Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 62 of 333
Found at i:18444163 original size:17 final size:15
Alignment explanation
Indices: 18444096--18444179 Score: 50
Period size: 16 Copynumber: 5.3 Consensus size: 15
18444086 GTGTATGTAT
18444096 TATA-TATATTTTTA
1 TATATTATATTTTTA
* *
18444110 -ATACTATATTATGTA
1 TATATTATATT-TTTA
18444125 TATATTATATTATATATA
1 TATATTATATT-T-T-TA
18444143 TATAGTTATTATATTTT-
1 TATA-TTA-TAT-TTTTA
18444160 TATATATATATTTTTA
1 TATAT-TATATTTTTA
18444176 -ATAT
1 TATAT
18444180 CACATTATTC
Statistics
Matches: 57, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
13 3 0.05
14 6 0.11
15 11 0.19
16 15 0.26
17 6 0.11
18 7 0.12
19 4 0.07
20 4 0.07
21 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (15 bp):
TATATTATATTTTTA
Found at i:18444380 original size:3 final size:3
Alignment explanation
Indices: 18444372--18444408 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
18444362 TTCTACGTTG
18444372 TAT TAT TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
18444409 CATTGTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:18444951 original size:133 final size:133
Alignment explanation
Indices: 18444711--18444951 Score: 365
Period size: 133 Copynumber: 1.8 Consensus size: 133
18444701 AACGGAGACG
* * *
18444711 ATGTTCGATGTTTAGCAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCTTGTTTGC
1 ATGTTCGACGTTCAGCAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGC
* * * * **
18444776 CCAAAATAATCGGATGTCTCTTTAGAATTTCGTTCATGTTTTCTAAAAACTTTTTAAATACGAAG
66 CCAAAATAATCGAATATCCCTTTAGAATTTCATTCACATTTTCTAAAAACTTTTTAAATACGAAG
18444841 GAA
131 GAA
* *
18444844 ATGTTCGACGTTCGGCAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGT
1 ATGTTCGACGTTCAGCAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGC
* *
18444909 GCAAAATAATCGAATATCCCTTTGGAATTTCATTCACATTTTC
66 CCAAAATAATCGAATATCCCTTTAGAATTTCATTCACATTTTC
18444952 CAAAGCGAGA
Statistics
Matches: 95, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
133 95 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (133 bp):
ATGTTCGACGTTCAGCAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGC
CCAAAATAATCGAATATCCCTTTAGAATTTCATTCACATTTTCTAAAAACTTTTTAAATACGAAG
GAA
Found at i:18445957 original size:2 final size:2
Alignment explanation
Indices: 18445950--18445974 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18445940 TTGGAGTAAA
18445950 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
18445975 AAAGTAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18448351 original size:7 final size:6
Alignment explanation
Indices: 18448330--18448364 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
18448320 CAAAGATTCA
18448330 AAAAAT -AAAAT AAAAAT AAAAAT AAAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAA
18448365 GTTAAAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:18448351 original size:12 final size:13
Alignment explanation
Indices: 18448329--18448364 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
18448319 GCAAAGATTC
18448329 AAAAAAT-AAAAT
1 AAAAAATAAAAAT
18448341 -AAAAATAAAAAT
1 AAAAAATAAAAAT
18448353 AAAAAATAAAAA
1 AAAAAATAAAAA
18448365 GTTAAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 5 0.23
13 11 0.50
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:18452085 original size:12 final size:12
Alignment explanation
Indices: 18452068--18452099 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
18452058 AAAAAATAAT
18452068 ATAATATTTATA
1 ATAATATTTATA
18452080 ATAATATTTATA
1 ATAATATTTATA
18452092 ATATATAT
1 ATA-ATAT
18452100 AACCTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATAATATTTATA
Found at i:18452250 original size:21 final size:20
Alignment explanation
Indices: 18452226--18452264 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
