTTCTTTG
* * *
1024750 TATTT TATTC TATTA TA-TT T-TTT TATTT TA-TT TATTT TATTAT TATAT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATT-T TATTT
* * * **
1024798 TAGTTT TGTTT TATTCT TA-TT TATTTT TATTT AATTT CATTT TCCTT
1 TA-TTT TATTT TATT-T TATTT TA-TTT TATTT TATTT TATTT TATTT
* * * * *
1024845 TGTTT TATTT TCGTTT TATGT TGTTT TATCTC TATTT T-TTAT TATTT
1 TATTT TATTT T-ATTT TATTT TATTT TAT-TT TATTT TATT-T TATTT
* *
1024892 TGTTT CATTTT TATTT
1 TATTT TA-TTT TATTT
1024908 ATGTTATCCT
Statistics
Matches: 113, Mismatches: 27, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
4 14 0.12
5 71 0.63
6 28 0.25
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:1024940 original size:16 final size:17
Alignment explanation
Indices: 1024919--1024960 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1024909 TGTTATCCTT
1024919 TTATTTATTATGTTTA-
1 TTATTTATTATGTTTAC
*
1024935 TTATTT-TTATTTTTAC
1 TTATTTATTATGTTTAC
1024951 TTA-TTATTAT
1 TTATTTATTAT
1024961 TTTTTCCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTTATTATGTTTAC
Found at i:1026107 original size:18 final size:18
Alignment explanation
Indices: 1026084--1026126 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1026074 ATTTAACGTT
1026084 AAGATTTGAAAATTTTAA
1 AAGATTTGAAAATTTTAA
1026102 AAGATTTGAAAATTTTAA
1 AAGATTTGAAAATTTTAA
1026120 AAG-TTTG
1 AAGATTTG
1026127 GGTACTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.40
Consensus pattern (18 bp):
AAGATTTGAAAATTTTAA
Found at i:1033523 original size:25 final size:25
Alignment explanation
Indices: 1033489--1033546 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
1033479 AGAACCTTTG
1033489 GAGTGCATTGGTCATGCTGGTATGC
1 GAGTGCATTGGTCATGCTGGTATGC
1033514 GAGTGCATTGGTCATGCTGGTATGC
1 GAGTGCATTGGTCATGCTGGTATGC
1033539 GAGTGCAT
1 GAGTGCAT
1033547 GAGCTATATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.17, C:0.16, G:0.36, T:0.31
Consensus pattern (25 bp):
GAGTGCATTGGTCATGCTGGTATGC
Found at i:1036353 original size:21 final size:21
Alignment explanation
Indices: 1036327--1036368 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1036317 GTTGATATGG
1036327 AATCAGCAAGGAAAAAGATTC
1 AATCAGCAAGGAAAAAGATTC
1036348 AATCAGCAAGGAAAAAGATTC
1 AATCAGCAAGGAAAAAGATTC
1036369 GGAAGTTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.19, T:0.14
Consensus pattern (21 bp):
AATCAGCAAGGAAAAAGATTC
Found at i:1045057 original size:19 final size:20
Alignment explanation
Indices: 1045034--1045083 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1045024 TTATAAATTT
1045034 AAAAAAATTAGAAAAAATA-
1 AAAAAAATTAGAAAAAATAC
* * *
1045053 TAAAAAATCAGAAAAATTAC
1 AAAAAAATTAGAAAAAATAC
1045073 AAAAAAATTAG
1 AAAAAAATTAG
1045084 TGTCATTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (20 bp):
AAAAAAATTAGAAAAAATAC
Found at i:1050584 original size:17 final size:20
Alignment explanation
Indices: 1050547--1050586 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
1050537 ATTTTATTTA
1050547 TTTTTATTTGTTTATAATAT
1 TTTTTATTTGTTTATAATAT
1050567 TTTTTA-TT-TTTA-AATAT
1 TTTTTATTTGTTTATAATAT
1050584 TTT
1 TTT
1050587 AGATATCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
19 2 0.10
20 6 0.30
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTATTTGTTTATAATAT
Found at i:1053637 original size:30 final size:29
Alignment explanation
Indices: 1053603--1053660 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
1053593 TAATTCTTTC
*
1053603 TTTTCAAAATTTTTATATATATACTTATTA
1 TTTTCAAAATATTTATATATATA-TTATTA
* *
1053633 TTTTCATAATATTTATATGTATATTATT
1 TTTTCAAAATATTTATATATATATTATT
1053661 TTATTAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTCAAAATATTTATATATATATTATTA
Found at i:1053698 original size:21 final size:20
Alignment explanation
