Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008925.1 Hibiscus syriacus cultivar Beakdansim tig00112230_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: 2702387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2471366 original size:11 final size:11
Alignment explanation
Indices: 2471350--2471378 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2471340 CAGTTAGTAA
2471350 AATAAAAAATG
1 AATAAAAAATG
2471361 AAT-AAAAATG
1 AATAAAAAATG
2471371 AATAAAAA
1 AATAAAAA
2471379 TAAAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (11 bp):
AATAAAAAATG
Found at i:2471369 original size:10 final size:10
Alignment explanation
Indices: 2471354--2471388 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
2471344 TAGTAAAATA
2471354 AAAAATGAAT
1 AAAAATGAAT
2471364 AAAAATGAAT
1 AAAAATGAAT
2471374 AAAAAT-AA-
1 AAAAATGAAT
2471382 AAAAATG
1 AAAAATG
2471389 GCAAGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 16 0.67
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (10 bp):
AAAAATGAAT
Found at i:2474086 original size:23 final size:23
Alignment explanation
Indices: 2474058--2474102 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2474048 TTGATGGCCA
2474058 AATATCTGACTCTATAAACAAAT
1 AATATCTGACTCTATAAACAAAT
2474081 AATATCTGACTCTATAAACAAA
1 AATATCTGACTCTATAAACAAA
2474103 GAGTATGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (23 bp):
AATATCTGACTCTATAAACAAAT
Found at i:2474479 original size:35 final size:35
Alignment explanation
Indices: 2474434--2474506 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
2474424 TTTCCGTTTA
*
2474434 AAAAATTCTAACACTAAGAGACATGAGAAAAACAT
1 AAAAATTCTAACACTAAAAGACATGAGAAAAACAT
*
2474469 AAAAATTCTAACACTAAAAGACATGAGAAAATCAT
1 AAAAATTCTAACACTAAAAGACATGAGAAAAACAT
2474504 AAA
1 AAA
2474507 TGAAACTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.59, C:0.14, G:0.10, T:0.18
Consensus pattern (35 bp):
AAAAATTCTAACACTAAAAGACATGAGAAAAACAT
Found at i:2475662 original size:15 final size:15
Alignment explanation
Indices: 2475642--2475673 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2475632 TTTATTGGTG
2475642 ATAATATTAAATATA
1 ATAATATTAAATATA
2475657 ATAATATTAAATATA
1 ATAATATTAAATATA
2475672 AT
1 AT
2475674 TAAGTCGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATATTAAATATA
Found at i:2477801 original size:14 final size:14
Alignment explanation
Indices: 2477782--2477822 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
2477772 TGACAAGAAT
2477782 GGATTAAATTGAAC
1 GGATTAAATTGAAC
2477796 GGATTAAATTGAAC
1 GGATTAAATTGAAC
*
2477810 GTATTAAATTGAA
1 GGATTAAATTGAA
2477823 GGCATAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (14 bp):
GGATTAAATTGAAC
Found at i:2480994 original size:3 final size:3
Alignment explanation
Indices: 2480986--2481059 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
2480976 TCTGCATTCT
2480986 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2481034 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2481060 TGAAATCGCG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2483827 original size:244 final size:248
Alignment explanation
Indices: 2483374--2483927 Score: 850
Period size: 244 Copynumber: 2.2 Consensus size: 248
2483364 TTTTTTGTCT
* * *
2483374 TTTTATTTTAACTAATAAATATCTTTTTAATTAATTATTTAATACTCTATATATTTTTCAAAAAA
1 TTTTATTTTAACTAATAAATATCTTTTTAATTAACTATTTAATACTCCATATATATTTCAAAAAA
** *
2483439 GGCTAAACTACATTTAGTATCCCAACTATAAGTTTTGTCCCATTTTAGTCTCCTAACTATTGTTT
66 AACTAAACTACATTTAGTATCCCAACTATAAGTTTTGTCCCATTTTAGTCACCTAACTATTGTTT
*
2483504 GTTTCAAAATCATACATAAAATTTAGTTTTAATTTCATTTTGGTATTCCACTATTAAAAATTAAT
131 GTCTCAAAATCATACATAAAATTTAGTTTTAATTTCATTTTGGTATTCCACTATTAAAAATTAAT
* * *
2483569 GGTAATACTAACATGTCATCATAAAATAATAAATATGACGCAAAGTTTTCTCC
196 GGTAATAATAACATGTCATCATAAAATAATAAATACGACACAAAGTTTTCTCC
*
2483622 TTTTATTTTAACTAATAAATATCTTTTTAATTAACAATTTAATACTCCATATATATTTCAAAAAA
1 TTTTATTTTAACTAATAAATATCTTTTTAATTAACTATTTAATACTCCATATATATTTCAAAAAA
* * ** *
2483687 AATTAAACTACATTTA-TATCCCAACTATCAGTTTTGTTTCGTTTTAGTCACC-AACTATT-TTT
66 AACTAAACTACATTTAGTATCCCAACTATAAGTTTTGTCCCATTTTAGTCACCTAACTATTGTTT
* *
2483749 -TCTCAAAATCGTACATAACATTTAGTTTTAATTTCATTTTGGTTATT-CACTATTAAAAATTAA
131 GTCTCAAAATCATACATAAAATTTAGTTTTAATTTCATTTTGG-TATTCCACTATTAAAAATTAA
* *
2483812 TGGTGATAATAACATGTCATCATAAAATAATAAATACGACACAAAGTTTTCTCT
195 TGGTAATAATAACATGTCATCATAAAATAATAAATACGACACAAAGTTTTCTCC
* *
2483866 TTTTATTTTAACTAATAAATATCTTTTTAATGAACTATTTAATACCCCATAT-TATTTTCAAA
1 TTTTATTTTAACTAATAAATATCTTTTTAATTAACTATTTAATACTCCATATATA-TTTCAAA
2483928 CGAAGATAAA
Statistics
Matches: 281, Mismatches: 23, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
243 2 0.01
244 160 0.57
245 7 0.02
246 7 0.02
247 31 0.11
248 74 0.26
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (248 bp):
TTTTATTTTAACTAATAAATATCTTTTTAATTAACTATTTAATACTCCATATATATTTCAAAAAA
AACTAAACTACATTTAGTATCCCAACTATAAGTTTTGTCCCATTTTAGTCACCTAACTATTGTTT
GTCTCAAAATCATACATAAAATTTAGTTTTAATTTCATTTTGGTATTCCACTATTAAAAATTAAT
GGTAATAATAACATGTCATCATAAAATAATAAATACGACACAAAGTTTTCTCC
Found at i:2483947 original size:81 final size:81
Alignment explanation
Indices: 2483854--2484009 Score: 278
Period size: 81 Copynumber: 1.9 Consensus size: 81
2483844 AATACGACAC
*
2483854 AAAGTTTTCTCTTTTTATTTTAACTAATAAATATCTTTTTAATGAACTATTTA-ATACCCCATAT
1 AAAGTTTTCTCTTTTTATTTTAACTAATAAATATCTTTTTAATGAACTATTTAGA-ACCCCATAA
2483918 TATTTTCAAACGAAGAT
65 TATTTTCAAACGAAGAT
*
2483935 AAAGTTTTCTCTTTTTATTTTAACTAATAAATATCTTTTTAATTAACTATTTAGAACCCCATAAT
1 AAAGTTTTCTCTTTTTATTTTAACTAATAAATATCTTTTTAATGAACTATTTAGAACCCCATAAT
2484000 ATTTTCAAAC
66 ATTTTCAAAC
2484010 AAAGCTAACC
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
81 71 0.99
82 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.46
Consensus pattern (81 bp):
AAAGTTTTCTCTTTTTATTTTAACTAATAAATATCTTTTTAATGAACTATTTAGAACCCCATAAT
ATTTTCAAACGAAGAT
Found at i:2484204 original size:329 final size:323
Alignment explanation
Indices: 2483610--2484254 Score: 934
Period size: 329 Copynumber: 2.0 Consensus size: 323
2483600 AATATGACGC
*
2483610 AAAGTTTTCTCCTTTTATTTTAACTAATAAATATCTTTTTAATTAACAATTTAATACTCCATATA
1 AAAGTTTTCTCCTTTTATTTTAACTAATAAATATCTTTTTAATTAACAATTTAATACCCCATATA
* * *
2483675 TATTTCAAAAAAAATTAAACTACATTTATATCCCAACTATCAGTTTTGTTTCGTTTTAGTCACCA
66 TATTTCAAAAAAAACTAAACTACATTTATATCCCAACTATCAATTTTGTTCCGTTTTAGTCACCA
* * * * * *
2483740 ACTATTTTTTCTCAAAATCGTACATAACATTTAGTTTTAATTTCATTTTGGTTATTCACTATTAA
131 ACTATTTTTTCTAAAAATCATACATAACATTTAGTTTTAATTTAATTTTAGTTATCCACCATTAA
* * *
2483805 AAATTAATGGTGATAATAACATGTCATCATAAAATAATAAATACGACACAAAGTTTTCTCTTTTT
196 AAACTAATGGTGATAATAACATGTCATCATAAAATAATAAATACGACACAAAGTTTTATCCTTTT
2483870 ATTTTAACTAATAAATATCTTTTTAATGAACTATTTAATACCCCATATTATTTTCAAACGAAGAT
261 ATTTTAACTAATAAATATCTTTTTAATGAACTATTTAATACCCCATA-TA-TTTCAAACGAAGAT
* *
2483935 AAAGTTTTCTCTTTTTATTTTAACTAATAAATATCTTTTTAATTAACTATTTAGA-ACCCCATA-
1 AAAGTTTTCTCCTTTTATTTTAACTAATAAATATCTTTTTAATTAACAATTTA-ATACCCCATAT
* * * * *
2483998 ATATTTTCAAACAAAGCTAACCTATATTTAGTATCCCAACTATCAATTTTGTTCCGTTTTGGTCA
65 ATA-TTTCAAAAAAAACTAAACTACATTTA-TATCCCAACTATCAATTTTGTTCCGTTTTAGTCA
* *
2484063 CCTAACTAGTTTTTGTTTAAAAATCATACATAACATTTAGTTTTGATTTAATTTTAGTTATCCAC
128 CC-AACTA-TTTTT-TCTAAAAATCATACATAACATTTAGTTTTAATTTAATTTTAGTTATCCAC
* * * **
2484128 CGTTAAAAACTAATGGTGATACTAACATGTCATCATAAAATAATAAATATGATGCAAAGTTTTAT
190 CATTAAAAACTAATGGTGATAATAACATGTCATCATAAAATAATAAATACGACACAAAGTTTTAT
* **
2484193 CCTTTTATTTTAACTAATAAATATCTTTTTAATTAACTATTTAATATTCCATATATTTCAAA
255 CCTTTTATTTTAACTAATAAATATCTTTTTAATGAACTATTTAATACCCCATATATTTCAAA
2484255 AAAGGCTAAA
Statistics
Matches: 284, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
324 3 0.01
325 79 0.28
326 34 0.12
327 12 0.04
328 7 0.02
329 149 0.52
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (323 bp):
AAAGTTTTCTCCTTTTATTTTAACTAATAAATATCTTTTTAATTAACAATTTAATACCCCATATA
TATTTCAAAAAAAACTAAACTACATTTATATCCCAACTATCAATTTTGTTCCGTTTTAGTCACCA
ACTATTTTTTCTAAAAATCATACATAACATTTAGTTTTAATTTAATTTTAGTTATCCACCATTAA
AAACTAATGGTGATAATAACATGTCATCATAAAATAATAAATACGACACAAAGTTTTATCCTTTT
ATTTTAACTAATAAATATCTTTTTAATGAACTATTTAATACCCCATATATTTCAAACGAAGAT
Found at i:2487924 original size:6 final size:6
Alignment explanation
Indices: 2487915--2487955 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
2487905 ATCATCAACC
* * *
2487915 TCATTA TCATTG TTACTA TCATTA TCATTA TCATTA TCATT
1 TCATTA TCATTA TCATTA TCATTA TCATTA TCATTA TCATT
2487956 GTTCATTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.51
Consensus pattern (6 bp):
TCATTA
Found at i:2488174 original size:23 final size:22
Alignment explanation
Indices: 2488148--2488202 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
2488138 CATGAAAGAT
*
2488148 CACGTAGAATTATCCCGAATGA
1 CACGTAGAATTATCCAGAATGA
*
2488170 CCACGTAGAATTATCTAGAATGA
1 -CACGTAGAATTATCCAGAATGA
2488193 CAGCGTAGAA
1 CA-CGTAGAA
2488203 CCCTCGACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (22 bp):
CACGTAGAATTATCCAGAATGA
Found at i:2488890 original size:19 final size:19
Alignment explanation
Indices: 2488868--2488910 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
2488858 CTGCGATATC
2488868 GATACTTTACTTCAGTATT
1 GATACTTTACTTCAGTATT
2488887 GATACTTTACTTCAGTATT
1 GATACTTTACTTCAGTATT
2488906 GATAC
1 GATAC
2488911 CCTTTCTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (19 bp):
GATACTTTACTTCAGTATT
Found at i:2492081 original size:2 final size:2
Alignment explanation
Indices: 2492074--2492103 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2492064 ATAAAATTAC
2492074 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
2492104 TCAATTAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2494222 original size:10 final size:10
Alignment explanation
Indices: 2494207--2494232 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2494197 GGTTTGCCGG
2494207 TGGTGGCGGA