18452216 AAAAAAAAGC
18452226 TATAATATTTTTATGAATAAA
1 TATAATATTTTTAT-AATAAA
*
18452247 TATATTATTTTTATAATA
1 TATAATATTTTTATAATA
18452265 TATAGCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TATAATATTTTTATAATAAA
Found at i:18453070 original size:14 final size:15
Alignment explanation
Indices: 18453051--18453083 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
18453041 ATTAAATAAA
18453051 AATTCAAATTG-ATT
1 AATTCAAATTGAATT
*
18453065 AATTCAACTTGAATT
1 AATTCAAATTGAATT
18453080 AATT
1 AATT
18453084 ACGGAGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (15 bp):
AATTCAAATTGAATT
Found at i:18458565 original size:32 final size:32
Alignment explanation
Indices: 18458524--18458586 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
18458514 ACTCTACGAG
18458524 TTAGATTTTGGAAAGGGTTTTTTTCTCGTGCT
1 TTAGATTTTGGAAAGGGTTTTTTTCTCGTGCT
18458556 TTAGATTTTGGAAAGGGTTTTTTTCTCGTGC
1 TTAGATTTTGGAAAGGGTTTTTTTCTCGTGC
18458587 AATATGTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.16, C:0.10, G:0.25, T:0.49
Consensus pattern (32 bp):
TTAGATTTTGGAAAGGGTTTTTTTCTCGTGCT
Found at i:18460348 original size:30 final size:30
Alignment explanation
Indices: 18460284--18460347 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
18460274 GTCAATATTC
18460284 AAAAATATATGAGTTACTTTTAATAATTAT
1 AAAAATATATGAGTTACTTTTAATAATTAT
* * *
18460314 AAAAATATCTGTA-TTATTTTTAA-AATTTT
1 AAAAATATATG-AGTTACTTTTAATAATTAT
18460343 AAAAA
1 AAAAA
18460348 AATTAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 10 0.33
30 19 0.63
31 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (30 bp):
AAAAATATATGAGTTACTTTTAATAATTAT
Found at i:18464594 original size:18 final size:18
Alignment explanation
Indices: 18464571--18464606 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
18464561 AACTACTGGC
18464571 AAAATAT-TTATAAAATTA
1 AAAATATGTT-TAAAATTA
18464589 AAAATATGTTTAAAATTA
1 AAAATATGTTTAAAATTA
18464607 TTGTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
AAAATATGTTTAAAATTA
Found at i:18464613 original size:13 final size:12
Alignment explanation
Indices: 18464586--18464621 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
18464576 ATTTATAAAA
18464586 TTAAAAATATGT
1 TTAAAAATATGT
*
18464598 TTAAAATTATTGT
1 TTAAAAATA-TGT
18464611 TTAAAAATATG
1 TTAAAAATATG
18464622 ATTATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TTAAAAATATGT
Found at i:18464874 original size:67 final size:67
Alignment explanation
Indices: 18464794--18464930 Score: 247
Period size: 67 Copynumber: 2.0 Consensus size: 67
18464784 TATAAAGCCA
18464794 AAGCAAGCCTGAAATTAGTCAATTTCGAATACACCAATTTTAAGTCAAGAAACAGGCAGCGCAAT
1 AAGCAAGCCTGAAATTAGTCAATTTCGAATACACCAATTTTAAGTCAAGAAACAGGCAGCGCAAT
18464859 GG
66 GG
* * *
18464861 AAGCAAGCTTGAAATTAGTCAATTTCGAATACGCCTATTTTAAGTCAAGAAACAGGCAGCGCAAT
1 AAGCAAGCCTGAAATTAGTCAATTTCGAATACACCAATTTTAAGTCAAGAAACAGGCAGCGCAAT
18464926 GG
66 GG
18464928 AAG
1 AAG
18464931 TTAAGAGAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (67 bp):
AAGCAAGCCTGAAATTAGTCAATTTCGAATACACCAATTTTAAGTCAAGAAACAGGCAGCGCAAT
GG
Found at i:18468128 original size:20 final size:21
Alignment explanation
Indices: 18468105--18468148 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18468095 CTCTCTTTTC
18468105 TTTTCTTTT-ACATTTTTCTT
1 TTTTCTTTTGACATTTTTCTT
**
18468125 TTTTCTTTTGATTTTTTTCTT
1 TTTTCTTTTGACATTTTTCTT
18468146 TTT
1 TTT
18468149 GACTGTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTGACATTTTTCTT
Found at i:18470133 original size:18 final size:18
Alignment explanation
Indices: 18470110--18470147 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
18470100 ATTACACATG
18470110 TCGTCTTTTGAATCATAC
1 TCGTCTTTTGAATCATAC
18470128 TCGTCTTTTGAATCATAC
1 TCGTCTTTTGAATCATAC
18470146 TC
1 TC
18470148 ACATTTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (18 bp):
