Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008025.1 Hibiscus syriacus cultivar Beakdansim tig00110500_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: 2744542
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1214021 original size:54 final size:54
Alignment explanation
Indices: 1213957--1214194 Score: 314
Period size: 54 Copynumber: 4.4 Consensus size: 54
1213947 GTATTTTACT
1213957 GTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCC
1 GTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCC
**
1214011 GTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTT
1 GTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCC
* * * *
1214065 GTATTGGCACTATATGTGCAATTTAAGAAATTAATAATGAGTTTATGAATTTCC
1 GTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCC
* * ** * * * *
1214119 ATATTGGCACTGTGTTTGCAATCCCACGTAATTCATAATGAGTTTGTGAATTACC
1 GTATTGGCACTGTGTGTGCAA-CTTAAGAAATTCATAATGAGTTTATGAATTTCC
* **
1214174 GTATTAGCACTACGTGTGCAA
1 GTATTGGCACTGTGTGTGCAA
1214195 ACCATAGGAT
Statistics
Matches: 158, Mismatches: 25, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
54 117 0.74
55 41 0.26
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37
Consensus pattern (54 bp):
GTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCC
Found at i:1224849 original size:18 final size:18
Alignment explanation
Indices: 1224826--1224865 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1224816 ATCCTTTTTT
*
1224826 TTTCTAATTCACGTTTAA
1 TTTCTAATTCACGATTAA
*
1224844 TTTCTAATTCATGATTAA
1 TTTCTAATTCACGATTAA
1224862 TTTC
1 TTTC
1224866 CTCGAATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTCTAATTCACGATTAA
Found at i:1227044 original size:24 final size:23
Alignment explanation
Indices: 1227017--1227072 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
1227007 AATCAATTAA
*
1227017 GGGAATTATCTTTTGTAATTTTTT
1 GGGAATTATCTTTTG-AATTTATT
*
1227041 GGGAATTATCTTTTGCATTTATT
1 GGGAATTATCTTTTGAATTTATT
*
1227064 AGGAATTAT
1 GGGAATTAT
1227073 ATTTAAGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (23 bp):
GGGAATTATCTTTTGAATTTATT
Found at i:1227068 original size:23 final size:24
Alignment explanation
Indices: 1227018--1227072 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
1227008 ATCAATTAAG
* *
1227018 GGAATTATCTTTTGTAATTTTTTG
1 GGAATTATCTTTTGTAATTTATTA
*
1227042 GGAATTATCTTTTG-CATTTATTA
1 GGAATTATCTTTTGTAATTTATTA
1227065 GGAATTAT
1 GGAATTAT
1227073 ATTTAAGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.53
Consensus pattern (24 bp):
GGAATTATCTTTTGTAATTTATTA
Found at i:1227674 original size:24 final size:24
Alignment explanation
Indices: 1227639--1227703 Score: 80
Period size: 23 Copynumber: 2.7 Consensus size: 24
1227629 TATTCAAACA
1227639 ATTAAGGGAATTATCTTTTGTAATTT
1 ATTAA-GGAATTATCTTTTG-AATTT
*
1227665 -TTAAGGAATTATCTTTTGCATTT
1 ATTAAGGAATTATCTTTTGAATTT
*
1227688 ACT-AGGAATTATCTTT
1 ATTAAGGAATTATCTTT
1227704 AAGCATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 17 0.47
24 15 0.42
25 4 0.11
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (24 bp):
ATTAAGGAATTATCTTTTGAATTT
Found at i:1227716 original size:23 final size:22
Alignment explanation
Indices: 1227645--1227718 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
1227635 AACAATTAAG
* *
1227645 GGAATTATCTTTTGTAATTTTTAA
1 GGAATTATCTTTAG-CATTTTT-A
* *
1227669 GGAATTATCTTTTGCATTTACTA
1 GGAATTATCTTTAGCATTT-TTA
1227692 GGAATTATCTTTAAGCATTTTTA
1 GGAATTATCTTT-AGCATTTTTA
1227715 GGAA
1 GGAA
1227719 GCTATAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 23 0.52
24 21 0.48
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (22 bp):
GGAATTATCTTTAGCATTTTTA
Found at i:1227821 original size:627 final size:616
Alignment explanation
Indices: 1226841--1228008 Score: 1594
Period size: 625 Copynumber: 1.9 Consensus size: 616
1226831 TTTTATTTTA
** **
1226841 TGGAGTCAAGGTTGAACTAATGGGCATGACTTGGGGCATGACTCCACTGATGTAGCGACTAGACA
1 TGGAGTCAAGGTTGAACTAATGGGCATGACTTAAGGCATGACTCCACTGACATAGCGACTAGACA
* *
1226906 ACATCTTCTAGAAGGTCCAGTCAACATTTTCGTGAAGAAAAAAACACATCCACAAATTCACACTT
66 ACATCTTCTAGAAGGTCCAATCAACATTTTCATGAAGAAAAAAACACATCCACAAATTCACACTT
*
1226971 AAATTTAGGAATTATCTTTATTTTTGAAATATTTTCAATCAATTAAGGGAATTATCTTTTGTAAT
131 AAATTTAGGAATTATCTTTATTTTTGAAATATTTTCAAACAATTAAGGGAATTATCTTTTGTAAT
** *
1227036 TTTTTGGGAATTATCTTTTGCATTTATTAGGAATTATATTTAAGCATTTAAGGGTTTTTAGGAAG
196 TTTTAAGGAATTATCTTTTGCATTTACTAGGAATTATATTTAAGC---T-A--GTTTTTAGGAAG
** ** ** * * *
1227101 CTATAAGTACCCTTTTGGGTAAGCTTTAAGCACATCTTGAATTCTCTGAATTTCTTTGTTTTTGC
255 CTATAAACACCCCCTCAGGTAAGCTTTAAGCACATCTCGAATTCTCTAAATTTCTTTGTTCTTGC
*
1227166 TTTCTTTCTTTTATAAAGTTTACTTTTCAAGTCTTTATTTTATTTTTCTTTAAAATGCTAAGTAT
320 TTTCTTTCTTTTATAAAGTTTACTTTTCAAGTATTTATTTTATTTTTCTTTAAAATGCTAAGTAT
* *
1227231 GATTTCTATCATACTTAGCTGA-TTTCTATCATAGCCAAAGGCTAAAGCGATGA-TTCAATTCCG
385 GATTT-TATCATACTTAGCTAAGTTT-T-TCATAGCCAAAGGCTAAAGCGATGACTT-AATTACG
* ** ***
1227294 ATGGTGAAAATTGAAAAGCATTTAATACCCTTTGGGTTACATTCTCAGTTTTCTGGAAACAAGGA
446 ATCGTGAAAATTGAAAAGCACCTAATACCCTTCAAGTTACATTCTCAGTTTTCTGGAAACAAGGA
*
1227359 TCGGTAATCAACTATCCTTTTATAAAAAGTGTATGTTGGATTGATAGTGTTTTCGATTAATAGTT
511 TCGGTAATCAACCATCCTTTTATAAAAAGTGTATGTTGGATTGATAGTGTTTTCGATTAATAGTT
1227424 GGGAGGAATGATTGGCTTATAACACATTTTTTATTTTTCTC
576 GGGAGGAATGATTGGCTTATAACACATTTTTTATTTTTCTC
* * * * *
1227465 TGGAGTCAAGGTTGGA-TCAATGGGCATGACTTAATGCATGACTCCACTGACATGGTGACTAGTC
1 TGGAGTCAAGGTTGAACT-AATGGGCATGACTTAAGGCATGACTCCACTGACATAGCGACTAGAC
** * * * * * *
1227529 CGCATCTTCTAGAAGGTTCAATCAACATTTTCATGAAGACATAAGACTCATCCGCAAATTCAGAC
65 AACATCTTCTAGAAGGTCCAATCAACATTTTCATGAAGA-AAAAAACACATCCACAAATTCACAC
**
1227594 TTAAATTTAGGAAATTATCTTTATTTTTGGGAT-TCTATTCAAACAATTAAGGGAATTATCTTTT
129 TTAAATTTAGG-AATTATCTTTATTTTTGAAATAT-T-TTCAAACAATTAAGGGAATTATCTTTT
*
1227658 GTAATTTTTAAGGAATTATCTTTTGCATTTACTAGGAATTATCTTTAAGC-A-TTTTTAGGAAGC
191 GTAATTTTTAAGGAATTATCTTTTGCATTTACTAGGAATTATATTTAAGCTAGTTTTTAGGAAGC
1227721 TATAAACACCCCCTCAGGTAAGCTTTGAA-CACATCTCGAATTCTCTAAATTTCTTTGTTCTTGC
256 TATAAACACCCCCTCAGGTAAGCTTT-AAGCACATCTCGAATTCTCTAAATTTCTTTGTTCTTGC
*
1227785 TTTTTTTTTCTTTTATAAAGTTTTACGTTTCTTTTCAAGTATTTATTTTATTTTTCTTTAAAATG
320 --TTTCTTTCTTTTATAAAG-TTTA-----CTTTTCAAGTATTTATTTTATTTTTCTTTAAAATG
*
1227850 CTAAGTATGATTTTATCATACTTAGCTAAGTTTTTCATAGCCAAAGGCTGAAGCGATGACTTAAT
377 CTAAGTATGATTTTATCATACTTAGCTAAGTTTTTCATAGCCAAAGGCTAAAGCGATGACTTAAT
* * * * *
1227915 TATGATCTTGAGAATTGAAAAGCACCTAATATCCTTCAAGTTACATTCTTAGTTTTCTGGAAACA
442 TACGATCGTGAAAATTGAAAAGCACCTAATACCCTTCAAGTTACATTCTCAGTTTTCTGGAAACA
*
1227980 AGGATCGGTAATCGACCATCCTTTTATAA
507 AGGATCGGTAATCAACCATCCTTTTATAA
1228009 TCAAAAACAT
Statistics
Matches: 475, Mismatches: 53, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
619 64 0.13
620 2 0.00
621 17 0.04
622 5 0.01
623 1 0.00
624 87 0.18
625 139 0.29
626 38 0.08
627 122 0.26
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (616 bp):
TGGAGTCAAGGTTGAACTAATGGGCATGACTTAAGGCATGACTCCACTGACATAGCGACTAGACA
ACATCTTCTAGAAGGTCCAATCAACATTTTCATGAAGAAAAAAACACATCCACAAATTCACACTT
AAATTTAGGAATTATCTTTATTTTTGAAATATTTTCAAACAATTAAGGGAATTATCTTTTGTAAT
TTTTAAGGAATTATCTTTTGCATTTACTAGGAATTATATTTAAGCTAGTTTTTAGGAAGCTATAA
ACACCCCCTCAGGTAAGCTTTAAGCACATCTCGAATTCTCTAAATTTCTTTGTTCTTGCTTTCTT
TCTTTTATAAAGTTTACTTTTCAAGTATTTATTTTATTTTTCTTTAAAATGCTAAGTATGATTTT
ATCATACTTAGCTAAGTTTTTCATAGCCAAAGGCTAAAGCGATGACTTAATTACGATCGTGAAAA
TTGAAAAGCACCTAATACCCTTCAAGTTACATTCTCAGTTTTCTGGAAACAAGGATCGGTAATCA
ACCATCCTTTTATAAAAAGTGTATGTTGGATTGATAGTGTTTTCGATTAATAGTTGGGAGGAATG
ATTGGCTTATAACACATTTTTTATTTTTCTC
Found at i:1230305 original size:36 final size:36
Alignment explanation
Indices: 1230265--1230335 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
1230255 AAGAGAAACT
* *
1230265 ATCTTAGGCGGGATGAAATTTGTT-TTAAAGAAAAAA
1 ATCTTAAGCGAGATGAAATTTGTTCTT-AAGAAAAAA
*
1230301 ATCTTAAGTGAGATGAAATTTGTTCTTAAGAAAAA
1 ATCTTAAGCGAGATGAAATTTGTTCTTAAGAAAAA
1230336 CGATCTTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 29 0.94
37 2 0.06
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (36 bp):
ATCTTAAGCGAGATGAAATTTGTTCTTAAGAAAAAA
Found at i:1231106 original size:17 final size:17
Alignment explanation
Indices: 1231080--1231117 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1231070 TGCTTTATTC
*
1231080 TCTTTTTTGAGTCTTT-A
1 TCTTTGTTGAGT-TTTCA
1231097 TCTTTGTTGAGTTTTCA
1 TCTTTGTTGAGTTTTCA
1231114 TCTT
1 TCTT
1231118 GTGAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.63
Consensus pattern (17 bp):
TCTTTGTTGAGTTTTCA
Found at i:1235812 original size:53 final size:52
Alignment explanation
Indices: 1235728--1235831 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 52
1235718 AATCCAAGCA
1235728 AAAACAAATTAAAATAATTTTGAACATAAATTGGAAATTCGAATTAAAGTTC
1 AAAACAAATTAAAATAATTTTGAACATAAATTGGAAATTCGAATTAAAGTTC
* * * *
1235780 AAAATAAATTCAAATAATTTTTTAACATAAATTGGGAATTCGAATTAAAGTT
1 AAAACAAATTAAAATAA-TTTTGAACATAAATTGGAAATTCGAATTAAAGTT
1235832 TGGGAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 15 0.32
53 32 0.68
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.34
Consensus pattern (52 bp):
AAAACAAATTAAAATAATTTTGAACATAAATTGGAAATTCGAATTAAAGTTC
Found at i:1236656 original size:198 final size:197
Alignment explanation
Indices: 1236332--1236890 Score: 719
Period size: 198 Copynumber: 2.8 Consensus size: 197
1236322 GAGCTATTAG
*** * * ** *
1236332 AATTGTTGAAATTTGTATCGATACAGTTATAAGTATATGTACCAAAATATCGGTACTGCATGAAT
1 AATTGTTGAAATTTGTATCGATAGTTTTATAAGTATATGTACCAAAGTATCAGTACTTTAGGAAT
* * * * *
1236397 TTAAAAGAATTGCAATAATAGTGGTTATAAAGTTTCGATACCTTACACACATGTGTCGATACGTG
66 TTAAAAGAATTGCAATAATAGTGGCTATAAAGTATCGATACCTTAGACACATGTATCGATACATG
* *
1236462 ACAATATAACAGGTTGAAATTTGACAAAACCGGTTTCAATTTGAAAAAAACTGTAAAGAGCTACC
131 ACAATATAACAGGTTCAAATTTGACAAAACCGGTTTCAATTTGAAAAAAACGGTAAAGAGCTACC
1236527 GA
196 GA
* *
1236529 AATTGTTGAAATTTGTATCGATATGTTTTATAAGTATATGTACCAAAGTGTCCGTACTTTAGGAA
1 AATTGTTGAAATTTGTATCGATA-GTTTTATAAGTATATGTACCAAAGTATCAGTACTTTAGGAA
* * *
1236594 TTTAAAAGAATTGCAATAATAGTGGCTATAAAATATCAATACCTTAGAAACATGTATCGATACAT
65 TTTAAAAGAATTGCAATAATAGTGGCTATAAAGTATCGATACCTTAGACACATGTATCGATACAT
* * * * * ** ** * *
1236659 GACAATACAACAAGTTTAAATTTTAGAAAATAGGTTTCAATTTGACGAAACCGGTAAGGAGCTAC
130 GACAATATAACAGGTTCAAATTTGACAAAACCGGTTTCAATTTGAAAAAAACGGTAAAGAGCTAC
*
1236724 CGG
195 CGA
* *
1236727 AATGGTTGAAATTTGTAAT-GATACTTTTATAAGTATATGTACCAAAGTATCAGTACTTTAGGAA
1 AATTGTTGAAATTTGT-ATCGATAGTTTTATAAGTATATGTACCAAAGTATCAGTACTTTAGGAA
* * * *
1236791 TTTCAAAGAATTTCAAT-ATAGT-GCTTATAAAGTATCGATACCTTAGACACGTGTATTGATACA
65 TTTAAAAGAATTGCAATAATAGTGGC-TATAAAGTATCGATACCTTAGACACATGTATCGATACA
1236854 TGACAATATAACAGGTTCCAAATTTGACAAAACCGGT
129 TGACAATATAACAGGTT-CAAATTTGACAAAACCGGT
1236891 AAAACGCTAC
Statistics
Matches: 310, Mismatches: 48, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
195 2 0.01
196 53 0.17
197 90 0.29
198 163 0.53
199 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.32
Consensus pattern (197 bp):