1 TGGTGGCGGA
2494217 TGGTGGCGGA
1 TGGTGGCGGA
2494227 TGGTGG
1 TGGTGG
2494233 GGCTTGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.62, T:0.23
Consensus pattern (10 bp):
TGGTGGCGGA
Found at i:2497952 original size:12 final size:10
Alignment explanation
Indices: 2497919--2497956 Score: 51
Period size: 9 Copynumber: 3.7 Consensus size: 10
2497909 ACAAACTTTC
2497919 TTATTTATTA
1 TTATTTATTA
2497929 TTA-TTATTA
1 TTATTTATTA
2497938 TTATTTGATTCA
1 TTATTT-ATT-A
2497950 TTATTTA
1 TTATTTA
2497957 ATAAAATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.36
10 5 0.20
11 4 0.16
12 7 0.28
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (10 bp):
TTATTTATTA
Found at i:2502235 original size:20 final size:20
Alignment explanation
Indices: 2502186--2502235 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
2502176 CGATGAACAA
2502186 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
* *
2502207 TATCAATACTGATGTGGAG-G
1 TATCGATACTGAT-TGAAGAG
2502227 TATCGATAC
1 TATCGATAC
2502236 CAAGAGGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.36
21 12 0.48
22 4 0.16
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:2502923 original size:21 final size:21
Alignment explanation
Indices: 2502897--2502940 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2502887 CCATTAGACA
2502897 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
*
2502918 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
2502939 GG
1 GG
2502941 CAATATGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.27, G:0.43, T:0.16
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:2505721 original size:20 final size:21
Alignment explanation
Indices: 2505683--2505741 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
2505673 ACCGTTAGAC
* *
2505683 AGGGGGAATCGGTACCCCCTG
1 AGGGGGAATCTGTACCCCTTG
*
2505704 AGGGGGAATCTGTTCCCCTTG
1 AGGGGGAATCTGTACCCCTTG
2505725 -GGGGGAATCTGTACCCC
1 AGGGGGAATCTGTACCCC
2505742 CTGGGCAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.17, C:0.27, G:0.36, T:0.20
Consensus pattern (21 bp):
AGGGGGAATCTGTACCCCTTG
Found at i:2505746 original size:20 final size:20
Alignment explanation
Indices: 2505684--2505746 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
2505674 CCGTTAGACA
*
2505684 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
* *
2505704 AGGGGGAATCTGTTCCCCTTG
1 -GGGGGAATCTGTACCCCCTG
2505725 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
2505745 GG
1 GG
2505747 CAATCTGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.21
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:2506811 original size:53 final size:53
Alignment explanation
Indices: 2506748--2506854 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
2506738 GTGCACTTTC
*
2506748 GACACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTT
1 GACACTATGTGTGCATCCATGGCATTCATAATGAGTTTGTGAATTACCATTTT
* *
2506801 GACACTATGTGTGCATTCATGGCATTGATAATGAGTTTGTGAATTACCATTTT
1 GACACTATGTGTGCATCCATGGCATTCATAATGAGTTTGTGAATTACCATTTT
2506854 G
1 G
2506855 TTACCTTGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (53 bp):
GACACTATGTGTGCATCCATGGCATTCATAATGAGTTTGTGAATTACCATTTT
Found at i:2507760 original size:21 final size:22
Alignment explanation
Indices: 2507729--2507774 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2507719 TTAACAAACA
* *
2507729 AAATAAATTAAGTAATAAAAGT
1 AAATAAATTAAATAAAAAAAGT
*
2507751 AAAT-AATTAAATAAAAAAATT
1 AAATAAATTAAATAAAAAAAGT
2507772 AAA
1 AAA
2507775 ATTGTTGGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (22 bp):
AAATAAATTAAATAAAAAAAGT
Found at i:2509967 original size:11 final size:11
Alignment explanation
Indices: 2509951--2509988 Score: 76
Period size: 11 Copynumber: 3.5 Consensus size: 11
2509941 TTTGTTGAAC
2509951 AAAATTGAAAA
1 AAAATTGAAAA
2509962 AAAATTGAAAA
1 AAAATTGAAAA
2509973 AAAATTGAAAA
1 AAAATTGAAAA
2509984 AAAAT
1 AAAAT
2509989 AGAATTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (11 bp):
AAAATTGAAAA
Found at i:2510430 original size:3 final size:3
Alignment explanation
Indices: 2510422--2510479 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
2510412 CTCCTCACTC
* * *
2510422 TCA TCA TCA TCA TCA TCG TCA CCA TCA TTA -CTA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC-A TCA TCA TCA TCA
2510467 TCA TCA TCA TCA T
1 TCA TCA TCA TCA T
2510480 GAACAAATAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
3 46 0.98
4 1 0.02
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:2516993 original size:22 final size:22
Alignment explanation
Indices: 2516961--2517017 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
2516951 ACTGAAAGGG
*
2516961 AGTATCGATACCACAATATAGA
1 AGTATCGATACCACAATATAAA
* *
2516983 AGTATCTATACCACAGTATAAA
1 AGTATCGATACCACAATATAAA
2517005 AGTATCGATACCA
1 AGTATCGATACCA
2517018 TGGTAAGGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (22 bp):
AGTATCGATACCACAATATAAA
Found at i:2517457 original size:54 final size:54
Alignment explanation
Indices: 2517354--2517471 Score: 157
Period size: 54 Copynumber: 2.2 Consensus size: 54
2517344 TGTAATCACT
* * * *
2517354 GTATGGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCC
1 GTATTGGCACCGTGTGTGCAACCCAAGAAATTCATAATAAGTTTATGAATTACC
* * *
2517408 GTATTGGCACCGTGTGTGCAAACCCACGTAATTCATAATAAG-TTGTGAATTACC
1 GTATTGGCACCGTGTGTGC-AACCCAAGAAATTCATAATAAGTTTATGAATTACC
2517462 GTATTGGCAC
1 GTATTGGCAC
2517472 TACGTGTGCA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 37 0.66
55 19 0.34
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (54 bp):
GTATTGGCACCGTGTGTGCAACCCAAGAAATTCATAATAAGTTTATGAATTACC
Found at i:2517695 original size:82 final size:82
Alignment explanation
Indices: 2517557--2518077 Score: 787
Period size: 82 Copynumber: 6.4 Consensus size: 82
2517547 CTGTTTTAAA
* *
2517557 ATAAAAGACTAAAAGCCTAGCTGTGCATTTGGTAGAAAGGTGCCAATAATGTCAGTTAGATGAAA
1 ATAAAAGACTAAAAGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
2517622 GGTTAAATGCCTTTGGG
66 GGTTAAATGCCTTTGGG
* *
2517639 ATAAAAGACTAAAAGCCTAGCCGTGCATTTGGCAGAAAGATGCCAATAATGCCAGTTAGATGAAA
1 ATAAAAGACTAAAAGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
2517704 GGTTAAATGCCTTTGGG
66 GGTTAAATGCCTTTGGG
* * * **
2517721 AAAAAAGACTAAATGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATAATG-CTTTTAGATGAAA
1 ATAAAAGACTAAAAGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
2517785 GGTTAAATGCCTTTGGG
66 GGTTAAATGCCTTTGGG
* *
2517802 ATAAAAGACTAAATGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
1 ATAAAAGACTAAAAGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
2517867 GGTTAAATGCCTTTGGG
66 GGTTAAATGCCTTTGGG
* * * * * *
2517884 ATAAAATATTAAAATCCTAGCTATGCATTTGGCAGAAAAGTGCTAATAATGCCAGTTAGATGAAA
1 ATAAAAGACTAAAAGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
2517949 GGTTAAATGCCTTTGGG
66 GGTTAAATGCCTTTGGG
* ** * **
2517966 ATAAAAGATTAAATTCCTAGCTGTGCATTTGGTAGAAAGGTGCCAATAATGATAGTTAGATGAAA
1 ATAAAAGACTAAAAGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
2518031 GGTTAAATGCCTTTGGG
66 GGTTAAATGCCTTTGGG
*
2518048 ATAAAAG--TAAAAATGCCTAGCTGTGTATTT
1 ATAAAAGACT-AAAA-GCCTAGCTGTGCATTT
2518078 TTGGTAGAAA
Statistics
Matches: 401, Mismatches: 35, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
80 1 0.00
81 79 0.20
82 321 0.80
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28
Consensus pattern (82 bp):
ATAAAAGACTAAAAGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
GGTTAAATGCCTTTGGG
Found at i:2517987 original size:245 final size:246
Alignment explanation
Indices: 2517557--2518077 Score: 832
Period size: 245 Copynumber: 2.1 Consensus size: 246
2517547 CTGTTTTAAA
* * *
2517557 ATAAAAGACTAAAAGCCTAGCTGTGCATTTGGTAGAAAGGTGCCAATAATGTCAGTTAGATGAAA
1 ATAAAAGACTAAATGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
*
2517622 GGTTAAATGCCTTTGGGATAAAAGACTAAAAGCCTAGCCGTGCATTTGGCAGAAAGATGCCAATA
66 GGTTAAATGCCTTTGGGATAAAAGACTAAAAGCCTAGCCATGCATTTGGCAGAAAGATGCCAATA
2517687 ATGCCAGTTAGATGAAAGGTTAAATGCCTTTGGGAAAAAAGACTAAATGCCTAGCTGTGCATTTG
131 ATGCCAGTTAGATGAAAGGTTAAATGCCTTTGGGAAAAAAGACTAAATGCCTAGCTGTGCATTTG
* * *
2517752 GCAGAAATGTGCCAATAATGCT-TTTAGATGAAAGGTTAAATGCCTTTGGG
196 GCAGAAAGGTGCCAATAATGATAGTTAGATGAAAGGTTAAATGCCTTTGGG
*
2517802 ATAAAAGACTAAATGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
1 ATAAAAGACTAAATGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
* * * * *
2517867 GGTTAAATGCCTTTGGGATAAAATATTAAAATCCTAGCTATGCATTTGGCAGAAA-AGTGCTAAT
66 GGTTAAATGCCTTTGGGATAAAAGACTAAAAGCCTAGCCATGCATTTGGCAGAAAGA-TGCCAAT
* * *
2517931 AATGCCAGTTAGATGAAAGGTTAAATGCCTTTGGGATAAAAGATTAAATTCCTAGCTGTGCATTT
130 AATGCCAGTTAGATGAAAGGTTAAATGCCTTTGGGAAAAAAGACTAAATGCCTAGCTGTGCATTT
*
2517996 GGTAGAAAGGTGCCAATAATGATAGTTAGATGAAAGGTTAAATGCCTTTGGG
195 GGCAGAAAGGTGCCAATAATGATAGTTAGATGAAAGGTTAAATGCCTTTGGG
* *
2518048 ATAAAAGTA-AAAATGCCTAGCTGTGTATTT
1 ATAAAAG-ACTAAATGCCTAGCTGTGCATTT
2518078 TTGGTAGAAA
Statistics
Matches: 253, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
244 1 0.00
245 199 0.79
246 52 0.21
247 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28
Consensus pattern (246 bp):
ATAAAAGACTAAATGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATAATGCCAGTTAGATGAAA
GGTTAAATGCCTTTGGGATAAAAGACTAAAAGCCTAGCCATGCATTTGGCAGAAAGATGCCAATA
ATGCCAGTTAGATGAAAGGTTAAATGCCTTTGGGAAAAAAGACTAAATGCCTAGCTGTGCATTTG
GCAGAAAGGTGCCAATAATGATAGTTAGATGAAAGGTTAAATGCCTTTGGG
Found at i:2518141 original size:47 final size:47
Alignment explanation
Indices: 2518075--2518186 Score: 120
Period size: 47 Copynumber: 2.3 Consensus size: 47
2518065 TAGCTGTGTA
* ** * *
2518075 TTTTTGGTAGAAATATGCCATTAA-GTCAAGTTAGATG-CTAACTGTG
1 TTTTTGGCAGAAAGGTGCCATTAATG-CAAGTAAGATGTCTAACGGTG
2518121 CTTTTTGGCAGAAAGGTGCCATTAATGCAAGTAAGATGTCTAACGGTG
1 -TTTTTGGCAGAAAGGTGCCATTAATGCAAGTAAGATGTCTAACGGTG
*
2518169 TAGTTTTGGCAAAAAGGT
1 T--TTTTGGCAGAAAGGT
2518187 TCCACTAACG