TCGTCTTTTGAATCATAC
Found at i:18472256 original size:22 final size:23
Alignment explanation
Indices: 18472231--18472276 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
18472221 CAACCAAATC
18472231 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
18472253 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
18472276 A
1 A
18472277 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:18472282 original size:23 final size:23
Alignment explanation
Indices: 18472238--18472282 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
18472228 ATCAATTCAA
*
18472238 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
18472261 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
18472283 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:18485326 original size:22 final size:22
Alignment explanation
Indices: 18485301--18485345 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
18485291 GTAAAAACTG
18485301 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
18485323 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
18485345 T
1 T
18485346 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:18489107 original size:22 final size:22
Alignment explanation
Indices: 18489079--18489123 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
18489069 AGGGGGAGTG
18489079 TAGGAATATTCTGT-GAATATTT
1 TAGGAATATTCTGTAG-ATATTT
*
18489101 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAGATATTT
18489123 T
1 T
18489124 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAGATATTT
Found at i:18496049 original size:356 final size:356
Alignment explanation
Indices: 18495396--18496458 Score: 2099
Period size: 356 Copynumber: 3.0 Consensus size: 356
18495386 TTCAAAACTC
18495396 AACCTTATCCTGCATGCATAAAATCAAATATATGATCTCATGGAAACAGAAATTAAATCATCTAT
1 AACCTTATCCTGCATGCATAAAATCAAATATATGATCTCATGGAAACAGAAATTAAATCATCTAT
*
18495461 CCCATAATGAGAATTGTCCCACCATTCTTTCTTCGTCTATAGGGAAGGTGTGGTAAGAAGTAAAA
66 CCCATAATGAGAATTGTCCCACCATTCTTTCTTCGTCTATAGGGAAGGTGTGGTAACAAGTAAAA
18495526 AAAAAAAAAAAAACAGCATCAAGAAGCAAATAAAATAACAGCATAGCCCAAAAAACTAATATGCT
131 AAAAAAAAAAAAACAGCATCAAGAAGCAAATAAAATAACAGCATAGCCCAAAAAACTAATATGCT
18495591 TCAATACATCTTCTAGGGTACAACATATCATGATACTTGTAACAAAGTAAAAAACCTTTCACCTT
196 TCAATACATCTTCTAGGGTACAACATATCATGATACTTGTAACAAAGTAAAAAACCTTTCACCTT
18495656 ATGCAACCAATTTTACTCCACAAAAGGAATGGACAAGGACTTTCTATTATTTCTACAAATTTACA
261 ATGCAACCAATTTTACTCCACAAAAGGAATGGACAAGGACTTTCTATTATTTCTACAAATTTACA
18495721 TCTATTGGTTCTTGAGCAATGAAATTTACTA
326 TCTATTGGTTCTTGAGCAATGAAATTTACTA
18495752 AACCTTATCCTGCATGCATAAAATCAAATATATGATCTCATGGAAACAGAAATTAAATCATCTAT
1 AACCTTATCCTGCATGCATAAAATCAAATATATGATCTCATGGAAACAGAAATTAAATCATCTAT
18495817 CCCATAATGAGAATTGTCCCACCATTCTTTCTTCGTCTATAGGGAAGGTGTGGTAACAAGTAAAA
66 CCCATAATGAGAATTGTCCCACCATTCTTTCTTCGTCTATAGGGAAGGTGTGGTAACAAGTAAAA
18495882 AAAAAAAAAAAAACAGCATCAAGAAGCAAATAAAATAACAGCATAGCCCAAAAAACTAATATGCT
131 AAAAAAAAAAAAACAGCATCAAGAAGCAAATAAAATAACAGCATAGCCCAAAAAACTAATATGCT
18495947 TCAATACATCTTCTAGGGTACAACATATCATGATACTTGTAACAAAGTAAAAAACCTTTCACCTT
196 TCAATACATCTTCTAGGGTACAACATATCATGATACTTGTAACAAAGTAAAAAACCTTTCACCTT
18496012 ATGCAACCAATTTTACTCCACAAAAGGAATGGACAAGGACTTTCTATTATTTCTACAAATTTACA
261 ATGCAACCAATTTTACTCCACAAAAGGAATGGACAAGGACTTTCTATTATTTCTACAAATTTACA
*
18496077 TCTATTGGTTCTTGAGCAATGAAATTTACTC
326 TCTATTGGTTCTTGAGCAATGAAATTTACTA
18496108 AACCTTATCCTGCATGCATAAAATCAAATATATGATCTCATGGAAACAGAAATTAAATCATCTAT
1 AACCTTATCCTGCATGCATAAAATCAAATATATGATCTCATGGAAACAGAAATTAAATCATCTAT
*
18496173 CCCATAATGAGAATTGTCCCACCATTCTTTCTTTGTCTATAGGGAAGGTGTGGTAACAAGTAAAA
66 CCCATAATGAGAATTGTCCCACCATTCTTTCTTCGTCTATAGGGAAGGTGTGGTAACAAGTAAAA
18496238 AAAAAAAAAAAAACAGCATCAAGAAGCAAATAAAATAACAGCATAGCCCAAAAAACTAATATGCT
131 AAAAAAAAAAAAACAGCATCAAGAAGCAAATAAAATAACAGCATAGCCCAAAAAACTAATATGCT