AATTGTTGAAATTTGTATCGATAGTTTTATAAGTATATGTACCAAAGTATCAGTACTTTAGGAAT
TTAAAAGAATTGCAATAATAGTGGCTATAAAGTATCGATACCTTAGACACATGTATCGATACATG
ACAATATAACAGGTTCAAATTTGACAAAACCGGTTTCAATTTGAAAAAAACGGTAAAGAGCTACC
GA
Found at i:1239086 original size:12 final size:12
Alignment explanation
Indices: 1239071--1239103 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1239061 GAAGAAGATC
1239071 AAGAGAAGGAAG
1 AAGAGAAGGAAG
*
1239083 AAGAGAAGGAGG
1 AAGAGAAGGAAG
1239095 AAGAGAAGG
1 AAGAGAAGG
1239104 TAGTAGGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (12 bp):
AAGAGAAGGAAG
Found at i:1239095 original size:15 final size:17
Alignment explanation
Indices: 1239053--1239098 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1239043 GGCAAAGAGG
1239053 AAGATGAGGAAGAAGATC
1 AAGA-GAGGAAGAAGATC
*
1239071 AAGAGAAGGAAGAAGA-G
1 AAGAG-AGGAAGAAGATC
1239088 AAG-GAGGAAGA
1 AAGAGAGGAAGA
1239099 GAAGGTAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 7 0.27
16 1 0.04
17 4 0.15
18 14 0.54
ACGTcount: A:0.54, C:0.02, G:0.39, T:0.04
Consensus pattern (17 bp):
AAGAGAGGAAGAAGATC
Found at i:1241028 original size:49 final size:49
Alignment explanation
Indices: 1240965--1241058 Score: 188
Period size: 49 Copynumber: 1.9 Consensus size: 49
1240955 GTTAGTTTGT
1240965 AAATTTTGTATGTGAATGAAATTATGTATGTGATTACCAAAGTTACAAC
1 AAATTTTGTATGTGAATGAAATTATGTATGTGATTACCAAAGTTACAAC
1241014 AAATTTTGTATGTGAATGAAATTATGTATGTGATTACCAAAGTTA
1 AAATTTTGTATGTGAATGAAATTATGTATGTGATTACCAAAGTTA
1241059 GCAAATATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (49 bp):
AAATTTTGTATGTGAATGAAATTATGTATGTGATTACCAAAGTTACAAC
Found at i:1241922 original size:21 final size:21
Alignment explanation
Indices: 1241896--1241969 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
1241886 AAGAAGTATT
1241896 GATACTTCTTATGACGTTATG
1 GATACTTCTTATGACGTTATG
1241917 GATACTTCTTATGACGTTATG
1 GATACTTCTTATGACGTTATG
* *
1241938 GATACTTCTTATGTCGATATG
1 GATACTTCTTATGACGTTATG
1241959 GATACTT-TTAT
1 GATACTTCTTAT
1241970 TCTAGTATGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 4 0.08
21 47 0.92
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.45
Consensus pattern (21 bp):
GATACTTCTTATGACGTTATG
Found at i:1242488 original size:179 final size:183
Alignment explanation
Indices: 1241959--1242728 Score: 722
Period size: 200 Copynumber: 4.1 Consensus size: 183
1241949 TGTCGATATG
*
1241959 GATACTTTTAT-T-CTA-GTATGATTCTCAAAC-AATTTGCACGTAAAATGTATCGATACACATA
1 GATACTTTTATATGCTATGTATGATTCTCAAACAAATTTGCACGCAAAATGTATCGATACACATA
* * * *
1242020 TATAAAGTATCAATACTTGGAATTTCAAAACCTATTCCTTTAAAGTAATTAGGTAAATTAACACT
66 TATAAAATATCGATACTTGGAATTTCAAAACCTATTACTTTAAAGTAA-TAGGTAAATTAACAAT
* * *
1242085 GTAAATGGTAAAAGACTACCAGTATAATGATAATAGACGTAAATACCAAGTATC
130 GTAAACGGTAAAAGTCTACCAGTATAATGATAATAGGCGTAAATACCAAGTATC
* *
1242139 AATACTCTTTATATGGGCATGGATACTTTTATTCTAGTATGCTTCTCAAAC-AATTTGCACGCAA
1 GATA--CTTT-TAT----AT-G---C---TA---T-GTATGATTCTCAAACAAATTTGCACGCAA
* * * * **
1242203 AATGTATC-A-ATACATGTATAAAGTATCGATGCTTGGAATTTTGAAACCTATTACTTTAAAGTA
48 AATGTATCGATACACATATATAAAATATCGATACTTGGAATTTCAAAACCTATTACTTTAAAGTA
** * *
1242266 ATAGGTAAATTAACAATGTAAAATGTAAAAGTATA-CAGGTATAATGATAATAGGCCTAAATACC
113 ATAGGTAAATTAACAATGTAAACGGTAAAAGTCTACCA-GTATAATGATAATAGGCGTAAATACC
*
1242330 AAGGATC
177 AAGTATC
*
1242337 GATACTTTTAT-T-CTA-GTATGCTTCTCAAAC-AATTTGCACGCAAAATGTATCGATACACATA
1 GATACTTTTATATGCTATGTATGATTCTCAAACAAATTTGCACGCAAAATGTATCGATACACATA
* * * *
1242398 TATAAAATATCTATACTTGAAATTTCAAAACCTATTACTTTAAAGTAATAGGTAACTTGACAATG
66 TATAAAATATCGATACTTGGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATG
** * *
1242463 TAAACGGTAAAAGTCTACTGGTATAATGATAATTGGTGTAAATACCAAGTATC
131 TAAACGGTAAAAGTCTACCAGTATAATGATAATAGGCGTAAATACCAAGTATC
* * *
1242516 GATGCTTTTATATAGGTATGGATATTTTTATTCTAATATGATTCTCAAAC-AATTTGCACCGTAA
1 GATACTTTTATAT-GCTAT-G---------------TATGATTCTCAAACAAATTTGCA-CG-CA
* *
1242580 AAAT-TATCGATACACATATATAAAATATCGATACATGGAATTTCGAAACCTATTACTTTAAAGT
47 AAATGTATCGATACACATATATAAAATATCGATACTTGGAATTTCAAAACCTATTACTTTAAAGT
* * * ** *
1242644 AATGGGTAAATTAACAATGTAAACGATAAAAGTCTACCAGTATATTGATAATAGGAATAAATACT
112 AATAGGTAAATTAACAATGTAAACGGTAAAAGTCTACCAGTATAATGATAATAGGCGTAAATACC
1242709 AAGTATC
177 AAGTATC
1242716 GATACTTTTATAT
1 GATACTTTTATAT
1242729 AGGTATCGAT
Statistics
Matches: 485, Mismatches: 58, Indels: 74
0.79 0.09 0.12
Matches are distributed among these distances:
177 36 0.07
178 1 0.00
179 115 0.24
180 4 0.01
182 8 0.02
183 3 0.01
184 1 0.00
185 1 0.00
188 1 0.00
190 1 0.00
193 1 0.00
195 3 0.01
196 6 0.01
197 2 0.00
198 62 0.13
199 69 0.14
200 132 0.27
201 39 0.08
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (183 bp):
GATACTTTTATATGCTATGTATGATTCTCAAACAAATTTGCACGCAAAATGTATCGATACACATA
TATAAAATATCGATACTTGGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATG
TAAACGGTAAAAGTCTACCAGTATAATGATAATAGGCGTAAATACCAAGTATC
Found at i:1243628 original size:2 final size:2
Alignment explanation
Indices: 1243621--1243648 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1243611 TAATGAGGAA
1243621 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
1243649 CTCCAGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1246206 original size:130 final size:131
Alignment explanation
Indices: 1245861--1246341 Score: 689
Period size: 130 Copynumber: 3.7 Consensus size: 131
1245851 CACGCAAAAT
* * * *
1245861 GTATCGATACACATATATAAAGTATCGATATTTATAATTTGGAAGCCTATTACTTTAAAGTAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
* * * *
1245926 TGTAAATTAACAATGTACAGGGTAAACATTTCTACCAGTATAATGAAAATAGGCGTAAATGTCCA
66 GGTAAATTAACAATGTACACGGTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
1245991 A
131 A
* * * * *
1245992 GTATCGATTCTTATATACAAAGTATCGATACTTATAATTTTGAAACATATTACTTTAAAGTAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
* * * *
1246057 GGTAAATTAACAATGTACACGATAAACGTTTCTATCGGTATAATGAAAATAGGCGTAAATGCCCT
66 GGTAAATTAACAATGTACACGGTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
1246122 A
131 A
* * * *
1246123 GTATAGATACTCATGTATAAAGTAT-GATACTTATAATTTCAAAACCTATTATTTTAAAGTAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
*
1246187 GGTAAATTAACAATGTACACGGTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTACA
66 GGTAAATTAACAATGTACACGGTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
1246252 A
131 A
* * * *
1246253 GCATCGATACT-GTCATAT-AAGTATCGATACTTCTAATTTCGAAACCAATTACTTTAAAGTAAT
1 GTATCGATACTCAT-ATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAAT
*
1246316 AGGTAAATTAACAATGTACATGGTAA
65 AGGTAAATTAACAATGTACACGGTAA
1246342 TATGTTGATA
Statistics
Matches: 309, Mismatches: 39, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
129 7 0.02
130 167 0.54
131 135 0.44
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.33
Consensus pattern (131 bp):
GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
GGTAAATTAACAATGTACACGGTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
A
Found at i:1250187 original size:43 final size:43
Alignment explanation
Indices: 1250135--1250223 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
1250125 ATTCAATGTA
*
1250135 ATGCAACACATATATGTAAATGAGTAATAATATTTAAGGCATT
1 ATGCAACACATAAATGTAAATGAGTAATAATATTTAAGGCATT
*
1250178 ATGCAACACATAAATGTAAATGAGTAATAATATTTAAGGTATT
1 ATGCAACACATAAATGTAAATGAGTAATAATATTTAAGGCATT
1250221 ATG
1 ATG
1250224 ACCACATTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.33
Consensus pattern (43 bp):
ATGCAACACATAAATGTAAATGAGTAATAATATTTAAGGCATT
Found at i:1250736 original size:22 final size:22
Alignment explanation
Indices: 1250705--1250748 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1250695 CCAAAATAAC
1250705 ATTCACAATAAACATCATATAT
1 ATTCACAATAAACATCATATAT
* *
1250727 ATTCATAATAAACTTCATATAT
1 ATTCACAATAAACATCATATAT
1250749 TATAACCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTCACAATAAACATCATATAT
Found at i:1251044 original size:2 final size:2
Alignment explanation
Indices: 1251037--1251096 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1251027 ATTTAAAGAA
1251037 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
1251079 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1251097 TATGTTTATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1251952 original size:19 final size:19
Alignment explanation
Indices: 1251928--1251976 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
1251918 TTACCAAATC
1251928 CAATTTCACATTCTAACAT
1 CAATTTCACATTCTAACAT
* *
1251947 CAATTTCAACACTCTAGCAT
1 CAATTTC-ACATTCTAACAT
*
1251967 TAATTT-ACAT
1 CAATTTCACAT
1251977 CATATTCCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 3 0.12
19 7 0.28
20 15 0.60
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (19 bp):
CAATTTCACATTCTAACAT
Found at i:1252459 original size:46 final size:46
Alignment explanation
Indices: 1252399--1252495 Score: 194
Period size: 46 Copynumber: 2.1 Consensus size: 46
1252389 CAAAAACCTC
1252399 AAAATCCATCATCAATTCATGAAACCATAACATGTTCATAAACCCT
1 AAAATCCATCATCAATTCATGAAACCATAACATGTTCATAAACCCT
1252445 AAAATCCATCATCAATTCATGAAACCATAACATGTTCATAAACCCT
1 AAAATCCATCATCAATTCATGAAACCATAACATGTTCATAAACCCT
1252491 AAAAT
1 AAAAT
1252496 TTGGGATCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.45, C:0.25, G:0.04, T:0.26
Consensus pattern (46 bp):
AAAATCCATCATCAATTCATGAAACCATAACATGTTCATAAACCCT
Found at i:1254947 original size:33 final size:32
Alignment explanation
Indices: 1254899--1254971 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
1254889 GCATTAATAT
* *
1254899 CATACATGTATGTATTACATGAATAAATT-ATA
1 CATACATATATGTATTAAAT-AATAAATTCATA
*
1254931 CATACATATCATGTATTAAATTATAAATTCATA
1 CATACATAT-ATGTATTAAATAATAAATTCATA
1254964 CATACATA
1 CATACATA
1254972 CATACATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 15 0.42
33 21 0.58
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.37
Consensus pattern (32 bp):
CATACATATATGTATTAAATAATAAATTCATA
Found at i:1254969 original size:4 final size:4
Alignment explanation
Indices: 1254960--1254986 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1254950 ATTATAAATT
1254960 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
1254987 TCTATGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:1255305 original size:61 final size:60
Alignment explanation
Indices: 1255176--1255314 Score: 149
Period size: 61 Copynumber: 2.3 Consensus size: 60
1255166 TTTCAGTAAA
* * * *
1255176 ATTTAAAATGAAAACATTTCCTCTTCTCTATTCACTCATAGTTTTAAAGTTTTAGTGAAT
1 ATTTAAAATGAAAACCTTCCCTCTTCTCTATTCACTCATAATTTTAAAGTTTTAATGAAT
* * *
1255236 ATTCAAAATGAAAACCTTCCCTCTT-TCTCTTCCCTCCATGAATTTTAAA-TATTTAATGAA-
1 ATTTAAAATGAAAACCTTCCCTCTTCTCTATTCACT-CAT-AATTTTAAAGT-TTTAATGAAT
*
1255296 ATTTTAAAATAAAAACCTT
1 A-TTTAAAATGAAAACCTT
1255315 TGATCTCGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 8 0.12
60 27 0.41
61 31 0.47
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.40
Consensus pattern (60 bp):
ATTTAAAATGAAAACCTTCCCTCTTCTCTATTCACTCATAATTTTAAAGTTTTAATGAAT