Indices: 1053656--1053698 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
1053646 TATATGTATA
*
1053656 TTATTTTATTAATGTTTCATT
1 TTATTTT-TTAATATTTCATT
*
1053677 TTATTTTTTAAGTATTTTATT
1 TTATTTTTTAA-TATTTCATT
1053698 T
1 T
1053699 CATTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (20 bp):
TTATTTTTTAATATTTCATT
Found at i:1056972 original size:15 final size:15
Alignment explanation
Indices: 1056952--1056983 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1056942 GATCAATACC
1056952 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1056967 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1056982 TT
1 TT
1056984 ATTTATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1064336 original size:21 final size:19
Alignment explanation
Indices: 1064289--1064351 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 19
1064279 GCTTGAAGAA
1064289 AAAAAAAAGAACAAAAAAAG
1 AAAAAAAAGAA-AAAAAAAG
*
1064309 AACAAAAAAGAAAAAAAATG
1 AA-AAAAAAGAAAAAAAAAG
**
1064329 -AGGAAAA-AAAAAAAAAG
1 AAAAAAAAGAAAAAAAAAG
1064346 AAAAAA
1 AAAAAA
1064352 GAGGGGGTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 9 0.26
18 7 0.20
19 1 0.03
20 9 0.26
21 9 0.26
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.02
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAAAG
Found at i:1064349 original size:11 final size:11
Alignment explanation
Indices: 1064284--1064353 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
1064274 ATTATGCTTG
1064284 AAGAAAAAAAA
1 AAGAAAAAAAA
*
1064295 AAGAACAAAAA
1 AAGAAAAAAAA
*
1064306 AAG-AACAAAA
1 AAGAAAAAAAA
1064316 AAGAAAAAAAA
1 AAGAAAAAAAA
*
1064327 TGAGGAAAAAAAA
1 --AAGAAAAAAAA
*
1064340 AA-AAAGAAAA
1 AAGAAAAAAAA
1064350 AAGA
1 AAGA
1064354 GGGGGTCAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
10 17 0.35
11 21 0.44
13 10 0.21
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.01
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1064748 original size:19 final size:17
Alignment explanation
Indices: 1064706--1064754 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
1064696 TATTTTCTCT
1064706 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
1064722 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
*
1064740 AAAATTCAACTTATT
1 -AAATTCAATTTATT
1064755 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 1 0.04
19 12 0.44
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:1065250 original size:115 final size:115
Alignment explanation
Indices: 1065048--1065501 Score: 784
Period size: 115 Copynumber: 4.0 Consensus size: 115
1065038 TACCACGTTA
1065048 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
*
1065113 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATTTGC
*
1065163 TCATAGTAGAAATAAGAAGACTCAATAGCAGCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* *
1065228 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAATATGAATTTGC
66 TTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATTTGC
*
1065278 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGG
1 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
*
1065343 TTTGGTATGAACCCCAAAAACCAATCATTAGATTTAAAAGATGAATTTGC
66 TTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATTTGC
* *
1065393 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* * * * *
1065458 TTCGGTAGGAACCAC-AGAACCAATCATTAGAATTGAAAGATGAA
66 TTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAA
1065502 CTGCATGATC
Statistics
Matches: 323, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
114 26 0.08
115 297 0.92
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (115 bp):
TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATTTGC
Found at i:1066657 original size:116 final size:110
Alignment explanation
Indices: 1066469--1066891 Score: 395
Period size: 116 Copynumber: 3.7 Consensus size: 110