18496303 TCAATACATCTTCTAGGGTACAACATATCATGATACTTGTAACAAAGTAAAAAACCTTTCACCTT
196 TCAATACATCTTCTAGGGTACAACATATCATGATACTTGTAACAAAGTAAAAAACCTTTCACCTT
18496368 ATGCAACCAATTTTACTCCACAAAAGGAATGGACAAGGACTTTCTATTATTTCTACAAATTTACA
261 ATGCAACCAATTTTACTCCACAAAAGGAATGGACAAGGACTTTCTATTATTTCTACAAATTTACA
18496433 TCTATTGGTTCTTGAGCAATGAAATT
326 TCTATTGGTTCTTGAGCAATGAAATT
18496459 ATAGTTTAAG
Statistics
Matches: 704, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
356 704 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (356 bp):
AACCTTATCCTGCATGCATAAAATCAAATATATGATCTCATGGAAACAGAAATTAAATCATCTAT
CCCATAATGAGAATTGTCCCACCATTCTTTCTTCGTCTATAGGGAAGGTGTGGTAACAAGTAAAA
AAAAAAAAAAAAACAGCATCAAGAAGCAAATAAAATAACAGCATAGCCCAAAAAACTAATATGCT
TCAATACATCTTCTAGGGTACAACATATCATGATACTTGTAACAAAGTAAAAAACCTTTCACCTT
ATGCAACCAATTTTACTCCACAAAAGGAATGGACAAGGACTTTCTATTATTTCTACAAATTTACA
TCTATTGGTTCTTGAGCAATGAAATTTACTA
Found at i:18501755 original size:27 final size:27
Alignment explanation
Indices: 18501694--18501744 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
18501684 ATTTTGAGTT
*
18501694 AATAAATTCTCTTTGAGTTTTTCTTTC
1 AATAATTTCTCTTTGAGTTTTTCTTTC
*
18501721 AAGAATTTCTC-TTGA-TTTTTCTTT
1 AATAATTTCTCTTTGAGTTTTTCTTT
18501745 TAGAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 4 0.18
27 9 0.41
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.57
Consensus pattern (27 bp):
AATAATTTCTCTTTGAGTTTTTCTTTC
Found at i:18504347 original size:42 final size:42
Alignment explanation
Indices: 18504285--18504372 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
18504275 GTTTCAGTTC
* * *
18504285 AACCTTAATGGGTTTTCGTTCAGCTC-TATTGAGCTTCTGTTT
1 AACCTTAATAGGTTTCCGTTCAGCTCTTA-TGAGCTTCTATTT
* *
18504327 AACCTTTATAGGTTTCCGTTCAGCTCTTATGAGCTTTTATTT
1 AACCTTAATAGGTTTCCGTTCAGCTCTTATGAGCTTCTATTT
18504369 AACC
1 AACC
18504373 CTTACGGGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 38 0.95
43 2 0.05
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.44
Consensus pattern (42 bp):
AACCTTAATAGGTTTCCGTTCAGCTCTTATGAGCTTCTATTT
Found at i:18504383 original size:42 final size:42
Alignment explanation
Indices: 18504294--18504406 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
18504284 CAACCTTAAT
* * * *
18504294 GGGTTTTCGTTCAGCTC-TATTGAGCTTCTGTTTAACCTTTAT
1 GGGTTTCCGTTCAGCTCTTA-TGAGCTTCTATTTAACCCTTAC
* *
18504336 AGGTTTCCGTTCAGCTCTTATGAGCTTTTATTTAACCCTTAC
1 GGGTTTCCGTTCAGCTCTTATGAGCTTCTATTTAACCCTTAC
* * * *
18504378 GGGTTTCTGTTTAGCACTTATGTGCTTCT
1 GGGTTTCCGTTCAGCTCTTATGAGCTTCT
18504407 GTGCAGCCTT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 56 0.97
43 2 0.03
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (42 bp):
GGGTTTCCGTTCAGCTCTTATGAGCTTCTATTTAACCCTTAC
Found at i:18511524 original size:42 final size:42
Alignment explanation
Indices: 18511452--18511560 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
18511442 CTTATATAAG
* * *
18511452 TTTCAGTTCAACCCTAATAGGTTTCTGTTCAGCTC-TATTGAGC
1 TTTC-GTTCAACCCTTATGGGTTTCCGTTCAGCTCTTA-TGAGC
* *
18511495 TTTTGTTTAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGC
1 TTTCGTTCAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGC
*
18511537 TTTCGTTCAACCCTTACGGGTTTC
1 TTTCGTTCAACCCTTATGGGTTTC
18511561 TGTTTAGCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 52 0.91
43 5 0.09
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.42
Consensus pattern (42 bp):
TTTCGTTCAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGC
Found at i:18511533 original size:21 final size:21
Alignment explanation
Indices: 18511503--18511560 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
18511493 GCTTTTGTTT
18511503 AACCCTTATGGGTTTCCGTTC
1 AACCCTTATGGGTTTCCGTTC
* * *
18511524 AGCTCTTATGAGCTTT-CGTTC
1 AACCCTTATG-GGTTTCCGTTC
*