Found at i:1261623 original size:38 final size:39
Alignment explanation
Indices: 1261580--1261654 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
1261570 CTAATGCTCA
* * *
1261580 TAATTATTATAAAAATC-AATTTATTAATTTAATAATCT
1 TAATTAATATAAAAAGCAAATTTATTAATATAATAATCT
*
1261618 TAATTAATATAGAAAGCAAATTTATTAATATAATAAT
1 TAATTAATATAAAAAGCAAATTTATTAATATAATAAT
1261655 AATTAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 14 0.44
39 18 0.56
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (39 bp):
TAATTAATATAAAAAGCAAATTTATTAATATAATAATCT
Found at i:1261680 original size:21 final size:21
Alignment explanation
Indices: 1261651--1261690 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1261641 ATTAATATAA
1261651 TAATAATTAAATTTATTAATC
1 TAATAATTAAATTTATTAATC
* **
1261672 TAATGATTATTTTTATTAA
1 TAATAATTAAATTTATTAA
1261691 CTATTCTTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
TAATAATTAAATTTATTAATC
Found at i:1268316 original size:26 final size:26
Alignment explanation
Indices: 1268287--1268338 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1268277 TCTGGTTATT
* *
1268287 CTGGGCCGGTTCTGTTTTGTTTGTAA
1 CTGGGCCGGTCCAGTTTTGTTTGTAA
1268313 CTGGGCCGGTCCAGTTTTGTTTGTAA
1 CTGGGCCGGTCCAGTTTTGTTTGTAA
1268339 TTGTTTGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.10, C:0.17, G:0.31, T:0.42
Consensus pattern (26 bp):
CTGGGCCGGTCCAGTTTTGTTTGTAA
Found at i:1268356 original size:3 final size:3
Alignment explanation
Indices: 1268348--1268425 Score: 86
Period size: 3 Copynumber: 25.7 Consensus size: 3
1268338 ATTGTTTGTA
* * *
1268348 AAT AAT AAT TAT AAT -AT AAT AAT AAT ATTT AAT AAT AAT ATTT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT
**
1268394 AAT AAT AAT AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1268426 AAACAAAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.03
3 56 0.90
4 4 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:1268382 original size:13 final size:13
Alignment explanation
Indices: 1268350--1268421 Score: 82
Period size: 13 Copynumber: 5.8 Consensus size: 13
1268340 TGTTTGTAAA
* *
1268350 TAATAATTATAATA
1 TAATAATAAT-ATT
1268364 TAATAATAATATT
1 TAATAATAATATT
1268377 TAATAATAATATT
1 TAATAATAATATT
1268390 TAATAAT-A-A--
1 TAATAATAATATT
1268399 TAATAATAAT-TT
1 TAATAATAATATT
1268411 TAATAATAATA
1 TAATAATAATA
1268422 ATAAAAACAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
9 7 0.14
10 1 0.02
11 1 0.02
12 11 0.22
13 22 0.43
14 9 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATAATAATATT
Found at i:1268745 original size:76 final size:76
Alignment explanation
Indices: 1268580--1269367 Score: 1391
Period size: 76 Copynumber: 10.4 Consensus size: 76
1268570 GAGGTCTTAA
*
1268580 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1268644 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * *
1268655 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTTAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1268720 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
1268731 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACTTCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1268796 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1268807 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1268872 AGGCTTTTTGG
66 AGGCTTTTTGG
**
1268883 AAACATCATGCACTATAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
1268948 TGGCTTTTTGG
66 AGGCTTTTTGG
1268959 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1269024 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
1269035 AAACATCATGCACTGCAGGACTTACAGATGTCCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1269100 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1269111 AAACATCATGCACTGCAGGACTTACAGATGACTCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1269176 AGGCTTTTTGG
66 AGGCTTTTTGG
1269187 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1269252 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1269263 AAACATCTTGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1269327 AGGCTTTTTGG
66 AGGCTTTTTGG
1269338 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
1269368 TGGGAAATAG
Statistics
Matches: 685, Mismatches: 27, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
75 103 0.15
76 582 0.85
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1270061 original size:22 final size:23
Alignment explanation
Indices: 1270036--1270090 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
1270026 AATAAAGCTT
*
1270036 TCATCTTTGAAAAGA-GAATCTA
1 TCATCTTTGAAAAAAGGAATCTA
*
1270058 TCATCTTT-AAAAAAGGAGTCTA
1 TCATCTTTGAAAAAAGGAATCTA
1270080 TCATCTTTGAA
1 TCATCTTTGAA
1270091 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 5 0.17
22 22 0.76
23 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (23 bp):
TCATCTTTGAAAAAAGGAATCTA
Found at i:1270539 original size:54 final size:53
Alignment explanation
Indices: 1270457--1270608 Score: 220
Period size: 54 Copynumber: 2.9 Consensus size: 53
1270447 AGAATAACAG
* * **
1270457 GTTCGTAAAACATTTGACAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGA
1 GTTCGTAAAACATTTGACAATACATTCATCCTTTTTTGTGGCTTCTGCTCAGA
*
1270510 TGTTCGTAAAACATTTGACAATACATTCATACTTTTTTGTGGCTTCTGCTCAGA
1 -GTTCGTAAAACATTTGACAATACATTCATCCTTTTTTGTGGCTTCTGCTCAGA
*
1270564 --T-GTAAAACATTTGACAACACATTCATCCTTTTTTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAATACATTCATCCTTTTTTGTGGCTTCTGC
1270609 CAAGATTTCT
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
50 42 0.46
51 1 0.01
54 48 0.53
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAATACATTCATCCTTTTTTGTGGCTTCTGCTCAGA
Found at i:1273303 original size:115 final size:115
Alignment explanation
Indices: 1272965--1273303 Score: 583
Period size: 115 Copynumber: 3.0 Consensus size: 115
1272955 GATCATGCAG
* * * *
1272965 TTCATCTTTCAATTCCAATGATTGG--TTTGGGGTTCCTACCGAACCAGATCATATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
1273028 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * *
1273078 TTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACTAGATCAGATAACTTAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
1273143 AACACTTCCAGAAGAGGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
1273193 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1273258 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
66 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
1273304 AACGTGGCAC
Statistics
Matches: 211, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
113 23 0.11
115 188 0.89
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1275484 original size:24 final size:24
Alignment explanation
Indices: 1275457--1275505 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1275447 CTTTTTTCTT
1275457 TTTTTCTCTCTTTTT-TTTGATGGA
1 TTTTTCT-TCTTTTTCTTTGATGGA
* *
1275481 TTTTTCTTTTTTTTCTTTGTTGGA
1 TTTTTCTTCTTTTTCTTTGATGGA
1275505 T
1 T
1275506 GAGTATAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.71
Consensus pattern (24 bp):
TTTTTCTTCTTTTTCTTTGATGGA
Found at i:1282541 original size:16 final size:17
Alignment explanation
Indices: 1282520--1282553 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1282510 CTGCTGTCCG
1282520 TGCTCTCT-CCTTTTTT
1 TGCTCTCTGCCTTTTTT
*
1282536 TGCTCTCTGTCTTTTTT
1 TGCTCTCTGCCTTTTTT
1282553 T
1 T
1282554 TTTCTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.00, C:0.26, G:0.09, T:0.65
Consensus pattern (17 bp):
TGCTCTCTGCCTTTTTT
Found at i:1282958 original size:3 final size:3
Alignment explanation
Indices: 1282950--1283014 Score: 78
Period size: 3 Copynumber: 21.7 Consensus size: 3
1282940 ACTGTTTATA
* *
1282950 AAT AAT AAT TAT AAT -AT AAT AAT AAT ATTT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
**
1282995 AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1283015 AAACAAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:1292966 original size:45 final size:45
Alignment explanation
Indices: 1292898--1293027 Score: 161
Period size: 45 Copynumber: 2.9 Consensus size: 45
1292888 TTGTCGTTAC
* * * * ** *
1292898 CGAAGCCAATCGCAATGACCCTAAACCTAATATGGAGAATGATAC
1 CGAAGCCGATGGCAAGGAGCCTAAACCTAATACAGAGAATGATAA
* * *
1292943 CGAAGCTGATGGTAAGGAGCCTAAACCTAATACAGAGAATGCTAA
1 CGAAGCCGATGGCAAGGAGCCTAAACCTAATACAGAGAATGATAA
*
1292988 CGAAGCCGATGGCAAGGAGCCTAAACCTAATAAAGAGAAT
1 CGAAGCCGATGGCAAGGAGCCTAAACCTAATACAGAGAAT
1293028 ATCGCTGAAG
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (45 bp):
CGAAGCCGATGGCAAGGAGCCTAAACCTAATACAGAGAATGATAA
Found at i:1293038 original size:45 final size:44
Alignment explanation
Indices: 1292897--1293064 Score: 149
Period size: 45 Copynumber: 3.8 Consensus size: 44
1292887 ATTGTCGTTA
* * * **
1292897 CCGAAGCCAATCGCAATGACCCTAAACCTAATATGGAGAATGAT
1 CCGAAGCCAATGGCAAGGAGCCTAAACCTAATAAAGAGAATGAT
** * * *
1292941 ACCGAAGCTGATGGTAAGGAGCCTAAACCTAATACAGAGAATGCT
1 -CCGAAGCCAATGGCAAGGAGCCTAAACCTAATAAAGAGAATGAT
* *
1292986 AACGAAGCCGATGGCAAGGAGCCTAAACCTAATAAAGAGAAT-AT
1 -CCGAAGCCAATGGCAAGGAGCCTAAACCTAATAAAGAGAATGAT
* * * *
1293030 CGCTGAAGCAAAAGGCAACGAGCCTAACCCTAATA
1 C-C-GAAGCCAATGGCAAGGAGCCTAAACCTAATA
1293065 CAAAAAAGTT
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
44 2 0.02
45 99 0.98
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.15
Consensus pattern (44 bp):
CCGAAGCCAATGGCAAGGAGCCTAAACCTAATAAAGAGAATGAT
Found at i:1293420 original size:26 final size:25
Alignment explanation
Indices: 1293386--1293446 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
1293376 TTTTTAAAAT
* *
1293386 ATTTTTGAAAACGTATATATAATATA
1 ATTTTTGAAAACATATAAAT-ATATA
*
1293412 TTTTTTGAAAACATATAAATATATA
1 ATTTTTGAAAACATATAAATATATA
1293437 ATTTTT-AAAA
1 ATTTTTGAAAA
1293447 TATTTTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 4 0.13
25 10 0.32
26 17 0.55
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (25 bp):
ATTTTTGAAAACATATAAATATATA
Found at i:1293464 original size:61 final size:61
Alignment explanation
Indices: 1293367--1293482 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 61
1293357 GAAAACACGT
**
1293367 AATATATGGTTTTTAAAATATTTTTGAAAACGTATATATAATATAT--TTTTTGAAAACATATA
1 AATATATAATTTTTAAAATATTTTTGAAAAC--ATATATAATATATAGTTTTT-AAAACATATA
*
1293429 AATATATAATTTTTAAAATA-TTTTGAAAATATATATAATATATAGTTTTTAAAA
1 AATATATAATTTTTAAAATATTTTTGAAAACATATATAATATATAGTTTTTAAAA
1293483 TATTTTGAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
59 13 0.27
60 4 0.08
61 14 0.29
62 18 0.37
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.46
Consensus pattern (61 bp):
AATATATAATTTTTAAAATATTTTTGAAAACATATATAATATATAGTTTTTAAAACATATA
Found at i:1293593 original size:76 final size:75
Alignment explanation
Indices: 1293412--1293681 Score: 331
Period size: 74 Copynumber: 3.6 Consensus size: 75
1293402 ATATAATATA
* * * *
1293412 TTTTTTGAAAACATATA-AATATATAATTTTTAAAATATTTTGAAA-ATATATATAATATATAGT
1 TTTTTTGAAAATATATATAATATATAGTTTTAAAAACATTTTGAAATATATATATAATATATAGT
*
1293475 TTTTAAAA--
66 TTTGAAAACG
*