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
47 32 0.58
48 9 0.16
49 14 0.25
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (47 bp):
TTTTTGGCAGAAAGGTGCCATTAATGCAAGTAAGATGTCTAACGGTG
Found at i:2522158 original size:3 final size:3
Alignment explanation
Indices: 2522150--2522258 Score: 157
Period size: 3 Copynumber: 36.0 Consensus size: 3
2522140 TTCATTTAAA
* *
2522150 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
2522198 ATT ATT ATT ATT ATT ATT A-T ATT AGT ATTT ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
2522243 ATAT ATT ATT ATT ATT
1 AT-T ATT ATT ATT ATT
2522259 TAATAAATAA
Statistics
Matches: 95, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
2 2 0.02
3 88 0.93
4 5 0.05
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2522751 original size:10 final size:10
Alignment explanation
Indices: 2522715--2522759 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
2522705 ACCCAGAAGG
2522715 ACAGAGAGCA
1 ACAGAGAGCA
* *
2522725 ACAGACAGCC
1 ACAGAGAGCA
2522735 ACAGAGAGCA
1 ACAGAGAGCA
* *
2522745 ACGGAGAACA
1 ACAGAGAGCA
2522755 ACAGA
1 ACAGA
2522760 AAAACAGACG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.49, C:0.24, G:0.27, T:0.00
Consensus pattern (10 bp):
ACAGAGAGCA
Found at i:2524652 original size:13 final size:15
Alignment explanation
Indices: 2524621--2524657 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2524611 TTATATGTTT
2524621 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
2524636 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
2524649 TA-TTTATTT
1 TATTTTATTT
2524658 TTCTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:2531816 original size:114 final size:113
Alignment explanation
Indices: 2531561--2531868 Score: 443
Period size: 114 Copynumber: 2.8 Consensus size: 113
2531551 ATGTAATTTG
*
2531561 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TT-G--G-A---CAGAATCT
1 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCCCA-AAACT
*
2531618 AATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGAC
65 AATCATTGGATTTGAAAAATGAATTTGCTCATAGTAGAAATAAGAAGAC
2531667 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACT
1 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GAACCCCAAAACT
*
2531732 AATCATTGGATTTGAAAAATGAATTTGCTCATAGTAGAAATAAGGAGAC
65 AATCATTGGATTTGAAAAATGAATTTGCTCATAGTAGAAATAAGAAGAC
* * * * *
2531781 CCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAGAACC
1 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GAACCCCAAAACT
* *
2531846 GATCATTGGAATTGAAAAATGAA
65 AATCATTGGATTTGAAAAATGAA
2531869 CTGCATGATC
Statistics
Matches: 182, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
106 44 0.24
107 2 0.01
108 1 0.01
111 1 0.01
112 1 0.01
114 131 0.72
115 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (113 bp):
CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCCCAAAACTA
ATCATTGGATTTGAAAAATGAATTTGCTCATAGTAGAAATAAGAAGAC
Found at i:2534363 original size:21 final size:22
Alignment explanation
Indices: 2534296--2534372 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
2534286 CATCTGCACT
*
2534296 TTTTAAAGATAATAGATTCTCA
1 TTTTAAAGATGATAGATTCTCA
* * * * * *
2534318 CTTCAGAGATGACAAATT-TCT
1 TTTTAAAGATGATAGATTCTCA
2534339 TTTTAAAGATGATAGATTCTC-
1 TTTTAAAGATGATAGATTCTCA
*
2534360 TTTTCAAAAATGA
1 TTTT-AAAGATGA
2534373 AAGCTTTATG
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
21 19 0.47
22 21 0.52
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (22 bp):
TTTTAAAGATGATAGATTCTCA
Found at i:2535167 original size:76 final size:76
Alignment explanation
Indices: 2535041--2535836 Score: 1439
Period size: 76 Copynumber: 10.5 Consensus size: 76
2535031 CTATTTCTTA
2535041 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2535106 AACCTTCGGGT
66 AGCCTTCGGGT
* * *
2535117 CATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
2535182 AACCTTCGAGT
66 AGCCTTCGGGT
* *
2535193 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2535258 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2535269 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2535334 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2535345 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2535410 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2535421 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTACGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2535486 AGCCTTCGGGT
66 AGCCTTCGGGT
2535497 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2535562 AGCCTTCGGGT
66 AGCCTTCGGGT
2535573 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2535638 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2535649 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2535714 AACCTTCGGGT
66 AGCCTTCGGGT
2535725 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
2535790 AAACCTTCGGGT
65 AAGCCTTCGGGT
* *
2535802 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
2535837 CATTTCCATC
Statistics
Matches: 699, Mismatches: 20, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
76 653 0.93
77 46 0.07
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:2535969 original size:3 final size:3
Alignment explanation
Indices: 2535961--2536073 Score: 172
Period size: 3 Copynumber: 37.0 Consensus size: 3
2535951 TTCATTTAAA
* *
2535961 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
2536009 ATT ATT ATT ATT ATT ATT ATT ATT AGT ATTT ATT ATT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
2536055 ATT ATAT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT
2536074 TAATAAATAA
Statistics
Matches: 100, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
3 95 0.95
4 5 0.05
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2538509 original size:17 final size:19
Alignment explanation
Indices: 2538470--2538514 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
2538460 ATCATAACAA
2538470 ACTAA-TAATAAACTAAAT
1 ACTAACTAATAAACTAAAT
*
2538488 CCTAACTAAT-AAC-AAAT
1 ACTAACTAATAAACTAAAT
2538505 ACTAACTAAT
1 ACTAACTAAT
2538515 CATTATTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 13 0.54
18 7 0.29
19 4 0.17
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.27
Consensus pattern (19 bp):
ACTAACTAATAAACTAAAT
Found at i:2538650 original size:36 final size:36
Alignment explanation
Indices: 2538609--2538849 Score: 283
Period size: 36 Copynumber: 6.7 Consensus size: 36
2538599 TTTTCGTTTG
*
2538609 ACTTGAATCGGAAGTGCTGATGCTTCATTCCGTTCA
1 ACTTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCA
* *
2538645 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCATTCGA
1 ACTTGAATCGGAAGTGCTGATGCTTCCTTCCGTTC-A
* * *
2538682 A-TTGAATCGGAAGTG-TCGATACCTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCT-GATGCTTCCTTCCGTTCA
* * *
2538717 ACTTGAATCGGAAGTG-TCGATACCTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCT-GATGCTTCCTTCCGTTCA
* * * *
2538753 ACTTGAATCAGAAGTGCCGATGCCTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCA
**
2538789 ACTTGAATCGGAAGTGCCAATGCTTCCTTCCGTTCA
1 ACTTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCA
2538825 ACTTGAATCGGAAGTGCAT-ATGCTT
1 ACTTGAATCGGAAGTGC-TGATGCTT
2538850 TCTTTCATTC
Statistics
Matches: 184, Mismatches: 16, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
35 1 0.01
36 181 0.98
37 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCA
Found at i:2538695 original size:72 final size:72
Alignment explanation
Indices: 2538611--2538841 Score: 322
Period size: 72 Copynumber: 3.2 Consensus size: 72
2538601 TTCGTTTGAC
* * *
2538611 TTGAATCGGAAGTGCTGATGCTTCATTCCGTTCAACTTGAATCGGAAGTGCCGATGCTTCCTTCC
1 TTGAATCGGAAGTGCTGATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCTTCC
*
2538676 ATTCGAA
66 GTTCGAA
* * * *
2538683 TTGAATCGGAAGTG-TCGATACCTCCTTCCGTTCGACTTGAATCGGAAGTGTCGATACCTCCTTC
1 TTGAATCGGAAGTGCT-GATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCTTC
*
2538747 CGTTCGAC
65 CGTTCGAA
* * *
2538755 TTGAATCAGAAGTGCCGATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGCCAATGCTTCCTTCC
1 TTGAATCGGAAGTGCTGATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCTTCC
2538820 GTTC-AA
66 GTTCGAA
2538826 CTTGAATCGGAAGTGC
1 -TTGAATCGGAAGTGC
2538842 ATATGCTTTC
Statistics
Matches: 138, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
71 2 0.01
72 136 0.99
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (72 bp):
TTGAATCGGAAGTGCTGATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCTTCC
GTTCGAA
Found at i:2538781 original size:108 final size:107
Alignment explanation
Indices: 2538576--2538841 Score: 336
Period size: 108 Copynumber: 2.5 Consensus size: 107
2538566 AAACGAACAC
* * * * * * *
2538576 TTGAAACGAAAGTGCGATACATCTTTTCGTTTGACTTGAATCGGAAGTGCTGATGCTTCATTCCG
1 TTGAATCGGAAGTGCGATACATCCTTCCGTTCGACTTGAATCGGAAGTGCTGATACCTCATTCCG
* *
2538641 TTCAACTTGAATCGGAAGTGCCGATGCTTCCTTCCATTCGAA
66 TTCAACTTGAATCAGAAGTGCCGATGCCTCCTTCCATTCGAA
* *
2538683 TTGAATCGGAAGTGTCGATACCTCCTTCCGTTCGACTTGAATCGGAAGTG-TCGATACCTCCTTC
1 TTGAATCGGAAGTG-CGATACATCCTTCCGTTCGACTTGAATCGGAAGTGCT-GATACCTCATTC
* * *
2538747 CGTTCGACTTGAATCAGAAGTGCCGATGCCTCCTTCCGTTCGAC
64 CGTTCAACTTGAATCAGAAGTGCCGATGCCTCCTTCCATTCGAA
* * * *
2538791 TTGAATCGGAAGTGCCAATGCTTCCTTCCGTTCAACTTGAATCGGAAGTGC
1 TTGAATCGGAAGTG-CGATACATCCTTCCGTTCGACTTGAATCGGAAGTGC
2538842 ATATGCTTTC
Statistics
Matches: 137, Mismatches: 19, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
107 13 0.09
108 124 0.91
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (107 bp):
TTGAATCGGAAGTGCGATACATCCTTCCGTTCGACTTGAATCGGAAGTGCTGATACCTCATTCCG
TTCAACTTGAATCAGAAGTGCCGATGCCTCCTTCCATTCGAA
Found at i:2540236 original size:44 final size:44
Alignment explanation
Indices: 2540187--2540284 Score: 178
Period size: 44 Copynumber: 2.2 Consensus size: 44
2540177 TTGAATGGAG
*
2540187 ATGGATATTGGATTAAAATCCATAATTATAGACATATATTTATA