18511545 AACCCTTACGGGTTTC
1 AACCCTTATGGGTTTC
18511561 TGTTTAGCAT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
20 4 0.14
21 20 0.71
22 4 0.14
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.38
Consensus pattern (21 bp):
AACCCTTATGGGTTTCCGTTC
Found at i:18512766 original size:30 final size:30
Alignment explanation
Indices: 18512725--18512782 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
18512715 TTGTCAAAAT
*
18512725 TTTTTTTATTATTTTAAAGACATTTGCTAA
1 TTTTGTTATTATTTTAAAGACATTTGCTAA
* *
18512755 TTTTGTTATTATTTTAGAGGCATTTGCT
1 TTTTGTTATTATTTTAAAGACATTTGCT
18512783 TGTTAAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.57
Consensus pattern (30 bp):
TTTTGTTATTATTTTAAAGACATTTGCTAA
Found at i:18512934 original size:12 final size:12
Alignment explanation
Indices: 18512904--18512936 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
18512894 TATATATTTT
18512904 AAAATT-ATATA
1 AAAATTAATATA
18512915 AAAA-TAATATA
1 AAAATTAATATA
18512926 AAAATTAATAT
1 AAAATTAATAT
18512937 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:18516704 original size:5 final size:5
Alignment explanation
Indices: 18516690--18516762 Score: 139
Period size: 5 Copynumber: 14.8 Consensus size: 5
18516680 AAGAATTAAG
18516690 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
18516739 TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATA
18516763 ATAAAACAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
4 4 0.06
5 64 0.94
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:18516936 original size:40 final size:40
Alignment explanation
Indices: 18516892--18516972 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
18516882 AGTTTCAAGC
18516892 TCAAATGGATAGTCAATTTAATTCTTTTTCTTATAATTTT
1 TCAAATGGATAGTCAATTTAATTCTTTTTCTTATAATTTT
18516932 TCAAATGGATAGTCAATTTAATTCTTTTTCTTATAATTTT
1 TCAAATGGATAGTCAATTTAATTCTTTTTCTTATAATTTT
18516972 T
1 T
18516973 ATGTTTTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (40 bp):
TCAAATGGATAGTCAATTTAATTCTTTTTCTTATAATTTT
Found at i:18524947 original size:16 final size:16
Alignment explanation
Indices: 18524926--18524979 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
18524916 ACACAATTCA
18524926 TAAAATATATATAAAT
1 TAAAATATATATAAAT
* *
18524942 TAAAATTTATA-AAAC
1 TAAAATATATATAAAT
*
18524957 AAATAATATATATAAAT
1 TAA-AATATATATAAAT
18524974 TCAAAA
1 T-AAAA
18524980 AAACTTAGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 5 0.17
16 17 0.59
17 5 0.17
18 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATATATATAAAT
Found at i:18531918 original size:34 final size:31
Alignment explanation
Indices: 18531875--18531948 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 31
18531865 TAAAGCATGT
* *
18531875 CATAATTAAAAGATGTAGATTAATAATACAAGA
1 CATAATTAAAACATGCA-ATTAATAA-ACAAGA
*
18531908 CATTAATT-AAACATGCATTTAATAAACAAGA
1 CA-TAATTAAAACATGCAATTAATAAACAAGA
18531939 CATAATTAAA
1 CATAATTAAA
18531949 GACTCATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 5 0.14
31 10 0.28
32 7 0.19
33 9 0.25
34 5 0.14
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.28
Consensus pattern (31 bp):
CATAATTAAAACATGCAATTAATAAACAAGA
Found at i:18531948 original size:15 final size:16
Alignment explanation
Indices: 18531893--18531948 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
18531883 AAAGATGTAG
18531893 ATTAA-TAATACAAGAC
1 ATTAATTAA-ACAAGAC
*
18531909 ATTAATTAAACATG-C
1 ATTAATTAAACAAGAC
18531924 ATTTAA-TAAACAAGAC
1 A-TTAATTAAACAAGAC
18531940 A-TAATTAAA
1 ATTAATTAAA
18531949 GACTCATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 3 0.09
15 13 0.38
16 15 0.44
17 3 0.09
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (16 bp):
ATTAATTAAACAAGAC
Found at i:18532159 original size:13 final size:13
Alignment explanation