1293483 TATTTTGAAAGTATATATATAATATATAGTTTTAAAAACATTTTGAAATATATATATAATATATA
1 TTTTTTGAAA--ATATATATAATATATAGTTTTAAAAACATTTTGAAATATATATATAATATATA
1293548 GTTTTGAAAACG
64 GTTTTGAAAACG
* * *
1293560 TTTTTTTGAAAGTATATATAATATATAGTTTTAAAAACATTTTTTAAAATATATATGTAATATA-
1 -TTTTTTGAAAATATATATAATATATAGTTTTAAAAACA--TTTTGAAATATATATATAATATAT
1293624 A-TTTTGAAAACG
63 AGTTTTGAAAACG
* *
1293636 -TTTTAGAAAATATATATAATATATA-TTTTAGAAAACATTTGGAAAT
1 TTTTTTGAAAATATATATAATATATAGTTTTA-AAAACATTTTGAAAT
1293682 TTTTTATATA
Statistics
Matches: 175, Mismatches: 14, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
71 9 0.05
72 7 0.04
73 11 0.06
74 54 0.31
75 25 0.14
76 38 0.22
77 1 0.01
78 30 0.17
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (75 bp):
TTTTTTGAAAATATATATAATATATAGTTTTAAAAACATTTTGAAATATATATATAATATATAGT
TTTGAAAACG
Found at i:1293670 original size:37 final size:36
Alignment explanation
Indices: 1293414--1293680 Score: 290
Period size: 37 Copynumber: 7.2 Consensus size: 36
1293404 ATAATATATT
* * * *
1293414 TTTTGAAAACATATA-AATATATAATTTTTAAAATA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
1293449 TTTTGAAAATATATATAATATATAGTTTTTAAAATA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
1293485 TTTTGAAAGTATATATATAATATATAGTTTTAAAAACA
1 TTTTGAAA--ATATATATAATATATAGTTTTGAAAACA
*
1293523 TTTTGAAATATATATATAATATATAGTTTTGAAAACGTTT
1 TTTTGAAA-ATATATATAATATATAGTTTTGAAAAC---A
* *
1293563 TTTTGAAAGTATATATAATATATAGTTTTAAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
1293599 TTTTTTAAAATATATATGTAATATA-A-TTTTGAAAACG
1 -TTTTGAAAATATATA--TAATATATAGTTTTGAAAACA
1293636 TTTTAGAAAATATATATAATATATA-TTTTAGAAAACA
1 TTTT-GAAAATATATATAATATATAGTTTT-GAAAACA
*
1293673 TTTGGAAA
1 TTTTGAAA
1293681 TTTTTTATAT
Statistics
Matches: 204, Mismatches: 16, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
35 21 0.10
36 40 0.20
37 68 0.33
38 35 0.17
39 32 0.16
40 8 0.04
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACA
Found at i:1299833 original size:21 final size:21
Alignment explanation
Indices: 1299807--1299869 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1299797 GTAGCAGTAT
* *
1299807 TGTAGCAAGGTATTGGTACCC
1 TGTAGCAGGGTATCGGTACCC
1299828 TGTAGCAGGGTATCGGTACCC
1 TGTAGCAGGGTATCGGTACCC
*
1299849 TGTAGCAGGGTATCGATACCC
1 TGTAGCAGGGTATCGGTACCC
1299870 CTAAAGCAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.25
Consensus pattern (21 bp):
TGTAGCAGGGTATCGGTACCC
Found at i:1299877 original size:22 final size:21
Alignment explanation
Indices: 1299831--1299877 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1299821 GGTACCCTGT
* **
1299831 AGCAGGGTATCGGTACCCTGT
1 AGCAGGGTATCGATACCCTAA
1299852 AGCAGGGTATCGATACCCCTAA
1 AGCAGGGTATCGATA-CCCTAA
1299874 AGCA
1 AGCA
1299878 ATCTGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.19
Consensus pattern (21 bp):
AGCAGGGTATCGATACCCTAA
Found at i:1301625 original size:17 final size:17
Alignment explanation
Indices: 1301603--1301647 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1301593 AATGATATGA
1301603 AAGGTAATGAAAGAATT
1 AAGGTAATGAAAGAATT
*
1301620 AAGGTAATAAAAGAATT
1 AAGGTAATGAAAGAATT
*
1301637 AAAGTAATGAA
1 AAGGTAATGAA
1301648 GTGATGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.20, T:0.22
Consensus pattern (17 bp):
AAGGTAATGAAAGAATT
Found at i:1303660 original size:13 final size:13
Alignment explanation
Indices: 1303642--1303676 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1303632 AAACTCTTTA
1303642 TTCTTCTTCTCCC
1 TTCTTCTTCTCCC
1303655 TTCTTCTTCTCCC
1 TTCTTCTTCTCCC
1303668 TTCTTCTTC
1 TTCTTCTTC
1303677 CTCCTCCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (13 bp):
TTCTTCTTCTCCC
Found at i:1305735 original size:21 final size:21
Alignment explanation
Indices: 1305705--1305746 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1305695 ATAGCAGTAA
1305705 TGTAGCAGGGTATCGATACCC
1 TGTAGCAGGGTATCGATACCC
*
1305726 TGTAGTAGGGTATCGATACCC
1 TGTAGCAGGGTATCGATACCC
1305747 CTGAAGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TGTAGCAGGGTATCGATACCC
Found at i:1307242 original size:99 final size:98
Alignment explanation
Indices: 1306929--1307213 Score: 457
Period size: 97 Copynumber: 2.9 Consensus size: 98
1306919 TTATAATAGT
*
1306929 ATATGTATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAATCGCCCGGCTTTATGGA
1 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAATCGCCCGGCTTTATGGA
*
1306994 TAAGATTCGGCTAGCCTGATAAAGGTGATTATA
66 TAAGATTCAGCTAGCCTGATAAAGGTGATTATA
* *
1307027 ATATATATACAATAAAGCTTGAGTTGTTCCTTTAGAGCAATTGG-TAATCGCCCGGCTTTATGGA
1 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAATCGCCCGGCTTTATGGA
*
1307091 TAAGATTCAGCTAGCCTGATAAAGGTGATTATG
66 TAAGATTCAGCTAGCCTGATAAAGGTGATTATA
* * *
1307124 ATATATATACAATAAAGCTTTAGTTGTCCCTCTAGAGCAATTGGTTAAATAC-CTCGGCTTTCTG
1 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTT-AAT-CGCCCGGCTTTATG
*
1307188 GATAAGATTCAGCTAGCCTAATAAAG
64 GATAAGATTCAGCTAGCCTGATAAAG
1307214 TCAAATTACA
Statistics
Matches: 173, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
97 92 0.53
98 42 0.24
99 38 0.22
100 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (98 bp):
ATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAATCGCCCGGCTTTATGGA
TAAGATTCAGCTAGCCTGATAAAGGTGATTATA
Found at i:1308935 original size:201 final size:200
Alignment explanation
Indices: 1308590--1309142 Score: 696
Period size: 201 Copynumber: 2.7 Consensus size: 200
1308580 ATTGTTCGCG
* *
1308590 GCATAGCTCAAGGCGAGAAGGGTTATTTGTCCACAAAAACTTTCAAGTTCGATTCCATTCATCTC
1 GCATAGCTCAAGGCGAGAAGGGTTATTTGTCAACAAAAACTTTCAAGTTCGATT-CATTCAACTC
* * * * * * * *
1308655 GATGACATATCAACCGCATAGTAACAGTGATGAACTAATTTTCGGTTGAAGCTTAAACTGAGGTC
65 GATGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGATTGAAGTTTAAACTGAGGTC
* *
1308720 TTTGAGTCAAGAAGAAGACCTAGATGGGCTGCGATTTAGCAACAAGGAACTATCTCCCAG-CTAA
130 TTTAAGTCAAGAAGAAGACCTAGATGGGCTGCGATTTAGCAACAAGGAACTATATCCCAGTC-AA
1308784 AATTACA
194 AATTACA
* * * ** *
1308791 GCATAGCTCAAGGTGAGAATGGATATCCGTCAACAAAAACTTTCAAGTTCGATTCAATTCAGCTC
1 GCATAGCTCAAGGCGAGAAGGGTTATTTGTCAACAAAAACTTTCAAGTTCGATTC-ATTCAACTC
* *
1308856 AATGACATATCAACCGCATGGTAGCAGCGAGGAATTACTTTCCGATTGAAGTTTAAACTGAGGTC
65 GATGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGATTGAAGTTTAAACTGAGGTC
* * * * *
1308921 TTTAAGTCAAGAAGAAGACCTAGCTTGGTTGCTATTTAGCAACAATGAACTATATCCCAGTCAAA
130 TTTAAGTCAAGAAGAAGACCTAGATGGGCTGCGATTTAGCAACAAGGAACTATATCCCAGTCAAA
* *
1308986 TTTCCA
195 ATTACA
* * *
1308992 GCATAGCTCAAGGCGAGAAGGGTTATTTGTCAACAAAAACCTTCGAGTTTGATTTCATTCAACTC
1 GCATAGCTCAAGGCGAGAAGGGTTATTTGTCAACAAAAACTTTCAAGTTCGA-TTCATTCAACTC
* * * * * *
1309057 GAGGGCATATCAACCACATGGTAGCATCGAGG-ACTACTTTTCCGATTGAATTTTCAAACCGAGG
65 GATGACATATCAACCGCATGGTAGCAGCGAGGAACTAC-TTTCCGATTGAAGTTT-AAACTGAGG
**
1309121 TCTTTAAACCAAGAAGAAGACC
128 TCTTTAAGTCAAGAAGAAGACC
1309143 AAGGTTGACT
Statistics
Matches: 302, Mismatches: 45, Indels: 9
0.85 0.13 0.03
Matches are distributed among these distances:
200 5 0.02
201 265 0.88
202 32 0.11
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (200 bp):
GCATAGCTCAAGGCGAGAAGGGTTATTTGTCAACAAAAACTTTCAAGTTCGATTCATTCAACTCG
ATGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGATTGAAGTTTAAACTGAGGTCT
TTAAGTCAAGAAGAAGACCTAGATGGGCTGCGATTTAGCAACAAGGAACTATATCCCAGTCAAAA
TTACA
Found at i:1309816 original size:25 final size:25
Alignment explanation
Indices: 1309746--1309828 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
1309736 TTTAAAATAT
*
1309746 TTTTGAAAACGCATATAT-A-ACATAG
1 TTTTGAAAA--CATATATAATATATAG
1309771 TTTTTGAAAAC--ATATAATATATAG
1 -TTTTGAAAACATATATAATATATAG
1309795 TTTTGAAAACATATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
*
1309820 TTTTTAAAA
1 TTTTGAAAA
1309829 TATTTTGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.08
23 11 0.22
24 6 0.12
25 21 0.41
26 9 0.18
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (25 bp):
TTTTGAAAACATATATAATATATAG
Found at i:1309917 original size:37 final size:35
Alignment explanation
Indices: 1309795--1310065 Score: 240
Period size: 36 Copynumber: 7.3 Consensus size: 35
1309785 TAATATATAG
* * *
1309795 TTTTGAAAACATATATAATATATAGTTTTTAAAATA
1 TTTTG-AAATATATATAATATATAGTTTTAAAAACA
* *
1309831 TTTTGAAAATATATATAATATATAGTTTTTAAAATA
1 TTTTG-AAATATATATAATATATAGTTTTAAAAACA
1309867 TTTTGAAAGTATATATGCAATATATAGTTTTAAAAACA
1 TTTTGAAA-TATATAT--AATATATAGTTTTAAAAACA
* * *
1309905 TTTTGAAATATATATATAATATATAATTTTGAAAACGTTT
1 TTTTG-AA-ATATATATAATATATAGTTTTAAAAAC---A
1309945 TTTTGAAAGTATATATATAATATATAGTTTTAAAAACA
1 TTTTG-AA--ATATATATAATATATAGTTTTAAAAACA
* * * *
1309983 TTTTTTAAA-ATATATATATAATATAATTTTGAAAACG
1 -TTTTGAAATATATATA-AT-ATATAGTTTTAAAAACA
1310020 TTTTAGAAAATATATATAATATATA-TTTTAGAAAACA
1 TTTT-G-AAATATATATAATATATAGTTTTA-AAAACA
*
1310057 TTTGGAAAT
1 TTTTGAAAT
1310066 TTTTTATATA
Statistics
Matches: 202, Mismatches: 17, Indels: 33
0.80 0.07 0.13
Matches are distributed among these distances:
35 14 0.07
36 59 0.29
37 44 0.22
38 30 0.15
39 20 0.10
40 9 0.04
41 26 0.13
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (35 bp):
TTTTGAAATATATATAATATATAGTTTTAAAAACA
Found at i:1309974 original size:78 final size:76
Alignment explanation
Indices: 1309805--1310064 Score: 336
Period size: 78 Copynumber: 3.4 Consensus size: 76
1309795 TTTTGAAAAC
* * * * *
1309805 ATATATAATATATAGTTTTTAAAATATTTTGAAAATATATATAATATATAGTTTTTAAAA--TAT
1 ATATATAATATATAGTTTTAAAAACATTTTGAAAATATATATAATATATAATTTTGAAAACGTTT
1309868 TTTGAAAGTAT
66 TTTGAAAGTAT
**
1309879 ATATGCAATATATAGTTTTAAAAACATTTTGAAATATATATATAATATATAATTTTGAAAACGTT
1 ATATATAATATATAGTTTTAAAAACATTTTGAAA-ATATATATAATATATAATTTTGAAAACG-T
1309944 TTTTTGAAAGTAT
64 TTTTTGAAAGTAT
*
1309957 ATATATAATATATAGTTTTAAAAACATTTTTTAAAATATATAT-ATAATATAATTTTGAAAACG-
1 ATATATAATATATAGTTTTAAAAACA-TTTTGAAAATATATATAAT-ATATAATTTTGAAAACGT
*
1310020 TTTTAGAAA--AT
64 TTTTTGAAAGTAT
*
1310031 ATATATAATATATA-TTTTAGAAAACATTTGGAAA
1 ATATATAATATATAGTTTTA-AAAACATTTTGAAA
1310065 TTTTTTATAT
Statistics
Matches: 166, Mismatches: 13, Indels: 15
0.86 0.07 0.08
Matches are distributed among these distances:
73 11 0.07
74 52 0.31
75 24 0.14
76 8 0.05
77 2 0.01
78 62 0.37
79 7 0.04
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (76 bp):
ATATATAATATATAGTTTTAAAAACATTTTGAAAATATATATAATATATAATTTTGAAAACGTTT
TTTGAAAGTAT
Found at i:1310143 original size:21 final size:19
Alignment explanation
Indices: 1310109--1310157 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
1310099 CTTTTTCTCG
*
1310109 TTTATATTTATTTATTACTT
1 TTTATTTTTATTTATT-CTT
*
1310129 ATTTATTTTTGTTTATTCTT
1 -TTTATTTTTATTTATTCTT
*
1310149 TTTGTTTTT
1 TTTATTTTT
1310158 TTCTTTAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.32
20 3 0.12
21 14 0.56
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTATTTTTATTTATTCTT
Found at i:1313014 original size:42 final size:42
Alignment explanation
Indices: 1312832--1313092 Score: 190
Period size: 42 Copynumber: 6.1 Consensus size: 42
1312822 TTTTACAGCC
* * * *