1066459 TTTCCAGTTC
1066469 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAA-TTCATAATGAGAAGAATTTGTT
* * *
1066534 CAACCTTTTGTTTGAATTCATCATTTGATGGATC-GACATTGCCAG-GTA
64 CAACCTTTTG-CTAAATCCATCATTTGATGGATCAG-CATTGCCAGAG-A
1066582 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTT
1 GAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAG-AAGAAG-AATTCATAATGAGAAGAATTT
* *
1066647 GTTCAACCTTTTGCTAAATCCATCATTTGATGGATCAGCTTTTCCAGAGA
61 GTTCAACCTTTTGCTAAATCCATCATTTGATGGATCAGCATTGCCAGAGA
* * **
1066697 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAG--TTCACAATGAGAAGAGCTTGTTCA
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAATTCATAATGAGAAGAATTTGTTCA
* ** * * * * * *
1066760 ACATTTTGCATAATTCTATCACAGAAAGAGATAGATTAGTATCAACCTTTCCAGAGA
66 ACCTTTTGC-TAA----ATC-C---ATCA-TTTGA-T-GGATCAGCATTGCCAGAGA
* * ** *
1066817 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAAAAGTTCATAATGAGAAGAGCTTATT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGAA-TTCATAATGAGAAGAATTTGTT
1066882 CAACCTTTTG
64 CAACCTTTTG
1066892 AATGACTCTA
Statistics
Matches: 266, Mismatches: 21, Indels: 35
0.83 0.07 0.11
Matches are distributed among these distances:
108 29 0.11
109 3 0.01
111 6 0.02
112 13 0.05
113 23 0.09
114 1 0.00
115 48 0.18
116 52 0.20
117 4 0.02
118 3 0.01
119 1 0.00
120 49 0.18
121 5 0.02
124 29 0.11
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (110 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAATTCATAATGAGAAGAATTTGTTCA
ACCTTTTGCTAAATCCATCATTTGATGGATCAGCATTGCCAGAGA
Found at i:1066733 original size:115 final size:116
Alignment explanation
Indices: 1066470--1066734 Score: 364
Period size: 115 Copynumber: 2.3 Consensus size: 116
1066460 TTCCAGTTCG
*
1066470 AGTTCATAATGAGAAGAACTCATCTGAAGAAG--G-AAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTG
* * * *
1066532 TTCAACCTTTTGTTTGAATTCATCATTTGATGGATCGACATTGCCAGGTAG
66 TTCAACCTTTTGTCTAAATCCATCATTTGATGGATCGACATTGCCAGGTAA
* **
1066583 AGTTCATAATGAGAAGAACTCGTCAT-CTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTT
1 AGTTCATAATGAGAAGAACTCATC-TGAAGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTT
* *
1066647 GTTCAACCTTTTG-CTAAATCCATCATTTGATGGATC-AGCTTTTCCAGAG-AA
65 GTTCAACCTTTTGTCTAAATCCATCATTTGATGGATCGA-CATTGCCAG-GTAA
1066698 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAA
1066735 GTTCACAATG
Statistics
Matches: 132, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
113 27 0.20
114 3 0.02
115 61 0.46
116 41 0.31
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (116 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTG
TTCAACCTTTTGTCTAAATCCATCATTTGATGGATCGACATTGCCAGGTAA
Found at i:1066905 original size:124 final size:124
Alignment explanation
Indices: 1066687--1066980 Score: 361
Period size: 124 Copynumber: 2.4 Consensus size: 124
1066677 TGGATCAGCT
1066687 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAG---AAGTTCACAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAAAAGTTCACAATGAGA
* * * * * **
1066748 AGAGCTTGTTCAACATTTTGCATAATTCTATCACAGAAAGAGATA-GATTAGTATCAACC
66 AGAGCTTATTCAACATTTTGAATAACTCTATCACAGAAAGAAATAGGA-CAACATCAACC
*
1066807 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAAAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAAAAGTTCACAATGAGA
* * * * *
1066872 AGAGCTTATTCAACCTTTTGAATGACTCTATCACATAAGGAAATAGGACAACATCATCC
66 AGAGCTTATTCAACATTTTGAATAACTCTATCACAGAAAGAAATAGGACAACATCAACC
* *
1066931 ---CCAGCGGAAAGTTCATAATGAGAATAACTCATCTGAAGAAAGAGAAGAAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGA-AAGAAA
1066981 TTATTCAACA
Statistics
Matches: 151, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
120 43 0.28
121 7 0.05
122 31 0.21
123 4 0.03
124 64 0.42
125 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.23