Indices: 18532143--18532167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18532133 TGTGGACAAA
18532143 ATAAATACATGTG
1 ATAAATACATGTG
18532156 ATAAATACATGT
1 ATAAATACATGT
18532168 ATATATACTA
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:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (13 bp):
ATAAATACATGTG
Found at i:18532363 original size:19 final size:21
Alignment explanation
Indices: 18532328--18532366 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
18532318 AAAATATTTT
18532328 AGTGGATTAGTTTTTTAAAAG
1 AGTGGATTAGTTTTTTAAAAG
18532349 AGTGGATT-G-TTTTTAAAA
1 AGTGGATTAGTTTTTTAAAA
18532367 TTAAATGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (21 bp):
AGTGGATTAGTTTTTTAAAAG
Found at i:18545678 original size:21 final size:22
Alignment explanation
Indices: 18545634--18545678 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
18545624 ATATTATTAG
** *
18545634 ATTATTATTATTATTATTTTAA
1 ATTATTATTATTATTAAATAAA
18545656 ATTA-TATTATTATTAAATAAA
1 ATTATTATTATTATTAAATAAA
18545677 AT
1 AT
18545679 AAATAGAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTATTATTATTATTAAATAAA
Found at i:18546600 original size:18 final size:19
Alignment explanation
Indices: 18546565--18546603 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
18546555 TGAGTATTGA
18546565 TATTGAATTGAATGAAAATG
1 TATTGAATTG-ATGAAAATG
18546585 TATTGAATTG-TGAAAATG
1 TATTGAATTGATGAAAATG
18546603 T
1 T
18546604 GTGAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (19 bp):
TATTGAATTGATGAAAATG
Found at i:18550327 original size:19 final size:20
Alignment explanation
Indices: 18550287--18550328 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
18550277 TTGATTCATG
18550287 TTTTCAATCTCATATCTCAA
1 TTTTCAATCTCATATCTCAA
18550307 TTTTCAATTCTCA-AT-TCAA
1 TTTTCAA-TCTCATATCTCAA
18550326 TTT
1 TTT
18550329 ATCGTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 9 0.43
21 5 0.24
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTCAATCTCATATCTCAA
Found at i:18550985 original size:15 final size:14
Alignment explanation
Indices: 18550959--18551000 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
18550949 CATGTATATT
18550959 ATATAATTCAATCA
1 ATATAATTCAATCA
18550973 ATATAATTTCAATCA
1 ATATAA-TTCAATCA
18550988 ATATAAATTCAAT
1 ATAT-AATTCAAT
18551001 AAATTCATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.23
15 18 0.69
16 2 0.08
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATAATTCAATCA
Found at i:18552160 original size:3 final size:3
Alignment explanation
Indices: 18552152--18552178 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18552142 TCAATTTATT
18552152 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
18552179 CAACAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18556265 original size:3 final size:3
Alignment explanation
Indices: 18556243--18556300 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
18556233 TGTTAAAATA
* *
18556243 TAT TAT TA- AAT TAT TGT TAT TAT TAT TAT TAT TAT T-T TA- TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18556287 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
18556301 AATAAAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 7 0.15
3 40 0.85
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:18556537 original size:18 final size:17
Alignment explanation
Indices: 18556510--18556546 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
18556500 GAAAACAGAG
*
18556510 AAGAAAAGAAGGAAAGA
1 AAGAAAAGAAAGAAAGA
18556527 AAGAGAAAGAAAGAAAGA
1 AAGA-AAAGAAAGAAAGA
18556545 AA
1 AA
18556547 AAATTAGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAAGAAAGA
Found at i:18556538 original size:14 final size:14
Alignment explanation
Indices: 18556510--18556544 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
18556500 GAAAACAGAG
*
18556510 AAGAAA-AGAAGGA