1312832 GAGGTCCTTAATTTCTTAAATCTCACTTTTTTACATTTATAATT
1 GAGGTCCCTAATTT-TTTAATCTTAC-TTTTTACCTTTATAATT
* * * ** * *
1312876 GATG-ACCTAAGTTTTTCAATCCCACTTTGTACATTTATAATT
1 GAGGTCCCTAA-TTTTTTAATCTTACTTTTTACCTTTATAATT
* * *
1312918 GAGCT-CCTAAGTGTTTTAATCTTACTTTCTACCTTTATAATT
1 GAGGTCCCTAA-TTTTTTAATCTTACTTTTTACCTTTATAATT
*
1312960 GAGGTCCCTAATTTTTTAATCTCACTTTTTACCTTTATAA-T
1 GAGGTCCCTAATTTTTTAATCTTACTTTTTACCTTTATAATT
* * * * * *
1313001 GGGGTCCGTTAATTTTATATTCTTACTTTTTAGCTTTAAAATT
1 GAGGTCC-CTAATTTTTTAATCTTACTTTTTACCTTTATAATT
* * *
1313044 AAGG-CCCATAATTTTTTTAAAT-TTGAATTCTTACCTTTATAATT
1 GAGGTCCC-TAA-TTTTTT-AATCTT-ACTTTTTACCTTTATAATT
1313088 GAGGT
1 GAGGT
1313093 TCTTAGATTT
Statistics
Matches: 172, Mismatches: 35, Indels: 19
0.76 0.15 0.08
Matches are distributed among these distances:
41 7 0.04
42 111 0.65
43 28 0.16
44 26 0.15
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (42 bp):
GAGGTCCCTAATTTTTTAATCTTACTTTTTACCTTTATAATT
Found at i:1314095 original size:16 final size:14
Alignment explanation
Indices: 1314057--1314099 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
1314047 TAATTTCAAC
*
1314057 AAATTAAAAAATAA
1 AAATTAAAATATAA
1314071 AAATTTAAAATATATA
1 AAA-TTAAAATATA-A
1314087 AAATATAAAATAT
1 AAAT-TAAAATAT
1314100 TTTTTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 10 0.40
16 12 0.48
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATTAAAATATAA
Found at i:1315209 original size:20 final size:20
Alignment explanation
Indices: 1315184--1315222 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1315174 GTAATCCTAT
1315184 TCACTGGTAATCTTACATTC
1 TCACTGGTAATCTTACATTC
*
1315204 TCACTGGTAATCTTGCATT
1 TCACTGGTAATCTTACATT
1315223 TCGTGAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (20 bp):
TCACTGGTAATCTTACATTC
Found at i:1316715 original size:26 final size:26
Alignment explanation
Indices: 1316682--1316747 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
1316672 CTGGCGGTAA
*
1316682 ATTTTAAT-TTATTGAATTGTTTTATTT
1 ATTTTAATATT-TTGAAAT-TTTTATTT
1316709 -TTTTAATATTTTGAAATTTTTATTT
1 ATTTTAATATTTTGAAATTTTTATTT
1316734 ATTTTAATAATTTT
1 ATTTTAAT-ATTTT
1316748 TTCGATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 8 0.23
26 20 0.57
27 7 0.20
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (26 bp):
ATTTTAATATTTTGAAATTTTTATTT
Found at i:1316761 original size:4 final size:4
Alignment explanation
Indices: 1316752--1316854 Score: 55
Period size: 4 Copynumber: 24.0 Consensus size: 4
1316742 AATTTTTTCG
** * *
1316752 ATTT ATTT ATTT -TGG ATTT ATTT ACTC ATTT ATTT CAAATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ---ATTT ATTT ATTT
* * * *
1316802 TTTT GGATTT ATTT ATTG ATTG ATTT GTTT CAAATTT ATTT ATTT ATTT
1 ATTT --ATTT ATTT ATTT ATTT ATTT ATTT ---ATTT ATTT ATTT ATTT
1316851 ATTT
1 ATTT
1316855 GAAGGGGTAT
Statistics
Matches: 76, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
3 1 0.01
4 65 0.86
6 3 0.04
7 7 0.09
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.65
Consensus pattern (4 bp):
ATTT
Found at i:1316769 original size:15 final size:15
Alignment explanation
Indices: 1316746--1316775 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1316736 TTTAATAATT
1316746 TTTTCGATTTATTTA
1 TTTTCGATTTATTTA
*
1316761 TTTTGGATTTATTTA
1 TTTTCGATTTATTTA
1316776 CTCATTTATT
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:0.20, C:0.03, G:0.10, T:0.67
Consensus pattern (15 bp):
TTTTCGATTTATTTA
Found at i:1318410 original size:15 final size:17
Alignment explanation
Indices: 1318390--1318428 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
1318380 TTAAACATGT
*
1318390 ATATGAAAGT-TATG-A
1 ATATGAAAGTGGATGAA
1318405 ATATGAAAGTGGATGAA
1 ATATGAAAGTGGATGAA
1318422 ATATGAA
1 ATATGAA
1318429 GCATTTGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 3 0.14
17 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.28
Consensus pattern (17 bp):
ATATGAAAGTGGATGAA
Found at i:1319201 original size:29 final size:29
Alignment explanation
Indices: 1319168--1319276 Score: 193
Period size: 29 Copynumber: 3.8 Consensus size: 29
1319158 TATGTGATAT
1319168 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1319197 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
1319226 GAGAAATGACATTAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
1319255 GAGAAATGACATAAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1319277 ACATATAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
28 7 0.09
29 71 0.91
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1319379 original size:15 final size:15
Alignment explanation
Indices: 1319361--1319393 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1319351 GAGGGTATAA
1319361 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
1319376 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
1319391 TAG
1 TAG
1319394 GAGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:1322878 original size:3 final size:3
Alignment explanation
Indices: 1322872--1322897 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1322862 CTCTTCATCA
1322872 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
1322898 ATGTACGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1324089 original size:29 final size:29
Alignment explanation
Indices: 1324050--1324159 Score: 204
Period size: 29 Copynumber: 3.8 Consensus size: 29
1324040 TATGTGATAT
1324050 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
1324080 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1324109 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1324138 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1324160 AGATATAAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.09
29 68 0.85
30 5 0.06
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1329361 original size:14 final size:14
Alignment explanation
Indices: 1329339--1329373 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1329329 CAATTTTTAT
*
1329339 TTTCCTTAATCTAC
1 TTTCATTAATCTAC
1329353 TTTCATTAATCTAC
1 TTTCATTAATCTAC
1329367 TTTCATT
1 TTTCATT
1329374 TATTTTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTCATTAATCTAC
Found at i:1330799 original size:19 final size:19
Alignment explanation
Indices: 1330775--1330820 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1330765 ATCCTAATTG
*
1330775 GAAGAAATGGGAAAGGTCT
1 GAAGAAATGGGAAAGGCCT
*
1330794 GAAGAAAAGGGAAAGGCCT
1 GAAGAAATGGGAAAGGCCT
*
1330813 GAGGAAAT
1 GAAGAAAT
1330821 CTTTATAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.37, T:0.11
Consensus pattern (19 bp):
GAAGAAATGGGAAAGGCCT
Found at i:1331605 original size:20 final size:20
Alignment explanation
Indices: 1331580--1331632 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1331570 GACCAACAAA
1331580 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
1331600 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
1331620 TTCGCAACGCGAA
1 TTCGCAACGCGAA
1331633 TATATAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:1331705 original size:20 final size:19
Alignment explanation
Indices: 1331682--1331921 Score: 223
Period size: 20 Copynumber: 12.1 Consensus size: 19
1331672 AATTTGTAAA
*
1331682 TCGCAACACAGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
*
1331702 TCGCAATGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
**
1331722 TCTAAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
*
1331742 TCGCAACGTGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
* *
1331762 TCGCAACACAAAGTCAAAT
1 TCGCAACGCGAAGTCAAAT
*
1331781 TCACAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
1331801 TCGCAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
* *
1331821 TCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
* *
1331841 TCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
1331861 TCGCAACGCGAATTTGT-AAA-
1 TCGCAACGCGAA---GTCAAAT
* *
1331881 TCTCAACACAGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
1331901 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCG-AAGTCAAAT
1331921 T
1 T
1331922 TTTTTGCGCG
Statistics
Matches: 187, Mismatches: 23, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
18 2 0.01
19 24 0.13
20 152 0.81
21 7 0.04
22 2 0.01
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.20
Consensus pattern (19 bp):
TCGCAACGCGAAGTCAAAT
Found at i:1331738 original size:40 final size:40
Alignment explanation
Indices: 1331657--1331921 Score: 265
Period size: 40 Copynumber: 6.7 Consensus size: 40
1331647 TGCGATTTTC
* *
1331657 CAAATTAGCAACGCGAATTTGT-AAA-TCGCAACAC-AGAAGT
1 CAAATTCGCAACGCG-A-TAGTCAAATTCGCAACACGA-AAGT
* ** * *
1331697 CAAATTCGCAATGCGATAGTCAAATTCTAAACGCGATAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAAGT
*
1331737 CAAATTCGCAACGTGATAGTCAAATTCGCAACAC-AAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAAGT
* * *
1331776 CAAATTCACAACGCGATAGTCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAAGT
* * * *
1331816 CAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAAGT
* *
1331856 CAAATTCGCAACGCGAATTTGT-AAA-TCTCAACAC-AGAAGT
1 CAAATTCGCAACGCG-A-TAGTCAAATTCGCAACACGA-AAGT
*
1331896 CAAATTCGCAACGCGAAAGTCAAATT
1 CAAATTCGCAACGCGATAGTCAAATT
1331922 TTTTTGCGCG
Statistics
Matches: 185, Mismatches: 31, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
38 5 0.03
39 44 0.24
40 129 0.70
41 5 0.03
42 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAAGT
Found at i:1331868 original size:60 final size:60
Alignment explanation
Indices: 1331694--1331921 Score: 282
Period size: 60 Copynumber: 3.8 Consensus size: 60
1331684 GCAACACAGA
** * * ** * *
1331694 AGTCAAATTCGCAATGCGATAGTCAAATTCTAAACGCGATAGTCAAATTCGCAACGTGAT
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAT
* *
1331754 AGTCAAATTCGCAACAC-AAAGTCAAATTCACAACGCGATAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAT
* *
1331813 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAATT
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCG-A-T
* * *
1331875 TGT-AAA-TCTCAACACAGAAGTCAAATTCGCAACGCGAAAGTCAAATT
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAATT
1331922 TTTTTGCGCG
Statistics
Matches: 150, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
59 55 0.37
60 88 0.59
61 4 0.03
62 3 0.02
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (60 bp):
AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAT
Found at i:1332442 original size:20 final size:19
Alignment explanation
Indices: 1332396--1332463 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
1332386 AAATCGCAAC
1332396 GCGATTTTAGTTTT-GCGTT
1 GCGATTTTA-TTTTCGCGTT
* *
1332415 GCGGTTTTCATTTTCGCTTT
1 GCGATTTT-ATTTTCGCGTT
1332435 GCGATTTTTATTTTCGCGTT
1 GCGA-TTTTATTTTCGCGTT
*
1332455 GCGAATTTA
1 GCGATTTTA
1332464 AGTTTCAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
19 15 0.37
20 22 0.54
21 4 0.10
ACGTcount: A:0.12, C:0.15, G:0.22, T:0.51
Consensus pattern (19 bp):
GCGATTTTATTTTCGCGTT
Found at i:1332469 original size:20 final size:20
Alignment explanation