1 ATGGATATTGGATTAAAATCCATAATTATAGACACATATTTATA
2540231 ATGGATATTGGATTAAAATCCATAATTATAGACACATATTTATA
1 ATGGATATTGGATTAAAATCCATAATTATAGACACATATTTATA
*
2540275 ATGTATATTG
1 ATGGATATTG
2540285 TTATCATAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (44 bp):
ATGGATATTGGATTAAAATCCATAATTATAGACACATATTTATA
Found at i:2545378 original size:20 final size:20
Alignment explanation
Indices: 2545353--2545391 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2545343 AGTAGAAAAG
2545353 AATTTGGGACCATGTAACTC
1 AATTTGGGACCATGTAACTC
2545373 AATTTGGGACCATGTAACT
1 AATTTGGGACCATGTAACT
2545392 TACCACCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (20 bp):
AATTTGGGACCATGTAACTC
Found at i:2558309 original size:16 final size:16
Alignment explanation
Indices: 2558269--2558302 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2558259 CAAAGAATCC
*
2558269 TTAACATATAATATTA
1 TTAACATAGAATATTA
2558285 TTAACATAGAATATTA
1 TTAACATAGAATATTA
2558301 TT
1 TT
2558303 GCCATAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (16 bp):
TTAACATAGAATATTA
Found at i:2559812 original size:37 final size:37
Alignment explanation
Indices: 2559738--2559812 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
2559728 AATGTTTTTA
* *** * *
2559738 CTTGAAATAAAATTTTATCTCGCTTGTGATTGTTTTC
1 CTTGAAATAAAATTTCATCTCGCTCAAGATAGGTTTC
*
2559775 CTTGAAATAGAATTTCATCTCGCTCAAGATAGGTTTC
1 CTTGAAATAAAATTTCATCTCGCTCAAGATAGGTTTC
2559812 C
1 C
2559813 ACGAAACTCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (37 bp):
CTTGAAATAAAATTTCATCTCGCTCAAGATAGGTTTC
Found at i:2560381 original size:44 final size:44
Alignment explanation
Indices: 2560299--2560398 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 44
2560289 ATCACATAAG
*
2560299 GAGTTGGATCAACATCACCATCTTGCTTGATTTCATCAT-GTAAA
1 GAGTTGGATCAACATCACCATCTTGCTTAATTTCATCATAG-AAA
* * *
2560343 GAGTTGGATCAACATCACTC-TTTTGTTTAA-TTCTATCATAGAAG
1 GAGTTGGATCAACATCAC-CATCTTGCTTAATTTC-ATCATAGAAA
*
2560387 GAGGTGGATCAA
1 GAGTTGGATCAA
2560399 TGTTCAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
43 3 0.06
44 43 0.90
45 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (44 bp):
GAGTTGGATCAACATCACCATCTTGCTTAATTTCATCATAGAAA
Found at i:2568553 original size:15 final size:15
Alignment explanation
Indices: 2568535--2568577 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2568525 GGAAAAGTGA
2568535 AAGAGATAATAAATG
1 AAGAGATAATAAATG
*
2568550 AAGAGGATAA-GAATG
1 AAGA-GATAATAAATG
2568565 AAGAGATAATAAA
1 AAGAGATAATAAA
2568578 GTCTCAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 5 0.21
15 14 0.58
16 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.16
Consensus pattern (15 bp):
AAGAGATAATAAATG
Found at i:2572950 original size:27 final size:27
Alignment explanation
Indices: 2572912--2572969 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
2572902 TAGCTATTAG
2572912 TGTTATTGTTTGGACTATTACTGTTAC
1 TGTTATTGTTTGGACTATTACTGTTAC
* * *
2572939 TGTTATTGTTTGGATTATTACTTTTAT
1 TGTTATTGTTTGGACTATTACTGTTAC
2572966 TGTT
1 TGTT
2572970 TCTAACTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.59
Consensus pattern (27 bp):
TGTTATTGTTTGGACTATTACTGTTAC
Found at i:2573676 original size:18 final size:20
Alignment explanation
Indices: 2573645--2573681 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2573635 GTAAATATAC
*
2573645 ATTTTAGATTAAAA-CAAAA
1 ATTTTAGATGAAAATCAAAA
2573664 ATTTTAG-TGAAAATCAAA
1 ATTTTAGATGAAAATCAAA
2573682 TTTTCGGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (20 bp):
ATTTTAGATGAAAATCAAAA
Found at i:2584423 original size:20 final size:21
Alignment explanation
Indices: 2584384--2584423 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2584374 ATAAAATAGT
* *
2584384 TTTTAATATTAAATAGAATTG
1 TTTTAAAATAAAATAGAATTG
2584405 TTTTAAAATAAAATA-AATT
1 TTTTAAAATAAAATAGAATT
2584424 TTTAGGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
TTTTAAAATAAAATAGAATTG
Found at i:2587066 original size:19 final size:20
Alignment explanation
Indices: 2587042--2587094 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
2587032 TGCAAAAATG
*
2587042 GTATCGATACCGTA-ATAGT
1 GTATCGATACCATAGATAGT
2587061 GTATCGATACCATAGTATAGT
1 GTATCGATACCATAG-ATAGT
*
2587082 ATATCGATACCAT
1 GTATCGATACCAT
2587095 GGTTGGGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (20 bp):
GTATCGATACCATAGATAGT
Found at i:2587535 original size:57 final size:57
Alignment explanation
Indices: 2587442--2587938 Score: 578
Period size: 57 Copynumber: 8.8 Consensus size: 57
2587432 ATGGTACTGA
*
2587442 GTGTGCAAAAAGTTAAGGAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
* * * *
2587499 GTGTACAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCATATGGGTAGTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
* * * * * * **
2587556 GTATACAACAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGCAAGTACACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
* * *
2587613 GTGTACAAAAAGTTAAGAAATTCATAATTAGTTTATG-AGTTTCGATTTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCG-TATGGGCACTTT
* * * * * * *
2587670 TTGCGCAAAAAGCTAAGAAATTCATACTAAGTTTATGAATTTTTGTAT-GTCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
* *
2587726 GTGTGC-AAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGTACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
* *
2587782 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTAT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
* * * * * *
2587839 GTGTGC--AAA-TTAAGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGAACTAT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
* * * ***
2587893 ATGTGCAAACA--TAAGAAATTCATAATAAGTAGGTGAATTTTCGTAT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTAT
2587939 TGTTAGTGGG
Statistics
Matches: 378, Mismatches: 56, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
54 44 0.12
55 71 0.19
56 30 0.08
57 228 0.60
58 5 0.01
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (57 bp):
GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTT
Found at i:2587805 original size:169 final size:168
Alignment explanation
Indices: 2587442--2587918 Score: 606
Period size: 169 Copynumber: 2.8 Consensus size: 168
2587432 ATGGTACTGA
* *
2587442 GTGTGCAAAAAGTTAAGGAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTTGTGTACAA
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAA-TTTCGTATGGGCACTTTGTGTGCAA
* * * * * *
2587507 AAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCATATGGGTAGTTTGTATACAACAAGTTAA
65 AAAGTTAAGAAATTCATACTAAGTTTATGAATTTTCGTAT-GGTACTTTGTGTGCAA-AAGTTAA
*
2587572 GAAATTCATAATTAGTTTATGAATTTCCGCAAGTACACTTT
128 GAAATTCATAATTAGTTTATGAATTTCCGCAAGGACACTTT
* * * * *
2587613 GTGTACAAAAAGTTAAGAAATTCATAATTAGTTTATGAGTTTCGATTTGGGCACTTTTTGCGCAA
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCG-TATGGGCACTTTGTGTGCAA
* *
2587678 AAAGCTAAGAAATTCATACTAAGTTTATGAATTTTTGTAT-GTCACTTTGTGTGCAAAAGTTAAG
65 AAAGTTAAGAAATTCATACTAAGTTTATGAATTTTCGTATGGT-ACTTTGTGTGCAAAAGTTAAG
* * **
2587742 AAATTCATAATTAGTTTATGAATTTCCGTATGGGTACTTT
129 AAATTCATAATTAGTTTATGAATTTCCGCAAGGACACTTT
*
2587782 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTATGTGTGC--
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTT-CGTATGGGCACTTTGTGTGCAA
* * * * *
2587845 AAA-TTAAGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGAACTATATGTGCAAACA--TAA
65 AAAGTTAAGAAATTCATACTAAGTTTATGAATTTTCGTAT-GGTACTTTGTGTGCAAA-AGTTAA
2587907 GAAATTCATAAT
128 GAAATTCATAAT
2587919 AAGTAGGTGA
Statistics
Matches: 267, Mismatches: 33, Indels: 17
0.84 0.10 0.05
Matches are distributed among these distances:
166 47 0.18
167 15 0.06
168 2 0.01
169 99 0.37
170 17 0.06
171 87 0.33
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (168 bp):
GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCGTATGGGCACTTTGTGTGCAAA
AAGTTAAGAAATTCATACTAAGTTTATGAATTTTCGTATGGTACTTTGTGTGCAAAAGTTAAGAA
ATTCATAATTAGTTTATGAATTTCCGCAAGGACACTTT
Found at i:2589712 original size:90 final size:89
Alignment explanation
Indices: 2589595--2589768 Score: 269
Period size: 90 Copynumber: 1.9 Consensus size: 89
2589585 TCCCGAATAT
* ** * *
2589595 TTAATTTCAATTAATTAAATATCGATTTAATTAATTTGAAATAATAAAATCCCTGAA-ATGATTA
1 TTAAATTCAATTAATTAAATAAAGATTTAATTAATTTGAAATAATAAAAACCCT-AATATGACTA
2589659 GGGTAACTTGGATATAAAAGAATTA
65 GGGTAACTTGGATATAAAAGAATTA
2589684 TTAAATTCTAATTAATTAAATAAAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
1 TTAAATTC-AATTAATTAAATAAAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
*
2589749 GGGTAACTTGGCTATAAAAG
65 GGGTAACTTGGATATAAAAG
2589769 GGTGTGTTAG
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 9 0.12
90 68 0.88
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATAAAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAG
GGTAACTTGGATATAAAAGAATTA
Found at i:2596565 original size:90 final size:90
Alignment explanation
Indices: 2596444--2596619 Score: 289
Period size: 90 Copynumber: 2.0 Consensus size: 90
2596434 TAATCCCGAA
* * * * *
2596444 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
2596509 TAGGGTAACTTGGATATAAAATGAT
66 TAGGGTAACTTGGATATAAAATGAT
*
2596534 TATTAAATTCCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
2596599 TAGGGTAACTTGGCTATAAAA
66 TAGGGTAACTTGGATATAAAA
2596620 GGGTGTGTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAATGAT
Found at i:2602958 original size:57 final size:57
Alignment explanation
Indices: 2602865--2603228 Score: 459
Period size: 57 Copynumber: 6.5 Consensus size: 57
2602855 ATGACACTAA
*
2602865 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCTGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCTATATGGGCACTTT
* ** ** * *
2602922 ATGCACAAAAAGTTGGGAATTTCATAATTAGTTTATGAATTTCTATATGGACACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCTATATGGGCACTTT
* ***
2602979 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCATATATTCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCTATATGGGCACTTT
* * * * * * *
2603036 GTGTGCAAAAAGCTAAGAAAATCATACTAAGTGTATGAATTTTTGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCTATATGGGCACTTT
*
2603093 GTGTGC-AAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCATATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCTATATGGGCACTTT
* * * * *
2603149 GTGTGCAAAAAGTTAAGAAATTTATAATTAGTTTATGAATTT-TCGTATGTGTACTAT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCT-ATATGGGCACTTT
2603206 GTGTGC--AAA-TTAAGAAATTCATA
1 GTGTGCAAAAAGTTAAGAAATTCATA
2603229 CTAAGTGTGT
Statistics
Matches: 261, Mismatches: 44, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
54 13 0.05
55 3 0.01
56 48 0.18
57 197 0.75
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (57 bp):
GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCTATATGGGCACTTT
Found at i:2603154 original size:170 final size:170
Alignment explanation
Indices: 2602860--2603268 Score: 556
Period size: 170 Copynumber: 2.4 Consensus size: 170
2602850 ACCAAATGAC
* * * * *
2602860 ACTAAGTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCTGTATGGGCACTTTATG
1 ACTATGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTTTATG
** ** * *
2602925 CACAAAAAGTTGGGAATTTCATAATTAGTTTATGAATTTCTATATGGACACTTTGTGTGCAAAAA
66 TGC-AAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCATATGGACACTTTGTGTGCAAAAA
2602990 GTTAAGAAATTCATAATTAGTTTATGAATTTCCATATAT-T
130 GTTAAGAAATTCATAATTAGTTTATGAATTTCCATATATGT
* * * *
2603030 CACTTTGTGTGCAAAAAGCTAAGAAAATCATACTAAGTGTATGAATTTTTGTATGGGCACTTTGT
1 -ACTATGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTTTAT
*
2603095 GTGCAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCATATGGGCACTTTGTGTGCAAAAA
65 GTGCAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCATATGGACACTTTGTGTGCAAAAA
* * * *
2603160 GTTAAGAAATTTATAATTAGTTTATGAATTTTCGTATGTGT
130 GTTAAGAAATTCATAATTAGTTTATGAATTTCCATATATGT
* * * *
2603201 ACTATGTGTGC--AAA-TTAAGAAATTCATACTAAGTGTGTGAATTTTGGTATGGGAACTATATG
1 ACTATGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTTTATG
2603263 TGCAAA
66 TGCAAA
2603269 CATAAGAAGC
Statistics
Matches: 209, Mismatches: 28, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
167 47 0.22
168 3 0.01
170 101 0.48
171 58 0.28
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.37
Consensus pattern (170 bp):
ACTATGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTTTATG
TGCAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCATATGGACACTTTGTGTGCAAAAAG
TTAAGAAATTCATAATTAGTTTATGAATTTCCATATATGT
Found at i:2635314 original size:19 final size:19
Alignment explanation
Indices: 2635290--2635360 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 19
2635280 TGCAAAAATG
*
2635290 GTATCGATACCGTGATAGA
1 GTATCGATACCATGATAGA
* *
2635309 GTATCGGTACCCTAGTATAGTA
1 GTATCGATACCAT-G-ATAG-A
*
2635331 TTATCGATACCAT-AGTATGA
1 GTATCGATACCATGA-TA-GA
2635351 GTATCGATAC
1 GTATCGATAC
2635361 TAATGAGCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
19 12 0.29
20 13 0.32
21 5 0.12
22 11 0.27
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (19 bp):
GTATCGATACCATGATAGA
Found at i:2635341 original size:22 final size:23
Alignment explanation
Indices: 2635310--2635354 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2635300 CGTGATAGAG
* *
2635310 TATCGGTACCCTAGTAT-AGTAT
1 TATCGATACCATAGTATGAGTAT
2635332 TATCGATACCATAGTATGAGTAT
1 TATCGATACCATAGTATGAGTAT
2635355 CGATACTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (23 bp):
TATCGATACCATAGTATGAGTAT
Found at i:2635768 original size:54 final size:54
Alignment explanation
Indices: 2635686--2636257 Score: 844
Period size: 54 Copynumber: 10.6 Consensus size: 54
2635676 CCAAATATGA
2635686 ACTAAGTGTGCAACCCAC-GAAATTCATCATATGTTGATGAATCACCGTTTCGGC
1 ACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAATCACCGTTTCGGC
*
2635740 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTTATGAATCACCGTTTCGGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAATCACCGTTTCGGC
* * * * *
2635794 ACTAAGTGTACAACCCACGGAATTCATCATATGTTGAAGAATCACCATTTTGGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAATCACCGTTTCGGC
* * * *
2635848 ACTAAGTGTGCAACCCACAAAATTCATCAAATATTGATGAATCACCATTTCGGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAATCACCGTTTCGGC
* *
2635902 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATAAATCACCATTTCGGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAATCACCGTTTCGGC
* *
2635956 ACTAACTGTGCAACCCACAGAATTCATCATATGTTGATGAATCACCGTTTCGAC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAATCACCGTTTCGGC
* * *
2636010 ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAATCACGGTTTTGGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAATCACCGTTTCGGC
* *
2636064 ACTAAGTGTGCAACCCAC-GAAATTCATCATATATTGATGAATCACCCTTTCGGC
1 ACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAATCACCGTTTCGGC
* * *
2636118 ACTAAGTGTGCAACCCATAGAATTCATCATATGTTGATGAATCACCGTTTTGGT
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAATCACCGTTTCGGC
* * *
2636172 ACTAAGTGTGCAACCCACAGAATTCATAATATGTTAATGAATCACCGTTTTGGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAATCACCGTTTCGGC
* * *
2636226 ACTATGTGTGCTAA-CCACATAATTCATAATAT
1 ACTAAGTGTGC-AACCCACAGAATTCATCATAT
2636258 TTTTATGAGT
Statistics
Matches: 471, Mismatches: 43, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
54 467 0.99
55 4 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (54 bp):
ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAATCACCGTTTCGGC
Found at i:2642920 original size:54 final size:54
Alignment explanation
Indices: 2642838--2643224 Score: 544
Period size: 54 Copynumber: 7.2 Consensus size: 54
2642828 CAAATAGGAT
*
2642838 CTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAATCACCGTTTCGGCA
1 CTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAATCACCGTTTCGGCA
* *
2642892 CTAAGTGTGCAACCCATGAAATTCATCATATGTTGATGAATCACCGTTTCGACA
1 CTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAATCACCGTTTCGGCA
* *
2642946 CTAAGTGTACAACCCAC-AGAATTCATCATATGTTGATGAATCACCATTTCGGCA
1 CTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAATCACCGTTTCGGCA
* ** * * * *
2643000 CTAAGTGTGTAGTCCAC-AGAATTCATCATATATTGATGAATCACTGTTTCAGTA
1 CTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAATCACCGTTTCGGCA
* * *
2643054 CTAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAATTACCGTTTCGGCA
1 CTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAATCACCGTTTCGGCA
* *
2643108 CTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAATCACCGTTTTGGCA
1 CTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAATCACCGTTTCGGCA
* * * *
2643162 CTAAGTGTGCAAGCCACGAAATTCATCATATATTGATGAATCACCATTTTGGCA
1 CTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAATCACCGTTTCGGCA
*
2643216 CTATGTGTG
1 CTAAGTGTG
2643225 AAAACTATAG
Statistics
Matches: 297, Mismatches: 34, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
53 1 0.00
54 296 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (54 bp):
CTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAATCACCGTTTCGGCA
Found at i:2646637 original size:20 final size:20
Alignment explanation
Indices: 2646588--2646637 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2646578 CAACATTAAT
*
2646588 AACAACAAATTAGCAATATC
1 AACACCAAATTAGCAATATC
* *
2646608 AGCACTAAATTAGCAATATC
1 AACACCAAATTAGCAATATC
2646628 AACACCAAAT
1 AACACCAAAT
2646638 CAGTAGCATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (20 bp):
AACACCAAATTAGCAATATC
Found at i:2658762 original size:23 final size:23
Alignment explanation
Indices: 2658736--2658780 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2658726 TATCTTATAT
*
2658736 GGCACTTAGGTGCATTTCTACGC
1 GGCACTTAGGTGCATTTATACGC
*
2658759 GGCACTTCGGTGCATTTATACG
1 GGCACTTAGGTGCATTTATACG
2658781 AACTGTGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (23 bp):
GGCACTTAGGTGCATTTATACGC
Found at i:2668754 original size:249 final size:252
Alignment explanation
Indices: 2668182--2668851 Score: 816
Period size: 254 Copynumber: 2.6 Consensus size: 252
2668172 GTCCTTTGGG
* * * *
2668182 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAAGTCATTTGTTAGTCTTTCGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGTCAGTCTTTCGAGCAA
* * *
2668247 AATGATAAG-TCTTTCAGGCCATCTATAAGACCTTTGGG-TAGATGATTTCATATAATTTGAAAA
66 GATGATAAGTTC-TTCAGGCCATCTATAAGACCTTTGGGCAAGATGATTTCATATATTTTGAAAA
* * *
2668310 ATGAGAAAGCGATTTTCAAAATTTCTCTTTTAATATTTTTAAATATGAATTTTTTGAAAAGTAAA
130 ATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATATTTTTAAATATGAATTTTTTGAAAAG-AAA
* * * ** *
2668375 GAAGTGATTTCCAAAGTTTCTTGCCTAATAAACTATTTCCAAAATTGGTAAGTTCTTCGGA
194 GAA--GATTTCCAAAGTGTCTTACCTAATAAAATATTTCCAAAATTGGTAAGTAATTCAGA
* * * * *
2668436 CCATCAGTAAGTCTTTCAAGCATGATGATTAAATCTTTCGGGCCGTCTGTCAGTCTTTCGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGTCAGTCTTTCGAGCAA
* * *
2668501 GATGATAAGTTCTTCAGGCCATCTATGAGACC-TTGGGCAATATGCTTTCATATATTTTGAAAAA
66 GATGATAAGTTCTTCAGGCCATCTATAAGACCTTTGGGCAAGATGATTTCATATATTTTGAAAAA
* * * ** * *
2668565 CGAGAAAATGATTTTCAATGTTTCTCATTTGGTATTTTCATAAA-ATGATTTTTTTTATAAA-AA
131 TGAGAAAGTGATTTTCAAAGTTTCTCATTTAATATTTT--TAAATATGAATTTTTTGA-AAAGAA
*
2668628 A-AA-A-TTCCAAAGTGTCTTACCTATTAAAATATTTCCAAAATTGGTAAGTAATTCAGA
193 AGAAGATTTCCAAAGTGTCTTACCTAATAAAATATTTCCAAAATTGGTAAGTAATTCAGA
** * * *
2668685 CCATCAGTAAACCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTATCAATCTTTTGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGTCAGTCTTTCGAGCAA
* * *
2668750 GATGATAAGTCCTTCAGGCCATCTATAAGACCTTTGGGCAAGATGATTTAATATGGTATTTGTAA
66 GATGATAAGTTCTTCAGGCCATCTATAAGACCTTTGGGCAAGATGATTTCATAT-AT-TTTG-AA
2668815 GAGAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAA
128 -A-AATGAGAAAGTGATTTTCAAAGTTTCTCATTTAA
2668852 AAAAAAGATG
Statistics
Matches: 353, Mismatches: 52, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