Consensus pattern (124 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAAAAGTTCACAATGAGA
AGAGCTTATTCAACATTTTGAATAACTCTATCACAGAAAGAAATAGGACAACATCAACC
Found at i:1067137 original size:3 final size:3
Alignment explanation
Indices: 1067129--1067185 Score: 71
Period size: 3 Copynumber: 18.3 Consensus size: 3
1067119 ACTTATTTAT
*
1067129 TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA -TA TATA TATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA
1067176 TTA TTA TTA T
1 TTA TTA TTA T
1067186 AAAATAAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 37 0.74
4 11 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1071386 original size:16 final size:16
Alignment explanation
Indices: 1071365--1071399 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1071355 ATGATTAAGC
1071365 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
* *
1071381 GCTGAATGGTTCAGAT
1 GCTGAATGATTCAAAT
1071397 GCT
1 GCT
1071400 CTGTATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (16 bp):
GCTGAATGATTCAAAT
Found at i:1076152 original size:31 final size:30
Alignment explanation
Indices: 1076097--1076162 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
1076087 TTAAAAATAT
*
1076097 AATT-TTTTTAAAATTACCTAAGCATGAC-
1 AATTATTTTTAAAATTACATAAGCATGACA
*
1076125 AATTATTTTTAAAATTATATATGAGCATGACA
1 AATTATTTTTAAAATTACATA--AGCATGACA
1076157 AATTAT
1 AATTAT
1076163 GAAGAACGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 4 0.12
29 14 0.44
31 8 0.25
32 6 0.19
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (30 bp):
AATTATTTTTAAAATTACATAAGCATGACA
Found at i:1078148 original size:4 final size:4
Alignment explanation
Indices: 1078139--1078174 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1078129 TTATCAAACA
* *
1078139 GTAT GTAT GTAT GTAT ATAT ATAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1078175 AGACAGAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:1080545 original size:2 final size:2
Alignment explanation
Indices: 1080538--1080600 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1080528 ATCTCAGTAA
1080538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1080580 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1080601 ACGTAGATAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1081462 original size:21 final size:19
Alignment explanation
Indices: 1081417--1081468 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 19
1081407 AAATCGATAA
* *
1081417 AATATTTATTTAAAATATT
1 AATATTTATTTAAAACATC
*
1081436 ATTATTTATACTTAAAACATC
1 AATATTTAT--TTAAAACATC
1081457 AATATTT-TTTAA
1 AATATTTATTTAA
1081469 TATTTACAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 4 0.15
19 8 0.30
20 1 0.04
21 14 0.52
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTTATTTAAAACATC
Found at i:1083586 original size:37 final size:37
Alignment explanation
Indices: 1083545--1083616 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
1083535 CTTAAGAATA
*
1083545 TTTTCACAGGCACTAAAGTTGCA-ATAATCAATCAATC
1 TTTTCACAAGCACTAAAGTTG-ATATAATCAATCAATC
*
1083582 TTTTCACAAGCACTAAAGTTGATTTAATCAATCAA
1 TTTTCACAAGCACTAAAGTTGATATAATCAATCAA
1083617 AACCCATGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 1 0.03
37 31 0.97
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (37 bp):
TTTTCACAAGCACTAAAGTTGATATAATCAATCAATC
Found at i:1093733 original size:22 final size:23
Alignment explanation
Indices: 1093705--1093753 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
1093695 TTTTTTAATT
1093705 TACATAAAAAGTAAAGGGT-AAA
1 TACATAAAAAGTAAAGGGTAAAA
1093727 TACATAAAAAGTAAAGGGTAAAA
1 TACATAAAAAGTAAAGGGTAAAA
1093750 TACA
1 TACA
1093754 CAAATGGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.59, C:0.06, G:0.16, T:0.18
Consensus pattern (23 bp):
TACATAAAAAGTAAAGGGTAAAA
Done.