Indices: 1332426--1332469 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1332416 CGGTTTTCAT
* * * *
1332426 TTTCGCTTTGCGATTTTTAT
1 TTTCGCGTTGCGAATTTAAG
1332446 TTTCGCGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
1332466 TTTC
1 TTTC
1332470 AGAAACTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:1334419 original size:4 final size:4
Alignment explanation
Indices: 1334410--1334451 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
1334400 TTTTTCGGCA
* * *
1334410 TTAT TTAT TTAT TTAT TTAC TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1334452 TCAGCGACCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:1334636 original size:21 final size:21
Alignment explanation
Indices: 1334595--1334693 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
1334585 GATGCACCTA
* * *
1334595 TCATCATTCAAGAGACGCCTC
1 TCATCGTTCAAGAGGCCCCTC
1334616 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
1334637 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * *
1334658 CCACCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
1334679 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
1334694 TCCTGCCCGC
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
20 3 0.05
21 56 0.90
22 3 0.05
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.21
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1334642 original size:42 final size:43
Alignment explanation
Indices: 1334591--1334713 Score: 130
Period size: 42 Copynumber: 2.9 Consensus size: 43
1334581 GCCCGATGCA
* * *
1334591 CCTATCATCATTCAAGAGA-CGCCTCCTATCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAGAGCCCCTCCCACCGTTCAAGAGGCC
*
1334633 CCTCTCATCA-TCGAAGA-AGCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCATTC-AAGAGAGCCCCTCCCACCGTTCAAGAGGCC
* * *
1334675 CCTATCATCGTTCAAGAG-G-TCCTGCCCGCCGTTCAAGAG
1 CCTATCATCATTCAAGAGAGCCCCT-CCCACCGTTCAAGAG
1334714 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
41 6 0.09
42 60 0.88
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.21
Consensus pattern (43 bp):
CCTATCATCATTCAAGAGAGCCCCTCCCACCGTTCAAGAGGCC
Found at i:1336172 original size:65 final size:65
Alignment explanation
Indices: 1336068--1336211 Score: 227
Period size: 66 Copynumber: 2.2 Consensus size: 65
1336058 TTTTACATTG
*
1336068 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTT-ATTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGATTGATTAATTGATTTGTA
* * * *
1336132 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTATTTTTTTGATTGATTAATTGATTTGT
1336197 A
65 A
1336198 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
1336212 GTTTCTAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 17 0.23
65 25 0.34
66 31 0.42
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (65 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGATTGATTAATTGATTTGTA
Found at i:1336307 original size:20 final size:20
Alignment explanation
Indices: 1336270--1336307 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1336260 GTTGAAGGTA
*
1336270 CAAATTCGCAACGTGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
1336290 CAAATTCGCGACGCGAAA
1 CAAATTCGCAACGCGAAA
1336308 TAAGTATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:1336391 original size:20 final size:20
Alignment explanation
Indices: 1336368--1336406 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1336358 GATTTTCGGT
*
1336368 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTATCGCG
1336388 TTGCGAATTTGACTATCGC
1 TTGCGAATTTGACTATCGC
1336407 AACGCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCG
Found at i:1336672 original size:39 final size:39
Alignment explanation
Indices: 1336618--1336706 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
1336608 ACTCAAGTTG
* *
1336618 TAGATTTTGATTTCCTTTTGCTTGGCACCGTATGAGATT
1 TAGATTTTGATTTCCTTTTGCTTGGAACCATATGAGATT
*
1336657 TAGATTTTGATTTCCTTTTGCTTGGAACCATATGAGCTT
1 TAGATTTTGATTTCCTTTTGCTTGGAACCATATGAGATT
*
1336696 TGGATTTTGAT
1 TAGATTTTGAT
1336707 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.19, C:0.13, G:0.20, T:0.47
Consensus pattern (39 bp):
TAGATTTTGATTTCCTTTTGCTTGGAACCATATGAGATT
Found at i:1337040 original size:18 final size:18
Alignment explanation
Indices: 1337017--1337053 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1337007 CAAAATTTAT
1337017 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1337035 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1337053 A
1 A
1337054 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1337504 original size:20 final size:20
Alignment explanation
Indices: 1337479--1337520 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1337469 TGTACAAGAT
* *
1337479 GAAAGTTAAATTCGCAATGC
1 GAAAGTCAAATTCGCAACGC
1337499 GAAAGTCAAATTCGCAACGC
1 GAAAGTCAAATTCGCAACGC
1337519 GA
1 GA
1337521 TTTTCGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
GAAAGTCAAATTCGCAACGC
Found at i:1337552 original size:20 final size:20
Alignment explanation
Indices: 1337529--1337571 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1337519 GATTTTCGGT
1337529 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
*
1337549 TTGCGAATTTGACTTTTGCG
1 TTGCGAATTTGACTTTCGCG
1337569 TTG
1 TTG
1337572 ATCGCAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:1337880 original size:18 final size:18
Alignment explanation
Indices: 1337857--1337892 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1337847 AAGCCGGTTG
*
1337857 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1337875 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1337893 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1340179 original size:24 final size:24
Alignment explanation
Indices: 1340152--1340211 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1340142 CCATCACATC
*
1340152 ATCAAAATTCGAGTATTCCCCAAG
1 ATCAAAATTCGAGTATTCACCAAG
* * * *
1340176 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTCACCAAG
*
1340200 ATCAAATTTCGA
1 ATCAAAATTCGA
1340212 ATACTGACTA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTCACCAAG
Found at i:1340941 original size:14 final size:15
Alignment explanation
Indices: 1340905--1340942 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1340895 GAAATCATTG
1340905 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1340920 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1340935 AAAAATTA
1 AAAAATTA
1340943 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1341129 original size:19 final size:19
Alignment explanation
Indices: 1341105--1341209 Score: 104
Period size: 19 Copynumber: 5.4 Consensus size: 19
1341095 ACCTAATGCA
1341105 AATTTGAAATTCAGTTGCG
1 AATTTGAAATTCAGTTGCG
*
1341124 AATTTGAAATTCAGTTGCT
1 AATTTGAAATTCAGTTGCG
*
1341143 AATTTGAAATTCCGCGTTGCG
1 AATTTGAAATT-C-AGTTGCG
** **
1341164 AATTTGACTTTGTGTTGCG
1 AATTTGAAATTCAGTTGCG
*
1341183 AATTTGACTATTGC-GTTGCG
1 AATTTGA-AATT-CAGTTGCG
1341203 AATTTGA
1 AATTTGA
1341210 CTATCGCGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
19 42 0.58
20 16 0.22
21 14 0.19
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (19 bp):
AATTTGAAATTCAGTTGCG
Found at i:1341169 original size:40 final size:39
Alignment explanation
Indices: 1341105--1341209 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 39
1341095 ACCTAATGCA
* *
1341105 AATTTGAAATTC-AGTTGCGAATTTGAAATTCAGTTGCT
1 AATTTGAAATTCGCGTTGCGAATTTGAAATTCAGTTGCG
** **
1341143 AATTTGAAATTCCGCGTTGCGAATTTGACTTTGTGTTGCG
1 AATTTGAAATT-CGCGTTGCGAATTTGAAATTCAGTTGCG
*
1341183 AATTTGACTATT-GCGTTGCGAATTTGA
1 AATTTGA-AATTCGCGTTGCGAATTTGA
1341210 CTATCGCGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
38 11 0.19
39 16 0.28
40 27 0.47
41 3 0.05
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (39 bp):
AATTTGAAATTCGCGTTGCGAATTTGAAATTCAGTTGCG
Found at i:1341183 original size:59 final size:60
Alignment explanation
Indices: 1341118--1341288 Score: 169
Period size: 60 Copynumber: 2.9 Consensus size: 60
1341108 TTGAAATTCA
* *
1341118 GTTGCGAATTTGA-AATT-CAGTTGCTAATTTGAA-ATTCCGCGTTGCGAATTTGACTT-TGT
1 GTTGCGAATTTGACAATTGC-GTTGCGAATTTGAATA-T-CGCGTTGCGAATTTGACTTCCGT
* *
1341177 GTTGCGAATTTGACTATTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCCGT
1 GTTGCGAATTTGACAATTGCGTTGCGAATTTGAATATCGCGTTGCGAATTTGACTTCCGT
* *
1341237 GTTGCG-ATTT-ACAAATTCGCGTTGCG-ATTT-ACAGATTCGCGTTGTGAATTTG
1 GTTGCGAATTTGAC-AATT-GCGTTGCGAATTTGA-ATA-TCGCGTTGCGAATTTG
1341289 GAAAATCGCA
Statistics
Matches: 96, Mismatches: 8, Indels: 15
0.81 0.07 0.13
Matches are distributed among these distances:
58 3 0.03
59 44 0.46
60 47 0.49
61 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (60 bp):
GTTGCGAATTTGACAATTGCGTTGCGAATTTGAATATCGCGTTGCGAATTTGACTTCCGT
Found at i:1341202 original size:20 final size:20
Alignment explanation
Indices: 1341118--1341231 Score: 128
Period size: 20 Copynumber: 5.8 Consensus size: 20
1341108 TTGAAATTCA
*
1341118 GTTGCGAATTTGA-AATT-C
1 GTTGCGAATTTGACTATTGC
* *
1341136 AGTTGCTAATTTGA-AATTCCGC
1 -GTTGCGAATTTGACTATT--GC
*
1341158 GTTGCGAATTTGACT-TTGT
1 GTTGCGAATTTGACTATTGC
1341177 GTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGACTATTGC
*
1341197 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATTGC
1341217 GTTGCGAATTTGACT
1 GTTGCGAATTTGACT
1341232 TCCGTGTTGC
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
19 32 0.38
20 37 0.44
21 14 0.17
22 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTATTGC
Found at i:1341210 original size:39 final size:40
Alignment explanation
Indices: 1341156--1341231 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
1341146 TTGAAATTCC
* *
1341156 GCGTTGCGAATTTGACT-TTGTGTTGCGAATTTGACTATT
1 GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATT
1341195 GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT
1 GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT
1341232 TCCGTGTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 17 0.50
40 17 0.50
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.39
Consensus pattern (40 bp):
GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATT
Found at i:1341260 original size:20 final size:20
Alignment explanation
Indices: 1341237--1341280 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1341227 TGACTTCCGT
1341237 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
1341257 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
1341277 GTTG
1 GTTG
1341281 TGAATTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:1346558 original size:3 final size:3
Alignment explanation
Indices: 1346550--1346632 Score: 51
Period size: 3 Copynumber: 27.7 Consensus size: 3
1346540 ATATTGGGGG
* * ** * * *
1346550 CAT CAT CAT CACT C-T GAT CAT CAC CAT CAT CAT CCC CAC CAC CAC
1 CAT CAT CAT CA-T CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
* * * *
1346595 CAC CAC CAT CAC CAT CAC CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1346633 ACCTTATCTA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
2 1 0.02
3 63 0.95
4 2 0.03
ACGTcount: A:0.31, C:0.46, G:0.01, T:0.22