249 131 0.37
250 19 0.05
251 1 0.00
252 4 0.01
253 9 0.03
254 140 0.40
255 42 0.12
256 7 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (252 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGTCAGTCTTTCGAGCAA
GATGATAAGTTCTTCAGGCCATCTATAAGACCTTTGGGCAAGATGATTTCATATATTTTGAAAAA
TGAGAAAGTGATTTTCAAAGTTTCTCATTTAATATTTTTAAATATGAATTTTTTGAAAAGAAAGA
AGATTTCCAAAGTGTCTTACCTAATAAAATATTTCCAAAATTGGTAAGTAATTCAGA
Found at i:2668773 original size:41 final size:42
Alignment explanation
Indices: 2668697--2668797 Score: 107
Period size: 41 Copynumber: 2.4 Consensus size: 42
2668687 ATCAGTAAAC
* *
2668697 CTTTCGAGCATGATGATTAAATCATTCAGGTCATCTATCAAT
1 CTTTCGAGCAAGATGATTAAATCATTCAGGCCATCTATCAAT
* * * * *
2668739 CTTTTGAGCAAGATGA-TAAGTCCTTCAGGCCATCTATAAGAC
1 CTTTCGAGCAAGATGATTAAATCATTCAGGCCATCTATCA-AT
*
2668781 CTTT-GGGCAAGATGATT
1 CTTTCGAGCAAGATGATT
2668798 TAATATGGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 29 0.59
42 20 0.41
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (42 bp):
CTTTCGAGCAAGATGATTAAATCATTCAGGCCATCTATCAAT
Found at i:2668878 original size:249 final size:243
Alignment explanation
Indices: 2668182--2668880 Score: 645
Period size: 249 Copynumber: 2.8 Consensus size: 243
2668172 GTCCTTTGGG
* * * *
2668182 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAAGTCATTTGTTAGTCTTTCGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGTCAGTCTTTCGAGCAA
* * * *
2668247 AATGATAAGTCTTTCAGGCCATCTATAAGACCTTTGGG-TAGATGATTTCATATAATTTGAAAAA
66 GATGATAAGTCCTTCAGGCCATCTATAAGACCTTTGGGCAAGATGATTTCATATTATTTGAAAAA
* * *
2668311 TGAGAAAGCGATTTTCAAAATTTCTCTTTTAATATTTTTAAATATGAATTTTTTGAAAAGTAAAG
131 TGAGAAAGTGATTTTCAAAGTTTCTCATTTAA-A-----AAA-ATG-A-----TGAAAAG-AAAG
*** * * * * ** *
2668376 --AAGTGATTTCCAAAGTTTCTTGCCTAATAAACTATTTCCAAAATTGGTAAGTTCTTCGGA
182 AAAAAAAAATTCCAAAGTGTCTTACCTAATAAAATATTTCCAAAATTGGTAAGTAATTCAGA
* * * * *
2668436 CCATCAGTAAGTCTTTCAAGCATGATGATTAAATCTTTCGGGCCGTCTGTCAGTCTTTCGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGTCAGTCTTTCGAGCAA
* * * *
2668501 GATGATAAGTTCTTCAGGCCATCTATGAGACC-TTGGGCAATATGCTTTCATA-TATTTTGAAAA
66 GATGATAAGTCCTTCAGGCCATCTATAAGACCTTTGGGCAAGATGATTTCATATTA-TTTGAAAA
* * * * ******* *
2668564 ACGAGAAAATGATTTTCAATGTTTCTCATTTGGTATTTTCATAAAATGAT-TTTTTTTATAAAAA
130 ATGAGAAAGTGATTTTCAAAGTTTCTCA-TT--TA-----AAAAAATGATGAAAAGAAAGAAAAA
*
2668628 AAAATTCCAAAGTGTCTTACCTATTAAAATATTTCCAAAATTGGTAAGTAATTCAGA
187 AAAATTCCAAAGTGTCTTACCTAATAAAATATTTCCAAAATTGGTAAGTAATTCAGA
** * * *
2668685 CCATCAGTAAACCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTATCAATCTTTTGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGTCAGTCTTTCGAGCAA
*
2668750 GATGATAAGTCCTTCAGGCCATCTATAAGACCTTTGGGCAAGATGATTTAATATGGTATTTGTAA
66 GATGATAAGTCCTTCAGGCCATCTATAAGACCTTTGGGCAAGATGATTTCATAT--TATTTG-AA
*
2668815 GAGAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAAAAAAAAGATGGAAAAGAAAGAAAAAAAA
128 -A-AATGAGAAAGTGATTTTCAAAGTTTCTCATTTAAAAAAATGAT-GAAAAGAAAGAAAAAAAA
2668880 A
190 A
2668881 GAAATGAAAG
Statistics
Matches: 354, Mismatches: 70, Indels: 47
0.75 0.15 0.10
Matches are distributed among these distances:
247 9 0.03
249 145 0.41
250 17 0.05
252 6 0.02
253 10 0.03
254 130 0.37
255 31 0.09
256 3 0.01
257 2 0.01
262 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (243 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGTCAGTCTTTCGAGCAA
GATGATAAGTCCTTCAGGCCATCTATAAGACCTTTGGGCAAGATGATTTCATATTATTTGAAAAA
TGAGAAAGTGATTTTCAAAGTTTCTCATTTAAAAAAATGATGAAAAGAAAGAAAAAAAAATTCCA
AAGTGTCTTACCTAATAAAATATTTCCAAAATTGGTAAGTAATTCAGA
Found at i:2668882 original size:14 final size:15
Alignment explanation
Indices: 2668863--2668904 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
2668853 AAAAAGATGG
2668863 AAAAGAAAGAAA-AA
1 AAAAGAAAGAAAGAA
2668877 AAAAGAAATGAAAGAA
1 AAAAGAAA-GAAAGAA
2668893 AAGGAAGAAAGA
1 AA--AAGAAAGA
2668905 GAAATTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.33
15 4 0.17
16 4 0.17
17 2 0.08
18 6 0.25
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (15 bp):
AAAAGAAAGAAAGAA
Found at i:2671404 original size:4 final size:4
Alignment explanation
Indices: 2671395--2671419 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2671385 GAGACTCTAA
2671395 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
2671420 AAAAAGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:2676035 original size:85 final size:85
Alignment explanation
Indices: 2675896--2676267 Score: 464
Period size: 85 Copynumber: 4.4 Consensus size: 85
2675886 CAAGGCGATG
* *
2675896 AGGGTTATCTGTCAAC-AA-ACCTTTGAGTTCGATTACATTCAACTCAAGGGCATATCAAA-TTA
1 AGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACTCAAAGGCATATCAAATTTA
2675958 GCAGCATAGATCAAGGCAAGA
66 -CAGCATAGATCAAGGCAAGA
* * *
2675979 AGGGTTATCTGTCAACAAAGGCCTTCGAGTTCGATTACATTCAACTCAATGACATATCAAATTTA
1 AGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACTCAAAGGCATATCAAATTTA
*
2676044 CAGCATA-ACTCAAGGCAATA
66 CAGCATAGA-TCAAGGCAAGA
* * **
2676064 AGGGTTATCTGTCAACAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCGCATCAAATTTA
1 AGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACTCAAAGGCATATCAAATTTA
* * * *
2676129 TAACATAGCTCAAGGCGAGA
66 CAGCATAGATCAAGGCAAGA
* * * *
2676149 AGGGTTATCTATCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATATA
1 AGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACTCAAAGGCATATCAAATTTA
* * * **
2676214 TAGCATAGCTAAAGGTGAGA
66 CAGCATAGATCAAGGCAAGA
* * *
2676234 AGAGTTATATGTCAACAATGACCTTCGAGTTCGA
1 AGGGTTATCTGTCAACAAAGACCTTCGAGTTCGA
2676268 AATTTATATC
Statistics
Matches: 253, Mismatches: 31, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
83 16 0.06
84 3 0.01
85 231 0.91
86 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (85 bp):
AGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACTCAAAGGCATATCAAATTTA
CAGCATAGATCAAGGCAAGA
Found at i:2676152 original size:170 final size:170
Alignment explanation
Indices: 2675871--2676267 Score: 512
Period size: 170 Copynumber: 2.3 Consensus size: 170
2675861 TAAAAGAACT
* * *
2675871 ATTTACAGTATATCTCAAGGCGATGAGGGTTATCTGTCAAC-AA-ACCTTTGAGTTCGATTACAT
1 ATTTACAGCATAACTCAAGGCGATAAGGGTTATCTGTCAACAAAGACCTTTGAGTTCGATTACAT
* * * * *
2675934 TCAACTCAAGGGCATATCAAATTAGCAGCATAGATCAAGGCAAGAAGGGTTATCTGTCAACAAAG
66 TCAACTCAAAGGCACATCAAATTAGCAACATAGATCAAGGCAAGAAGGGTTATCTATCAACAAAA
* *
2675999 GCCTTCGAGTTCGATTACATTCAACTCAATGACATATCAA
131 ACCTTCGAGTTCGATTACATTCAACTCAAAGACATATCAA
*
2676039 ATTTACAGCATAACTCAAGGCAATAAGGGTTATCTGTCAACAAAGACCTTTGAGTTCGATTACAT
1 ATTTACAGCATAACTCAAGGCGATAAGGGTTATCTGTCAACAAAGACCTTTGAGTTCGATTACAT
* * * * *
2676104 TCAGCTCAAAGGCGCATCAAATTTA-TAACATAGCTCAAGGCGAGAAGGGTTATCTATCAACAAA
66 TCAACTCAAAGGCACATCAAA-TTAGCAACATAGATCAAGGCAAGAAGGGTTATCTATCAACAAA
* *
2676168 AACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAA
130 AACCTTCGAGTTCGATTACATTCAACTCAAAGACATATCAA
* * * * * * * * * *
2676209 ATATATAGCATAGCTAAAGGTGAGAAGAGTTATATGTCAACAATGACCTTCGAGTTCGA
1 ATTTACAGCATAACTCAAGGCGATAAGGGTTATCTGTCAACAAAGACCTTTGAGTTCGA
2676268 AATTTATATC
Statistics
Matches: 197, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
168 37 0.19
169 2 0.01
170 155 0.79
171 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (170 bp):
ATTTACAGCATAACTCAAGGCGATAAGGGTTATCTGTCAACAAAGACCTTTGAGTTCGATTACAT
TCAACTCAAAGGCACATCAAATTAGCAACATAGATCAAGGCAAGAAGGGTTATCTATCAACAAAA
ACCTTCGAGTTCGATTACATTCAACTCAAAGACATATCAA
Found at i:2676318 original size:145 final size:145
Alignment explanation
Indices: 2676122--2676396 Score: 392
Period size: 145 Copynumber: 1.9 Consensus size: 145
2676112 AAGGCGCATC
*
2676122 AAATTTATAACATAGCTCAAGGCGAGAAGGGTTATCTATCAACAAAAACCTTCGAGTTCGATTAC
1 AAATTTATAACATAACTCAAGGCGAGAAGGGTTATCTATCAACAAAAACCTTCGAGTTCGATTAC
* *
2676187 ATTCAGCTCAAAGGCATATCAAATATATAGCATAGCTAAAGGT-GAGAAGAGTTATATGTCAACA
66 ATTCAGCTCAAAGGCATATCAAATATACAGCATAGCTAAA-GTCGAGAAAAGTTATATGTCAACA
2676251 ATGACCTTCGAGTTCG
130 ATGACCTTCGAGTTCG
* * * * * *
2676267 AAATTTATATCATAACTCAAGGCGATAAGGGTTATCTGTCAA-AAAATACCTTTGAGTTTGATTC
1 AAATTTATAACATAACTCAAGGCGAGAAGGGTTATCTATCAACAAAA-ACCTTCGAGTTCGATTA
* * * * *
2676331 CATTCAGCTCAAGGGCATGTCAAATTTACAGCATAGCTTAAGTCGAGAAAAGTTATCTGTCAACA
65 CATTCAGCTCAAAGGCATATCAAATATACAGCATAGCTAAAGTCGAGAAAAGTTATATGTCAACA
2676396 A
130 A
2676397 AAAACTGTCG
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
144 6 0.05
145 108 0.95
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (145 bp):
AAATTTATAACATAACTCAAGGCGAGAAGGGTTATCTATCAACAAAAACCTTCGAGTTCGATTAC
ATTCAGCTCAAAGGCATATCAAATATACAGCATAGCTAAAGTCGAGAAAAGTTATATGTCAACAA
TGACCTTCGAGTTCG
Found at i:2677302 original size:38 final size:37
Alignment explanation
Indices: 2677177--2677311 Score: 173
Period size: 37 Copynumber: 3.5 Consensus size: 37
2677167 ATATATATAT
*
2677177 ATATATATTAAAATATA-TTTTTAGAAAACAATTTTTGAAA
1 ATATATA-TAATATATAGTTTTT-GAAAAC--TTTTTGAAA
* * *
2677217 ATGTATATATTATATAGTTTTTGAAAACGTTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAACTTTTTGAAA
*
2677254 ATATATATAATATATAGTTTTTGAAAACTTTTTTAAAA
1 ATATATATAATATATAGTTTTTGAAAAC-TTTTTGAAA
2677292 ATATATATAATATATAGTTT
1 ATATATATAATATATAGTTT
2677312 GAAAATATTT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
37 34 0.40
38 27 0.32
39 13 0.15
40 11 0.13
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTGAAAACTTTTTGAAA
Found at i:2677333 original size:3 final size:3
Alignment explanation
Indices: 2677325--2677365 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
2677315 AATATTTTTG
2677325 ATT ATT ATT ATT ATT ATT ATTT ATT -TT ATT -TT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT A
2677366 ATTTTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.18
3 25 0.74
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:2677354 original size:5 final size:5
Alignment explanation
Indices: 2677329--2677375 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