Consensus pattern (3 bp):
CAT
Found at i:1346577 original size:6 final size:6
Alignment explanation
Indices: 1346568--1346629 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
1346558 TCACTCTGAT
* * *
1346568 CATCAC CATCAT CATC-C C--CAC CACCAC CACCAC CATCAC CATCAC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC
* *
1346613 CATCAT CATCAT CATCA
1 CATCAC CATCAC CATCA
1346630 TCAACCTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 1 0.02
6 45 0.92
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CATCAC
Found at i:1346581 original size:12 final size:12
Alignment explanation
Indices: 1346550--1346632 Score: 69
Period size: 12 Copynumber: 6.7 Consensus size: 12
1346540 ATATTGGGGG
1346550 CATCATCATCAC
1 CATCATCATCAC
*
1346562 TC-TGATCATCAC
1 -CATCATCATCAC
1346574 CATCATCATCCCCAC
1 CATCATCAT---CAC
* * *
1346589 CACCACCACCAC
1 CATCATCATCAC
*
1346601 CATCACCATCAC
1 CATCATCATCAC
*
1346613 CATCATCATCAT
1 CATCATCATCAC
1346625 CATCATCA
1 CATCATCA
1346633 ACCTTATCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
11 1 0.02
12 46 0.81
13 1 0.02
15 9 0.16
ACGTcount: A:0.31, C:0.46, G:0.01, T:0.22
Consensus pattern (12 bp):
CATCATCATCAC
Found at i:1347693 original size:52 final size:52
Alignment explanation
Indices: 1347603--1347723 Score: 147
Period size: 52 Copynumber: 2.3 Consensus size: 52
1347593 GGAGTGATTT
* *
1347603 TAGGTTAAAGTGGTATA-AGGTTCGTTAAGGTGAAAGTGG-CAAAGGATTTTG
1 TAGGTTAAAGTGGTTTAGAGGTTCGTTAAGGTGAAAGTGGTC-AAGGATTATG
* ** * *
1347654 TAGGTTAAAGTGGTTTAGAGTTTTTTTAAGGTGAGAGTGGTCAAGGGTTATG
1 TAGGTTAAAGTGGTTTAGAGGTTCGTTAAGGTGAAAGTGGTCAAGGATTATG
*
1347706 TAGGTTAAAATGGTTTAG
1 TAGGTTAAAGTGGTTTAG
1347724 GGTAAGGTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
51 16 0.27
52 43 0.72
53 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (52 bp):
TAGGTTAAAGTGGTTTAGAGGTTCGTTAAGGTGAAAGTGGTCAAGGATTATG
Found at i:1349080 original size:26 final size:25
Alignment explanation
Indices: 1349037--1349085 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1349027 TTATCATCAA
1349037 AAAATTAAAATAACATAAACTAAAAC
1 AAAATTAAAATAACATAAA-TAAAAC
* **
1349063 AAAATTTAAATATTATAAATAAA
1 AAAATTAAAATAACATAAATAAA
1349086 TAAACTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAATTAAAATAACATAAATAAAAC
Found at i:1349551 original size:4 final size:4
Alignment explanation
Indices: 1349542--1349685 Score: 123
Period size: 4 Copynumber: 35.8 Consensus size: 4
1349532 ATATCCCTTC
** * **
1349542 AAAT AAAT AAAT AAAT AAAT TCA- AAAT AACT AAAT AAAT AAAT TCA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
1349588 AAAT AATT AAAT AAAT AATTT GAAAT AAAT AAAT GAAT AAAT AAAT GAAT
1 AAAT AAAT AAAT AAAT AA-AT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
1349638 AAAT AAATT CAAAA AAAT AAAT CAA- AAAT AAAT AAAT AAAT ATAT AAA
1 AAAT AAA-T -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1349686 ATTAAAACAA
Statistics
Matches: 109, Mismatches: 24, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
3 4 0.04
4 97 0.89
5 3 0.03
6 5 0.05
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1349575 original size:23 final size:23
Alignment explanation
Indices: 1349542--1349705 Score: 133
Period size: 23 Copynumber: 7.7 Consensus size: 23
1349532 ATATCCCTTC
1349542 AAATAAATAAATAAATAAATTCA
1 AAATAAATAAATAAATAAATTCA
*
1349565 AAATAACTAAATAAATAAATTCA
1 AAATAAATAAATAAATAAATTCA
*
1349588 AAATAATTAAATAAAT-AATT--
1 AAATAAATAAATAAATAAATTCA
*
1349608 ---TGAAATAAATAAATGAA-T--
1 AAAT-AAATAAATAAATAAATTCA
*
1349626 AAATAAATGAATAAATAAATTCA
1 AAATAAATAAATAAATAAATTCA
*
1349649 AAA-AAATAAATCAA-AAA-T--
1 AAATAAATAAATAAATAAATTCA
*
1349667 AAATAAATAAATATATAAAATT-A
1 AAATAAATAAATAAAT-AAATTCA
* *
1349690 AAACAAATCAATAAAT
1 AAATAAATAAATAAAT
1349706 GAAAATTACT
Statistics
Matches: 116, Mismatches: 12, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.01
18 15 0.13
19 11 0.09
20 14 0.12
21 8 0.07
22 14 0.12
23 53 0.46
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (23 bp):
AAATAAATAAATAAATAAATTCA
Found at i:1349809 original size:16 final size:17
Alignment explanation
Indices: 1349778--1349811 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1349768 GTCTCGCCAT
*
1349778 AATAATATGAGGGAGAG
1 AATAATATGAGAGAGAG
1349795 AATAAT-TGAGAGAGAG
1 AATAATATGAGAGAGAG
1349811 A
1 A
1349812 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (17 bp):
AATAATATGAGAGAGAG
Found at i:1350433 original size:86 final size:86
Alignment explanation
Indices: 1350288--1350456 Score: 241
Period size: 86 Copynumber: 2.0 Consensus size: 86
1350278 AAACTCTCAG
* * * * *
1350288 TCATCTGATAATGAACGCTCAATCACATGTTGCAATCGTTGGTGCTCGAACCCGTAACCATTAAG
1 TCATCTGACAATGAACGCTCAAGCACATGGTACAATCGTTGGTGCTCGAACCCGTAACCATTAAA
*
1350353 AATAACGACAATTTTTTTCAA
66 AATAACAACAATTTTTTTCAA
* *
1350374 TCATCTGACAATGAACGCTTAAGCACCTGGTACAATCGCTT-GTGCTCGAACCCGTAACCATTAA
1 TCATCTGACAATGAACGCTCAAGCACATGGTACAATCG-TTGGTGCTCGAACCCGTAACCATTAA
*
1350438 AAATAACAATAATTTTTTT
65 AAATAACAACAATTTTTTT
1350457 AACCATTTAG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 71 0.97
87 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (86 bp):
TCATCTGACAATGAACGCTCAAGCACATGGTACAATCGTTGGTGCTCGAACCCGTAACCATTAAA
AATAACAACAATTTTTTTCAA
Found at i:1359071 original size:59 final size:58
Alignment explanation
Indices: 1358960--1359071 Score: 131
Period size: 59 Copynumber: 1.9 Consensus size: 58
1358950 AATTAGTAAC
*
1358960 AAAATATTTTTTTTCTTAATAAAAAATTAATTTCATTATTTGATAACTAAATTTTTAA
1 AAAATATTTTTTTTCTTAATAAAAAATTAATTTCATTATTTGATAACAAAATTTTTAA
* * *
1359018 AAAATATTTTTTAATT-TTAA-AAATAATTTATTTTCATATATTTTATAA-AAAATT
1 AAAATATTTTTT--TTCTTAATAAA-AAATTAATTTCAT-TATTTGATAACAAAATT
1359072 CTAAAATTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
58 15 0.33
59 20 0.43
60 11 0.24
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.51
Consensus pattern (58 bp):
AAAATATTTTTTTTCTTAATAAAAAATTAATTTCATTATTTGATAACAAAATTTTTAA
Found at i:1359077 original size:58 final size:57
Alignment explanation
Indices: 1358960--1359077 Score: 125
Period size: 58 Copynumber: 2.0 Consensus size: 57
1358950 AATTAGTAAC
* *
1358960 AAAATATTTTTTTTCTTAATAAAAAATTAATTTCATTATTTGATAACTAAATTTTTAA
1 AAAATATTTTTTTTCTTAATAAAAAATTAATTTCATTATTTGATAAC-AAAATTCTAA
* * *
1359018 AAAATATTTTTTAATT-TTAA-AAATAATTTATTTTCATATATTTTATAA-AAAATTCTAA
1 AAAATATTTTTT--TTCTTAATAAA-AAATTAATTTCAT-TATTTGATAACAAAATTCTAA
1359076 AA
1 AA
1359078 TTTCTAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
58 25 0.49
59 15 0.29
60 11 0.22
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (57 bp):
AAAATATTTTTTTTCTTAATAAAAAATTAATTTCATTATTTGATAACAAAATTCTAA
Found at i:1361299 original size:20 final size:20
Alignment explanation
Indices: 1361274--1361314 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1361264 AGTGGATGGG
*
1361274 ATTTAGGAATATGAGTTTGT
1 ATTTAGGAATATGAGCTTGT
1361294 ATTTAGGAATATGAGCTTGT
1 ATTTAGGAATATGAGCTTGT
1361314 A
1 A
1361315 AGGTCAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTAGGAATATGAGCTTGT
Found at i:1363457 original size:10 final size:10
Alignment explanation
Indices: 1363439--1363513 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
1363429 CATTTAATAA
*
1363439 ATAAGCGAAC
1 ATAAACGAAC
1363449 ATAAACGAAC
1 ATAAACGAAC
1363459 AT----GAAC
1 ATAAACGAAC
1363465 ATAAACGAAC
1 ATAAACGAAC
** *
1363475 ACGAAC-ATAA
1 ATAAACGA-AC
1363485 ATGAACACGAAC
1 AT-AA-ACGAAC
1363497 ATAAACGAAC
1 ATAAACGAAC
1363507 ATAAACG
1 ATAAACG
1363514 TTGGAGACCT
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.56, C:0.20, G:0.13, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1363466 original size:16 final size:16
Alignment explanation
Indices: 1363444--1363507 Score: 110
Period size: 16 Copynumber: 4.0 Consensus size: 16
1363434 AATAAATAAG
1363444 CGAACATAAACGAACA
1 CGAACATAAACGAACA
*
1363460 TGAACATAAACGAACA
1 CGAACATAAACGAACA
*
1363476 CGAACATAAATGAACA
1 CGAACATAAACGAACA
1363492 CGAACATAAACGAACA
1 CGAACATAAACGAACA
1363508 TAAACGTTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.56, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:1364625 original size:14 final size:14
Alignment explanation
Indices: 1364608--1364634 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1364598 ATAGAACATA
1364608 AACGAACATAACCT
1 AACGAACATAACCT
1364622 AACGAACATAACC
1 AACGAACATAACC
1364635 GAACATTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.30, G:0.07, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCT
Found at i:1365435 original size:114 final size:114
Alignment explanation
Indices: 1365224--1365646 Score: 481
Period size: 114 Copynumber: 3.8 Consensus size: 114
1365214 ATCTCTAATT
* *
1365224 GTTTTTCAGGTTACACTAATTATCAGTCATG-ATTTT--TTTTTTAATGTT-GATGTTAGTG-TT
1 GTTTTTCAGGTTACACTAATTATCAGTCATGAATTTTCATTATCTAATGTTAG-TGTTAGTGTTT
*
1365284 TAATAATCTTATAC-TCTTAGTTTATTAATATCAAATTCCGGGCATTTCTTA
65 TAATAATCTTATACGT-TTAGTTTATTAATA-CAAATTCTGGGCATTTCTTA
* *
1365335 GTTTTTCGGGTTACACTAATTATCAGTCATGAATTTTCATTATCTATTGTTAGTGTT-GTGTTTT
1 GTTTTTCAGGTTACACTAATTATCAGTCATGAATTTTCATTATCTAATGTTAGTGTTAGTGTTTT
* * *
1365399 AATAATCTTATGCGTTTGGTTTATTAATAAAAAATTCTGGGCATTTCTTA
66 AATAATCTTATACGTTTAGTTTATTAAT-ACAAATTCTGGGCATTTCTTA
* * * * * *
1365449 GTTTTTCGGGCTACACTAATTATCAGTTA-CAATTTTCATTATCTAACGTTAATGTTAGTGTTTT
1 GTTTTTCAGGTTACACTAATTATCAGTCATGAATTTTCATTATCTAATGTTAGTGTTAGTGTTTT
1365513 AATTATAATCTTATACGTTTAGTTTA-T-AT-CAAATTCTGGGCATTTCTTA
66 -A--ATAATCTTATACGTTTAGTTTATTAATACAAATTCTGGGCATTTCTTA
* *
1365562 GTTTTTCAGGTTACACTAATTA-CAGTCATGAATTTTTATTATCGAAT-TTA-----A-TGTTTT
1 GTTTTTCAGGTTACACTAATTATCAGTCATGAATTTTCATTATCTAATGTTAGTGTTAGTGTTTT
* *
1365619 -ATAATCATATACGTTTAGTTTGTTAATA
66 AATAATCTTATACGTTTAGTTTATTAATA
1365647 GGCTTAATTA
Statistics
Matches: 271, Mismatches: 26, Indels: 36
0.81 0.08 0.11
Matches are distributed among these distances:
102 20 0.07
103 1 0.00
104 2 0.01
106 6 0.02
107 1 0.00
111 30 0.11
112 13 0.05
113 79 0.29
114 92 0.34
115 6 0.02
116 1 0.00
117 20 0.07
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.48
Consensus pattern (114 bp):
GTTTTTCAGGTTACACTAATTATCAGTCATGAATTTTCATTATCTAATGTTAGTGTTAGTGTTTT
AATAATCTTATACGTTTAGTTTATTAATACAAATTCTGGGCATTTCTTA
Found at i:1369414 original size:36 final size:36
Alignment explanation
Indices: 1369365--1369505 Score: 212
Period size: 36 Copynumber: 3.9 Consensus size: 36
1369355 TGAATAAGAA
**
1369365 GAACGAAAGGAAGCATCAACACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCCGCACTTTCGATTCAAAGT
* *
1369401 GAACGAAAAGAAGCATCCGCACTTTCGATTC-AAGAA
1 GAACGAAAGGAAGCATCCGCACTTTCGATTCAAAG-T
*
1369437 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCCGCACTTTCGATTCAAAGT
*
1369473 GAACGGAAGGAAGCATCCGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCCGCACTTTCGATTCAA
1369506 TTGTTCATCT
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
35 3 0.03
36 88 0.94
37 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.18
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCCGCACTTTCGATTCAAAGT
Found at i:1369453 original size:72 final size:72
Alignment explanation
Indices: 1369360--1369505 Score: 256
Period size: 72 Copynumber: 2.0 Consensus size: 72
1369350 GAAGGTGAAT
1369360 AAGAAGAACGAAAGGAAGCATCAACACTTTCGATTCAAAGTGAACGAAAAGAAGCATCCGCACTT
1 AAGAAGAACGAAAGGAAGCATCAACACTTTCGATTCAAAGTGAACGAAAAGAAGCATCCGCACTT
1369425 TCGATTC
66 TCGATTC
** * *
1369432 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
1 AAGAAGAACGAAAGGAAGCATCAACACTTTCGATTCAAAGTGAACGAAAAGAAGCATCCGCACTT
1369497 TCGATTC
66 TCGATTC
1369504 AA
1 AA
1369506 TTGTTCATCT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.18
Consensus pattern (72 bp):
AAGAAGAACGAAAGGAAGCATCAACACTTTCGATTCAAAGTGAACGAAAAGAAGCATCCGCACTT
TCGATTC
Found at i:1369584 original size:26 final size:27
Alignment explanation
Indices: 1369555--1369606 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1369545 GAATGTTAGA
*
1369555 CTGTTAAAG-AACATGCACGTGTATTG
1 CTGTTAAAGAAACATGCACATGTATTG
*
1369581 CTGTTAAAGAAATATGCACATGTATT
1 CTGTTAAAGAAACATGCACATGTATT
1369607 AAGCAGTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (27 bp):
CTGTTAAAGAAACATGCACATGTATTG
Found at i:1379485 original size:26 final size:28
Alignment explanation
Indices: 1379424--1379485 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
1379414 GAGTATTGCT
*
1379424 GAGCTCGACTCGACTCGAAAACTTTGCAA
1 GAGCTCGACTCGACTCGAAAACTTCGC-A
1379453 TGAAGCTCGACTCGACTCGAAAAC-TCGC-
1 -G-AGCTCGACTCGACTCGAAAACTTCGCA
1379481 GAGCT
1 GAGCT
1379486 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
30 4 0.13
31 21 0.70
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTTCGCA
Found at i:1388767 original size:165 final size:164
Alignment explanation
Indices: 1388589--1389560 Score: 1123
Period size: 165 Copynumber: 5.9 Consensus size: 164
1388579 TTGAATATAA
* * * ** ** *
1388589 TCGAACTCGAAGGTCTTCGGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTGAAGGATGT
1 TCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * *
1388654 GCCCTCCAAGCTGAGAGTAATTGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
66 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
*
1388719 ATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAG
131 ATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAG
* * * * *
1388754 TCGAACTCGAAGGTCTTTTGG-TCATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* *
1388818 TGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
65 TGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
*
1388883 TATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
130 TATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAG
* * * * * *
1388919 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * * * * * * * *
1388984 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTG
66 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTA
* * * * *
1389048 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
127 AGCTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAG
** * * * *
1389088 TCGAACTCGGGGGTCTTT-G--G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * * * * * * * *
1389149 GCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTA
66 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTA
* * *
1389213 AGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
127 AGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAG
* *
1389252 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* *
1389317 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTATCGACTTAAGCT
66 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
1389382 ATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
131 ATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAG
* * * * *
1389417 TCGAACTCAAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* *
1389481 TGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTATCGACTTAAGC
65 TGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
1389546 TATGCTGCAAATGAT
130 TATGCTGCAAATGAT
1389561 TGTTTAAAAA
Statistics
Matches: 701, Mismatches: 85, Indels: 42
0.85 0.10 0.05
Matches are distributed among these distances:
164 59 0.08
165 486 0.69
166 19 0.03
167 3 0.00
168 85 0.12
169 49 0.07
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (164 bp):
TCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
ATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAG
Found at i:1388964 original size:249 final size:249
Alignment explanation
Indices: 1388690--1389519 Score: 1338
Period size: 249 Copynumber: 3.3 Consensus size: 249
1388680 TCGAGGGTCT
* * * * * * *
1388690 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
1 TTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
*
1388755 CGAACTCGAAGGTCTTTTGGTCATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
66 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
*
1388820 CCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
1388885 TACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
196 TACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
*
1388939 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1389004 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
66 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
1389069 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
1389134 TACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
196 TACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
*
1389188 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
** * * * *
1389253 CGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
66 CGAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
*
1389317 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTATCGACTTAAGCT
130 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
*
1389382 ATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
195 ATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
* ** * * * * * * * * *
1389437 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
**
1389502 TCGAACTCGGGGGTCTTT
65 TCGAACTCGAAGGTCTTT
1389520 GGCAGATAGC
Statistics
Matches: 545, Mismatches: 33, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
248 5 0.01
249 511 0.94
250 27 0.05
251 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (249 bp):
TTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
TACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
Found at i:1389359 original size:414 final size:412
Alignment explanation
Indices: 1388589--1389560 Score: 1380
Period size: 414 Copynumber: 2.3 Consensus size: 412
1388579 TTGAATATAA
* * ** * *
1388589 TCGAACTCGAAGGTC-TTCGGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTGAAGGATG
1 TCGAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
* * * *
1388653 TGCCCTCCAAGCTGAGAGTAATTGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
65 TGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
* * *
1388718 TATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCATAGAT
130 TATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGAC
* * * * * *
1388783 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCG
195 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCG
** * * *
1388848 GGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGA
260 AAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCCTCGAGCTGA
* * * *
1388913 GCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAA
325 GCGTAATCGAACTCAAAGGTC--TTGTTGGCAGACAACCCTTATAGACTTAAGCTATGCTGCAAA
1388978 TGATATGCC-TTGGAGCTGAGCGTAG
388 TGATATGCCGTT-GAGCTGAGCGTAG
1389003 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1389068 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
66 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
* **
1389133 ATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGAC
131 ATACTGCAAATGATGTGCC-TTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGAC
* * * *
1389197 AACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCG
195 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCG
* *
1389261 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
260 AAGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCCTCG-A
* *** * * *
1389326 GCTGAGTGTAATCGAACTCGGGGGTC-T-TTGGCAGATAGCCCTTATCGACTTAAGCTATGCTGC
320 GCTGAGCGTAATCGAACTCAAAGGTCTTGTTGGCAGACAACCCTTATAGACTTAAGCTATGCTGC
*
1389389 AAATGATGTGCCGTTGAGCTGAGCGTAG
385 AAATGATATGCCGTTGAGCTGAGCGTAG
*
1389417 TCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
*
1389482 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTATCGACTTAAGCT
66 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
*
1389547 ATGCTGCAAATGAT
131 ATACTGCAAATGAT
1389561 TGTTTAAAAA
Statistics
Matches: 502, Mismatches: 48, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
413 26 0.05
414 397 0.79
415 10 0.02
417 47 0.09
418 22 0.04
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (412 bp):
TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
ATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGACA
ACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGA
AGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCCTCGAGCTGAG
CGTAATCGAACTCAAAGGTCTTGTTGGCAGACAACCCTTATAGACTTAAGCTATGCTGCAAATGA
TATGCCGTTGAGCTGAGCGTAG
Found at i:1392947 original size:18 final size:19
Alignment explanation
Indices: 1392906--1392950 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1392896 AGTTAATGTG
1392906 AATGCAAAGAAAATAAGAA
1 AATGCAAAGAAAATAAGAA
1392925 AATGCAAAGAAAATAAG-A
1 AATGCAAAGAAAATAAGAA
1392943 AATGCAAA
1 AATGCAAA
1392951 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.67, C:0.07, G:0.16, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAAGAA
Found at i:1394752 original size:2 final size:2
Alignment explanation
Indices: 1394745--1394780 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1394735 ATCATGCAAC
1394745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1394781 AAACACATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1405998 original size:15 final size:15
Alignment explanation
Indices: 1405980--1406017 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1405970 AAGGAAAATA
1405980 ATTAAAATATCAGT-G
1 ATTAAAATAT-AGTAG
*
1405995 ATTAAAATATAGTAT
1 ATTAAAATATAGTAG
1406010 ATTAAAAT
1 ATTAAAAT
1406018 TAAAAGCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.37
Consensus pattern (15 bp):
ATTAAAATATAGTAG
Found at i:1406967 original size:45 final size:45
Alignment explanation
Indices: 1406897--1406994 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
1406887 TGGAACGGGG
*
1406897 ACGTGGAGGGACTGCTGGCAGTGCTGGAAGCTACTGGAAATTGCA
1 ACGTGGAGGGACTGCTGGCAATGCTGGAAGCTACTGGAAATTGCA
* * * * *
1406942 ACGTGGAGGGGCTGTTGGGAATGCTGGAAGCTACTGGAATTTGTA
1 ACGTGGAGGGACTGCTGGCAATGCTGGAAGCTACTGGAAATTGCA
1406987 ACGTGGAG
1 ACGTGGAG
1406995 CTGCTGGAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.23, C:0.14, G:0.40, T:0.22
Consensus pattern (45 bp):
ACGTGGAGGGACTGCTGGCAATGCTGGAAGCTACTGGAAATTGCA
Done.