2677319 TTTTTGATTA
*
2677329 TTATT ATTATT ATTA-T TTATT TTATT TTATT TTA-T TAATT TTATT TT
1 TTATT -TTATT -TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
2677376 TTTCCAGGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
4 6 0.16
5 22 0.59
6 9 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:2677363 original size:19 final size:20
Alignment explanation
Indices: 2677329--2677375 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
2677319 TTTTTGATTA
*
2677329 TTATTATTATTATTATTTATT
1 TTATT-TTATTATTATTAATT
2677350 TTATTTTATT-TTATTAATT
1 TTATTTTATTATTATTAATT
2677369 TTATTTT
1 TTATTTT
2677376 TTTCCAGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 15 0.60
20 5 0.20
21 5 0.20
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTTATTATTATTAATT
Found at i:2677369 original size:9 final size:9
Alignment explanation
Indices: 2677326--2677378 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
2677316 ATATTTTTGA
2677326 TTATTATTA-
1 TTATT-TTAT
2677335 TTATTATTAT
1 TTATT-TTAT
2677345 TTATTTTATT
1 TTATTTTA-T
2677355 TTATTTTAT
1 TTATTTTAT
*
2677364 TAATTTTAT
1 TTATTTTAT
2677373 TT-TTTT
1 TTATTTT
2677379 CCAGGTCCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
8 4 0.10
9 22 0.55
10 14 0.35
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTATTTTAT
Found at i:2678562 original size:18 final size:19
Alignment explanation
Indices: 2678522--2678569 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
2678512 TAGGTTATTT
*
2678522 TTATTTTTTATTATTACTA
1 TTATTTTTTAATATTACTA
*
2678541 -TATTTTTTAATATT-TTA
1 TTATTTTTTAATATTACTA
*
2678558 TTATTTATTAAT
1 TTATTTTTTAAT
2678570 TTATTTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTTTTTAATATTACTA
Found at i:2679963 original size:28 final size:28
Alignment explanation
Indices: 2679931--2679994 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
2679921 GTGAGGGTTT
2679931 GAACTTAAGACCATTATTAAAGGGTCTA
1 GAACTTAAGACCATTATTAAAGGGTCTA
2679959 GAACTTAAGACCATTATTAAAGGGTCTA
1 GAACTTAAGACCATTATTAAAGGGTCTA
*
2679987 AAACTTAA
1 GAACTTAA
2679995 TACATTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (28 bp):
GAACTTAAGACCATTATTAAAGGGTCTA
Found at i:2684730 original size:22 final size:22
Alignment explanation
Indices: 2684705--2684748 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2684695 TGTTATATTG
2684705 TTTATAACATTTTAGGTCGCGC
1 TTTATAACATTTTAGGTCGCGC
* *
2684727 TTTATAATATTTTAGGTTGCGC
1 TTTATAACATTTTAGGTCGCGC
2684749 CTTTCCTTAA
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:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (22 bp):
TTTATAACATTTTAGGTCGCGC
Found at i:2686050 original size:43 final size:43
Alignment explanation
Indices: 2685943--2686126 Score: 181
Period size: 43 Copynumber: 4.3 Consensus size: 43
2685933 TGGTAACAAA
** * * * *
2685943 AAACGCCGCAATAGGTAACGATATATAGTGGCG-TTTGTCCAAC
1 AAACGCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTTCC-AC
*
2685986 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCAC
1 AAACGCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTTCCAC
* * * *
2686029 AAACGCCGCAATAGGTATTGAGATTTAACAGTGTTTTTTTACAC
1 AAACGCCGCAATAGGTATTGAGATTTAGCGGCG-TTTTTTCCAC
* * * * * *
2686073 AAACACCGCAATATGTCTTGAGATTTTGCGGCATTTTTCCCAC
1 AAACGCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTTCCAC
*
2686116 AAACGCTGCAA
1 AAACGCCGCAA
2686127 AAGATCTGGT
Statistics
Matches: 115, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
43 75 0.65
44 40 0.35
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTTCCAC
Found at i:2686082 original size:44 final size:43
Alignment explanation
Indices: 2685984--2686098 Score: 149
Period size: 44 Copynumber: 2.7 Consensus size: 43
2685974 CGTTTGTCCA
* * * *
2685984 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC
1 ACAAACGCCGCAATAGGTATTGAGATTTAACAGCGTTTTTTAC
*
2686027 ACAAACGCCGCAATAGGTATTGAGATTTAACAGTGTTTTTTTAC
1 ACAAACGCCGCAATAGGTATTGAGATTTAACAGCG-TTTTTTAC
* * *
2686071 ACAAACACCGCAATATGTCTTGAGATTT
1 ACAAACGCCGCAATAGGTATTGAGATTT
2686099 TGCGGCATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
43 31 0.49
44 32 0.51
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTATTGAGATTTAACAGCGTTTTTTAC
Found at i:2689022 original size:41 final size:41
Alignment explanation
Indices: 2688867--2689167 Score: 365
Period size: 41 Copynumber: 7.3 Consensus size: 41
2688857 TTGTGTTTAC
*
2688867 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
2688908 AAATG-CACTGAAGTACGAGTCTTTAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
2688948 AAATGCCACTGAAGT-TGAGTCTATAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
2688988 AAACGCCACTGAATTACAAGTCTTTAGCAGCGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A
* *
2689030 CAAACGCCACTAAAGTACGAGTCGTTAGTGGCGTTTGTATAA
1 -AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
2689072 AAACGCCACTAAAGTACGAGTCGTTAGTGGCGTTTGTACAAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTA-TAA
*
2689114 AAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
2689155 AAAC-CCTACTAAA
1 AAACGCC-ACTAAA
2689168 TGATTTTAGT
Statistics
Matches: 225, Mismatches: 29, Indels: 12
0.85 0.11 0.05
Matches are distributed among these distances:
40 73 0.32
41 80 0.36
42 39 0.17
43 33 0.15
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:2689149 original size:83 final size:82
Alignment explanation
Indices: 2688871--2689167 Score: 375
Period size: 83 Copynumber: 3.6 Consensus size: 82
2688861 GTTTACAAAC
* * *
2688871 GCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAAAAATG-CACTGAAGTACGAGTCTTTAGC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGC
* *
2688935 GACGTTTGTATAAAAAT
66 GGCGTTTGTAAAAAAAT
* * * * * * *
2688952 GCCACTGAAGT-TGAGTCTATAGCGGCGTTTATATAAAAACGCCACTGAATTACAAGTCTTTAGC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGC
* *
2689016 AGCGTTTGTAAACACAAAC
66 GGCGTTTGTAAA-A-AAAT
* * * *
2689035 GCCACTAAAGTACGAGTCGTTAGTGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCGTTAGT
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGC
2689100 GGCGTTTGTACAAAAAAT
66 GGCGTTTGTA-AAAAAAT
2689118 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC-CCTACTAAA
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCC-ACTAAA
2689168 TGATTTTAGT
Statistics
Matches: 183, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
80 25 0.14
81 39 0.21
82 3 0.02
83 61 0.33
84 53 0.29
85 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (82 bp):
GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGC
GGCGTTTGTAAAAAAAT
Found at i:2689268 original size:42 final size:40
Alignment explanation
Indices: 2689209--2689411 Score: 178
Period size: 41 Copynumber: 4.9 Consensus size: 40
2689199 GACTATATAT
*
2689209 TTAACA-TTTTGCGGCGTTTATACAAAAAAATGCCACTATTGA
1 TTAACACTATTGCGGCGTTT-T--AAAAAAATGCCACTATTGA
* * * *
2689251 TT-ACATTATTGTGGCGTTTGTTAAAAAACGCCACTATTGA
1 TTAACACTATTGCGGCGTTT-TAAAAAAATGCCACTATTGA
* ** *
2689291 TTAAAACTATTGCGGCGTTTTTGTAAAAACGCCACTATTGA
1 TTAACACTATTGCGGCG-TTTTAAAAAAATGCCACTATTGA
* ** *
2689332 TTAACACTATTGCGCCGTTTGTCTAAAAATGCCACTATTTA
1 TTAACACTATTGCGGCGTTT-TAAAAAAATGCCACTATTGA
*
2689373 TTATA-AATATTGCGGCGTTTTAAGAATAAATGCCACTAT
1 TTA-ACACTATTGCGGCGTTTTAA-AA-AAATGCCACTAT
2689412 ATGTGTAATC
Statistics
Matches: 135, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
40 23 0.17
41 82 0.61
42 30 0.22
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (40 bp):
TTAACACTATTGCGGCGTTTTAAAAAAATGCCACTATTGA
Found at i:2689277 original size:41 final size:40
Alignment explanation
Indices: 2689233--2689411 Score: 184
Period size: 41 Copynumber: 4.4 Consensus size: 40
2689223 CGTTTATACA
* * *
2689233 AAAAAATGCCACTATTGATT-ACATTATTGTGGCGTTTGTT
1 AAAAAATGCCACTATTGATTAAAACTATTGCGGCGTTT-TT
*
2689273 AAAAAACGCCACTATTGATTAAAACTATTGCGGCGTTTTT
1 AAAAAATGCCACTATTGATTAAAACTATTGCGGCGTTTTT
* * * *
2689313 GTAAAAACGCCACTATTGATTAACACTATTGCGCCGTTTGTCT
1 -AAAAAATGCCACTATTGATTAAAACTATTGCGGCGTTT-T-T
* *
2689356 -AAAAATGCCACTATTTATTATAAA-TATTGCGGCGTTTTA
1 AAAAAATGCCACTATTGATTA-AAACTATTGCGGCGTTTTT
2689395 AGAATAAATGCCACTAT
1 A-AA-AAATGCCACTAT
2689412 ATGTGTAATC
Statistics
Matches: 119, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
40 22 0.18
41 81 0.68
42 15 0.13
43 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (40 bp):
AAAAAATGCCACTATTGATTAAAACTATTGCGGCGTTTTT
Found at i:2689366 original size:82 final size:81
Alignment explanation
Indices: 2689234--2689393 Score: 225
Period size: 82 Copynumber: 2.0 Consensus size: 81
2689224 GTTTATACAA
* * * *
2689234 AAAAATGCCACTATTGATTACATTATTGTGGCGTTTGTTAAAAAACGCCACTATTGATTA-AAAC
1 AAAAACGCCACTATTGATTACACTATTGCGCCGTTTGTTAAAAAACGCCACTATTGATTATAAA-
2689298 TATTGCGGCGTTTTTGT
65 TATTGCGGCGTTTTTGT
* *
2689315 AAAAACGCCACTATTGATTAACACTATTGCGCCGTTTGTCT-AAAAATGCCACTATTTATTATAA
1 AAAAACGCCACTATTGATT-ACACTATTGCGCCGTTTGT-TAAAAAACGCCACTATTGATTATAA
2689379 ATATTGCGGCGTTTT
64 ATATTGCGGCGTTTT
2689394 AAGAATAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
81 18 0.26
82 48 0.69
83 4 0.06
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (81 bp):
AAAAACGCCACTATTGATTACACTATTGCGCCGTTTGTTAAAAAACGCCACTATTGATTATAAAT
ATTGCGGCGTTTTTGT
Found at i:2689465 original size:42 final size:41
Alignment explanation
Indices: 2689419--2689576 Score: 171
Period size: 42 Copynumber: 3.8 Consensus size: 41
2689409 TATATGTGTA
*
2689419 ATCTATTACGGCGTTTGTGGTTGAAACGCCGCTAATTTACC
1 ATCTATTACGGCGTTTGTGGTTAAAACGCCGCTAATTTACC
* * *
2689460 GATCTATTGCGGCGTTT-TGGCTAAAACGCCACTATATGTTA--
1 -ATCTATTACGGCGTTTGTGGTTAAAACGCCGCTA-AT-TTACC
* *
2689501 ATCTATTGCGGCGTTTGTGG-TATAAATGCCGCTAATTTACC
1 ATCTATTACGGCGTTTGTGGTTA-AAACGCCGCTAATTTACC
* *
2689542 ACTCTATTACGGCGTTTGTTGTAAAAACGCCGCTA
1 A-TCTATTACGGCGTTTGTGGTTAAAACGCCGCTA
2689577 TATATCAACT
Statistics
Matches: 98, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
39 3 0.03
40 20 0.20
41 27 0.28
42 44 0.45
43 4 0.04
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (41 bp):
ATCTATTACGGCGTTTGTGGTTAAAACGCCGCTAATTTACC
Found at i:2689518 original size:82 final size:83
Alignment explanation
Indices: 2689404--2689600 Score: 249
Period size: 82 Copynumber: 2.4 Consensus size: 83
2689394 AAGAATAAAT
*
2689404 GCCACTATATGTGTAATCTATTACGGCGTTTGTGGT-TGAAACGCCGCTAATTTACCGA-TCTAT
1 GCCACTATATGT-TAATCTATTGCGGCGTTTGTGGTAT-AAACGCCGCTAATTTACC-ACTCTAT
*
2689467 TGCGGCGTTT-TGGCT-AAAAC
63 TACGGCGTTTGTGG-TAAAAAC
*
2689487 GCCACTATATGTTAATCTATTGCGGCGTTTGTGGTATAAATGCCGCTAATTTACCACTCTATTAC
1 GCCACTATATGTTAATCTATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTCTATTAC
*
2689552 GGCGTTTGTTGTAAAAAC
66 GGCGTTTGTGGTAAAAAC
* * * *
2689570 GCCGCTATATATCAACTCTATTGCAGCGTTT
1 GCCACTATATGTTAA-TCTATTGCGGCGTTT
2689601 TTACAACAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
81 1 0.01
82 54 0.53
83 32 0.32
84 14 0.14
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (83 bp):
GCCACTATATGTTAATCTATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTCTATTAC
GGCGTTTGTGGTAAAAAC
Found at i:2689588 original size:42 final size:41
Alignment explanation
Indices: 2689297--2689600 Score: 163
Period size: 42 Copynumber: 7.3 Consensus size: 41
2689287 TTGATTAAAA
* * * *
2689297 CTATTGCGGCGTTT-TTGTAAAAACGCCACTAT-TGATTAACA
1 CTATTGCGGCGTTTGTGGTAAAAACGCCGCTATAT-ATCAA-T
* * * * * * *
2689338 CTATTGCGCCGTTTGT-CTAAAAATGCCACTATTTATTATAA
1 CTATTGCGGCGTTTGTGGTAAAAACGCCGCTATATATCA-AT
* * * * * *
2689379 ATATTGCGGCGTTT-TAAG-AATAAATGCCACTATATGTGTAAT
1 CTATTGCGGCGTTTGT-GGTAA-AAACGCCGCTATATAT-CAAT
* ** * * *
2689421 CTATTACGGCGTTTGTGGTTGAAACGCCGCTAATTTACCGAT
1 CTATTGCGGCGTTTGTGGTAAAAACGCCGCT-ATATATCAAT
* * *
2689463 CTATTGCGGCGTTT-TGGCT-AAAACGCCACTATATGTTAAT
1 CTATTGCGGCGTTTGTGG-TAAAAACGCCGCTATATATCAAT
* * * * *
2689503 CTATTGCGGCGTTTGTGGTATAAATGCCGCTAATTTACCACT
1 CTATTGCGGCGTTTGTGGTAAAAACGCCGCT-ATATATCAAT
* *
2689545 CTATTACGGCGTTTGTTGTAAAAACGCCGCTATATATCAACT
1 CTATTGCGGCGTTTGTGGTAAAAACGCCGCTATATATCAA-T
*
2689587 CTATTGCAGCGTTT
1 CTATTGCGGCGTTT
2689601 TTACAACAAA
Statistics
Matches: 202, Mismatches: 46, Indels: 29
0.73 0.17 0.10
Matches are distributed among these distances:
40 21 0.10
41 75 0.37
42 100 0.50
43 6 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (41 bp):
CTATTGCGGCGTTTGTGGTAAAAACGCCGCTATATATCAAT
Found at i:2689590 original size:124 final size:125
Alignment explanation
Indices: 2689297--2689601 Score: 295
Period size: 124 Copynumber: 2.4 Consensus size: 125
2689287 TTGATTAAAA
* * * * * *
2689297 CTATTGCGGCGTTT-TTGTAAAAACGCCACTATTGATTAACACTATTGCGCCG-TTTGTCTAAAA
1 CTATTACGGCGTTTGTTGTAAAAACGCCGCTATT-ATCAACTCTATTGCGGCGTTTTGGCTAAAA
* *
2689360 ATGCCACTATTTATTATAAATATTGCGGCGTTTTAAGAATAAATGCCACTATATGTGTAAT
65 ACGCCACTATATATTATAAATATTGCGGCGTTTTAAGAATAAATGCCACTATATGTGTAAT
* ** * *
2689421 CTATTACGGCGTTTGTGGTTGAAACGCCGCTAATTTACCGA-TCTATTGCGGCGTTTTGGCT-AA
1 CTATTACGGCGTTTGTTGTAAAAACGCCGCT-A-TTATCAACTCTATTGCGGCGTTTTGGCTAAA
* ** * * *
2689484 AACGCCACTATATGTTA-ATCTATTGCGGCGTTTGT-GGTATAAATGCCGCTA-AT-T-TACCAC
64 AACGCCACTATATATTATAAATATTGCGGCGTTT-TAAGAATAAATGCCACTATATGTGTA--A-
2689544 T
125 T
*
2689545 CTATTACGGCGTTTGTTGTAAAAACGCCGCTATATATCAACTCTATTGCAGCGTTTT
1 CTATTACGGCGTTTGTTGTAAAAACGCCGCTAT-TATCAACTCTATTGCGGCGTTTT
2689602 TACAACAAAC
Statistics
Matches: 146, Mismatches: 25, Indels: 20
0.76 0.13 0.10
Matches are distributed among these distances:
121 2 0.01
122 2 0.01
123 8 0.05
124 84 0.58
125 39 0.27
126 9 0.06
127 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (125 bp):
CTATTACGGCGTTTGTTGTAAAAACGCCGCTATTATCAACTCTATTGCGGCGTTTTGGCTAAAAA
CGCCACTATATATTATAAATATTGCGGCGTTTTAAGAATAAATGCCACTATATGTGTAAT
Found at i:2690571 original size:26 final size:29
Alignment explanation
Indices: 2690504--2690574 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
2690494 CAGTCCCCAC
2690504 GTAGGTCGCCATGCACTCCCATCGACCTGT
1 GTAGGTCGCCATGCACTCCCATC-ACCTGT
* * *
2690534 ATAGGTTGCCATGCACTCCCA-C-CGTG-
1 GTAGGTCGCCATGCACTCCCATCACCTGT
2690560 GTAGGTCGCCATGCA
1 GTAGGTCGCCATGCA
2690575 TGCCATTAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 13 0.36
27 3 0.08
29 1 0.03
30 19 0.53
ACGTcount: A:0.18, C:0.34, G:0.25, T:0.23
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCCATCACCTGT
Found at i:2691010 original size:30 final size:30
Alignment explanation
Indices: 2690964--2691032 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
2690954 AATTGCATGC
*
2690964 ATGGCGACCTATACAGGTCGCTAGGAGTGA
1 ATGGCGACCCATACAGGTCGCTAGGAGTGA
* * *
2690994 ATGGTGACCCATACAGGTCGCTGGGAGTGT
1 ATGGCGACCCATACAGGTCGCTAGGAGTGA
2691024 ATGGCGACC
1 ATGGCGACC
2691033 TACATAGGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.22, G:0.35, T:0.20
Consensus pattern (30 bp):
ATGGCGACCCATACAGGTCGCTAGGAGTGA
Found at i:2692276 original size:25 final size:25
Alignment explanation
Indices: 2692234--2692289 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
2692224 CGACATAGGC
2692234 ATAATGGTGCCATCATTGGGCA-CTA
1 ATAATGGTGCCATCATTGGGCATC-A
* * * *
2692259 ATAATGTTGTCATTATTGTGCATCA
1 ATAATGGTGCCATCATTGGGCATCA
2692284 ATAATG
1 ATAATG
2692290 CATCTATCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (25 bp):
ATAATGGTGCCATCATTGGGCATCA
Found at i:2692491 original size:13 final size:13
Alignment explanation
Indices: 2692473--2692497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2692463 TTTAATGTAT
2692473 ATTTTATTGTTTC
1 ATTTTATTGTTTC
2692486 ATTTTATTGTTT
1 ATTTTATTGTTT
2692498 TTATTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (13 bp):
ATTTTATTGTTTC
Found at i:2692871 original size:111 final size:104
Alignment explanation
Indices: 2692548--2693155 Score: 410
Period size: 102 Copynumber: 5.8 Consensus size: 104
2692538 TGTGTTCACA
* *
2692548 TGGTTTGGTAAGTTT--TTT-AAATTT-TTGTGTAATTTTATTTTTTATTTTAAATA-ATAATTA
1 TGGTTTGGTAAGTTTAGTTTAAAATTTATTGT-TTA-TTTATTTTTTATTGTAAATATA-AATTA
* * *
2692608 TTAGACTATTTATTTTGATTTTACATATTAAGTTGTATTTGAG
63 TTAGACTATTTATTTTGATTTTATATATTAA-ATATATTTGAG
* *
2692651 TAGTTTGGTAAGTTTAG-TTAAAA-TTA-TATTT-TTTATTTTTTATTG-AGCAATATAAATTAT
1 TGGTTTGGTAAGTTTAGTTTAAAATTTATTGTTTATTTATTTTTTATTGTA--AATATAAATTAT
* *
2692711 TAGACTAATTATTTT--TTTTATAGATTAAATCATATTTGAG
64 TAGACTATTTATTTTGATTTTATATATTAAAT-ATATTTGAG
2692751 TGGTTTGGTAAGTTTAGTTTAAAATTTATTGTTTAGGGTTTAGTGTTTTTATTGTAAATATAAAT
1 TGGTTTGGTAAGTTTAGTTTAAAATTTATTGTTTA---TTTA-T-TTTTTATTGTAAATATAAAT
**
2692816 TAATTAGACTATTTATTTTGATTTTATATATTAAACTATATTCAAG
61 T-ATTAGACTATTTATTTTGATTTTATATATTAAA-TATATTTGAG
* * * * * *
2692862 TGGTTTGGTAATTTTAATTT-AAATTT-TGTGTAATT-TTTAGCATAATTGTTATTTTTAATTTA
1 TGGTTTGGTAAGTTTAGTTTAAAATTTAT-TGT--TTATTT---AT--TTTTTATTGTAAATATA
* * * *
2692924 AATTCTAATTAGTAAACTATTTATTTTTTATTTTACATATTAAGTTGTATTTGAG
58 AA-T-T-ATTAG---ACTATTTA-TTTTGATTTTATATATTAA-ATATATTTGAG
* * *
2692979 TAGTTTTGTAAGTTTAGTTT-AAA-TT-TTATTT-TTTATTTTTTATTG-AGTAATATAAATTAT
1 TGGTTTGGTAAGTTTAGTTTAAAATTTATTGTTTATTTATTTTTTATTGTA--AATATAAATTAT
* * * * * * *
2693039 TGGACTATTTATTTTAATATTACAGATTTAATCGTATTTGAG
64 TAGACTATTTATTTTGATTTTATATATTAAAT-ATATTTGAG
* *
2693081 TGGTTTGGTAAGTTTAGTCT--AA---A-T-TTTA-TTA-TTTTTGTTGTAAATATAAATTAATT
1 TGGTTTGGTAAGTTTAGTTTAAAATTTATTGTTTATTTATTTTTTATTGTAAATATAAATT-ATT
2693137 AGACTATTTATTTTGATTT
65 AGACTATTTATTTTGATTT
2693156 AACAATTTTT
Statistics
Matches: 412, Mismatches: 50, Indels: 92
0.74 0.09 0.17
Matches are distributed among these distances:
96 10 0.02
97 27 0.07
98 7 0.02
99 2 0.00
100 36 0.09
101 22 0.05
102 68 0.17
103 28 0.07
104 6 0.01
105 3 0.01
106 4 0.01
107 5 0.01
108 22 0.05
109 33 0.08
110 13 0.03
111 54 0.13
112 4 0.01
113 12 0.03
115 2 0.00
116 11 0.03
117 43 0.10
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (104 bp):
TGGTTTGGTAAGTTTAGTTTAAAATTTATTGTTTATTTATTTTTTATTGTAAATATAAATTATTA
GACTATTTATTTTGATTTTATATATTAAATATATTTGAG
Found at i:2697691 original size:19 final size:19
Alignment explanation
Indices: 2697667--2697705 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2697657 ATTATATTCA
* *
2697667 ATTTTTTGTGATAAGTTTT
1 ATTTTTAGTGATAAATTTT
*
2697686 ATTTTTAGTTATAAATTTT
1 ATTTTTAGTGATAAATTTT
2697705 A
1 A
2697706 ATTATATTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (19 bp):
ATTTTTAGTGATAAATTTT
Found at i:2702087 original size:190 final size:189
Alignment explanation
Indices: 2701697--2702091 Score: 473
Period size: 190 Copynumber: 2.1 Consensus size: 189
2701687 GGTGACATTA
* * *
2701697 TATATAATGATGTTATGCATAATCATCATTCATAATATTATTAGTTAATGATATATTATGTCACT
1 TATATAGTGATGTTATGCATAAACATCATTCATAATATTATTAGTAAATGATATATTATGTCACT
* **
2701762 AAAAATGTGTATCTCTTTAGTCACATATAAGTTGATTTTAATGTATTATTTGTGACAATATAAAT
66 AAAAATGTGTATCTCTTTAGTCACATATAAGTTGATTTTAATATATTATCAGTGACAATATAAAT
* **
2701827 AATCAGTAATGGAATCTTATTTAATTTAGTAACGTAACTAACTGTCATATAATATAAAT
131 AATCAGTAATGAAATCTTATACAATTTAGTAACGTAACTAACTGTCATATAATATAAAT
* * *
2701886 CATAAAGTGATGTTATGCATAAACATCATTCATAATATTATTAGGTAACAT-TTATATTATGTCA
1 TATATAGTGATGTTATGCATAAACATCATTCATAATATTATTA-GTAA-ATGATATATTATGTCA
* * **
2701950 CTAAAAATGTGAATATCTTTTTCA-TCACATATATGTTGATTTTAATATATTATCAGTGATGATA
64 CTAAAAATGTG--TATCTCTTT-AGTCACATATAAGTTGATTTTAATATATTATCAGTGACAATA
* * * *
2702014 TAAATCATCCA-TAATGAAAT-TTA-ACAATTTAGTGACAG-AA-TTACTTGTCAT-TGAATATC
126 TAAATAAT-CAGTAATGAAATCTTATACAATTTAGTAAC-GTAACTAAC-TGTCATAT-AATATA
2702073 AAT
187 AAT
2702076 TATATAGTGATGTTAT
1 TATATAGTGATGTTAT
2702092 ATATAAATGT
Statistics
Matches: 175, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
189 43 0.25
190 66 0.38
191 6 0.03
192 57 0.33
193 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (189 bp):
TATATAGTGATGTTATGCATAAACATCATTCATAATATTATTAGTAAATGATATATTATGTCACT
AAAAATGTGTATCTCTTTAGTCACATATAAGTTGATTTTAATATATTATCAGTGACAATATAAAT
AATCAGTAATGAAATCTTATACAATTTAGTAACGTAACTAACTGTCATATAATATAAAT
Done.