1 AAGAAAGAGAAAGA
18556523 AAGAAAGAGAAAGA
1 AAGAAAGAGAAAGA
18556537 AAGAAAGA
1 AAGAAAGA
18556545 AAAAATTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AAGAAAGAGAAAGA
Found at i:18556785 original size:19 final size:19
Alignment explanation
Indices: 18556761--18556828 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 19
18556751 GGAGAAGGAT
18556761 TAAATTGTAGAATAGACTA
1 TAAATTGTAGAATAGACTA
*
18556780 TAAATTGT-GTCATAGGGACTAAA
1 TAAATTGTAG-AATA--GACT--A
*
18556803 TTAAATTGTAGAATAGGCTA
1 -TAAATTGTAGAATAGACTA
18556823 TAAATT
1 TAAATT
18556829 TTGTATAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
18 1 0.03
19 17 0.44
20 1 0.03
21 4 0.10
22 3 0.08
23 1 0.03
24 11 0.28
25 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.34
Consensus pattern (19 bp):
TAAATTGTAGAATAGACTA
Found at i:18556806 original size:43 final size:44
Alignment explanation
Indices: 18556759--18556849 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 44
18556749 TAGGAGAAGG
* *
18556759 ATTAAATTGTAGAATAGACTATAAA-TTGTGTCATAGGGACTAA
1 ATTAAATTGTAGAATAGACTATAAATTTGTATAATAGGGACTAA
*
18556802 ATTAAATTGTAGAATAGGCTATAAATTTTGTATAATAGGGACTAA
1 ATTAAATTGTAGAATAGACTATAAA-TTTGTATAATAGGGACTAA
18556847 ATT
1 ATT
18556850 GCAAGAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 24 0.56
45 19 0.44
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (44 bp):
ATTAAATTGTAGAATAGACTATAAATTTGTATAATAGGGACTAA
Found at i:18556818 original size:24 final size:24
Alignment explanation
Indices: 18556759--18556849 Score: 67
Period size: 21 Copynumber: 4.1 Consensus size: 24
18556749 TAGGAGAAGG
18556759 ATTAAATTGTAGAATA--GACT--
1 ATTAAATTGTAGAATAGGGACTAA
*
18556779 A-TAAATTGT-GTCATAGGGACTAA
1 ATTAAATTGTAG-AATAGGGACTAA
*
18556802 ATTAAATTGTAGAATAGGCTA-TAA
1 ATTAAATTGTAGAATAGG-GACTAA
*
18556826 ATT---TTGTATAATAGGGACTAA
1 ATTAAATTGTAGAATAGGGACTAA
18556847 ATT
1 ATT
18556850 GCAAGAAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
18 1 0.02
19 11 0.19
20 2 0.04
21 21 0.37
23 1 0.02
24 19 0.33
25 2 0.04
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (24 bp):
ATTAAATTGTAGAATAGGGACTAA
Found at i:18557267 original size:18 final size:18
Alignment explanation
Indices: 18557232--18557281 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
18557222 TGAGTATTGA
18557232 TATTGAATTGAATGAAAATG
1 TATTGAATTG--TGAAAATG
18557252 TATTGAATTGTGAAAATG
1 TATTGAATTGTGAAAATG
18557270 T-TTGAATATGTG
1 TATTGAAT-TGTG
18557282 GATTGAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.21
18 13 0.45
20 10 0.34
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.40
Consensus pattern (18 bp):
TATTGAATTGTGAAAATG
Found at i:18558502 original size:18 final size:19
Alignment explanation
Indices: 18558475--18558522 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
18558465 AAGTATGCTC
*
18558475 GAGAATATGT-CTATTGAA
1 GAGAACATGTCCTATTGAA
*
18558493 GAGATCATGTGCCTATTGAA
1 GAGAACATGT-CCTATTGAA
18558513 GAGAACATGT
1 GAGAACATGT
18558523 GCAAAAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.32
20 17 0.68
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (19 bp):
GAGAACATGTCCTATTGAA
Found at i:18558510 original size:20 final size:20
Alignment explanation
Indices: 18558485--18558524 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
18558475 GAGAATATGT
*
18558485 CTATTGAAGAGATCATGTGC
1 CTATTGAAGAGAACATGTGC
18558505 CTATTGAAGAGAACATGTGC
1 CTATTGAAGAGAACATGTGC
18558525 AAAAGATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (20 bp):
CTATTGAAGAGAACATGTGC
Found at i:18561374 original size:3 final size:3
Alignment explanation
Indices: 18561366--18561488 Score: 62
Period size: 3 Copynumber: 40.7 Consensus size: 3
18561356 TTCATGTATA
* *
18561366 TAT TAT TAT T-T ATAT TAT TGT TAT TAT TA- TAT TA- TAT ATAT TCT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * * *
18561410 CTCCA- TATT TAT T-T ATAT TAT TAC TAT CAT TAT TAT TAC TAT CAT
1 -T--AT TA-T TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
18561455 TAT T-T TAC TAT TAT T-T ATAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
18561489 CAATTATCAT
Statistics
Matches: 91, Mismatches: 14, Indels: 30
0.67 0.10 0.22
Matches are distributed among these distances:
2 10 0.11
3 71 0.78
4 10 0.11
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:18561405 original size:26 final size:26
Alignment explanation
Indices: 18561336--18561407 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 26
18561326 ATTATTTTTG
18561336 GTATTAT-TTATATATATTTTTTCAT
1 GTATTATATTATATATATTTTTTCAT
*
18561361 GTATATATTATTATTTATATTATTGTT-AT
1 GTAT-TA-TATTATATATATT-TT-TTCAT
18561390 -TATTATATTATATATATT
1 GTATTATATTATATATATT
18561408 CTCTCCATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 4 0.10
26 14 0.35
27 3 0.08
28 13 0.32
29 4 0.10
30 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (26 bp):
GTATTATATTATATATATTTTTTCAT
Found at i:18561407 original size:14 final size:13
Alignment explanation
Indices: 18561337--18561481 Score: 62
Period size: 12 Copynumber: 11.5 Consensus size: 13
18561327 TTATTTTTGG
18561337 TATTATTTATATA
1 TATTATTTATATA
*
18561350 TATTTTTTCATGTATA
1 TATTATTT-A--TATA
*
18561366 TATTA-TTATTTA
1 TATTATTTATATA
18561378 TATTATTGT-TAT-
1 TATTATT-TATATA
18561390 TATTATATTATATA
1 TATTAT-TTATATA
* * **
18561404 TATTCTCTCCATA
1 TATTATTTATATA
18561417 T-TTATTTATAT-
1 TATTATTTATATA
*
18561428 TATTA-CTATCAT-
1 TATTATTTAT-ATA
18561440 TATTA-TTACTAT-
1 TATTATTTA-TATA
* *
18561452 CATTATTT-TA-C
1 TATTATTTATATA
18561463 TATTATTTATAT-
1 TATTATTTATATA
18561475 TATTATT
1 TATTATT
18561482 ATTATTACAA
Statistics
Matches: 101, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
11 13 0.13
12 48 0.48
13 22 0.22
14 8 0.08
15 2 0.02
16 8 0.08
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (13 bp):
TATTATTTATATA
Found at i:18561422 original size:47 final size:47
Alignment explanation
Indices: 18561369--18561488 Score: 140
Period size: 47 Copynumber: 2.6 Consensus size: 47
18561359 ATGTATATAT
* *
18561369 TATTATTTATATTATTGTTATTATTA-TATTA-TAT-A-TATTCTCTCC
1 TATTATTTATATTATTATTATTATTATTATTACTATCATTATT-T-TAC
* *
18561414 ATATTTATTTATATTATTACTATCATTATTATTACTATCATTATTTTAC
1 -TA-TTATTTATATTATTATTATTATTATTATTACTATCATTATTTTAC
18561463 TATTATTTATATTATTATTATTATTA
1 TATTATTTATATTATTATTATTATTA
18561489 CAATTATCAT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
46 2 0.03
47 43 0.68
48 7 0.11
49 5 0.08
50 2 0.03
51 4 0.06
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.60
Consensus pattern (47 bp):
TATTATTTATATTATTATTATTATTATTATTACTATCATTATTTTAC
Found at i:18561495 original size:15 final size:15
Alignment explanation
Indices: 18561425--18561488 Score: 78
Period size: 15 Copynumber: 4.3 Consensus size: 15
18561415 TATTTATTTA
*
18561425 TATTATTACTATCAT
1 TATTATTACTATTAT
*
18561440 TATTATTACTATCAT
1 TATTATTACTATTAT
18561455 TATT-TTACTATTAT
1 TATTATTACTATTAT
*
18561469 T-TATATTATTATTAT
1 TAT-TATTACTATTAT
18561484 TATTA
1 TATTA
18561489 CAATTATCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.02
14 11 0.25
15 31 0.70
16 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATTACTATTAT
Found at i:18561559 original size:3 final size:3
Alignment explanation
Indices: 18561553--18561583 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
18561543 ATTATTACCC
*
18561553 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
18561584 ATTTTCACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:18561859 original size:21 final size:20
Alignment explanation
Indices: 18561835--18561882 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
18561825 CGTTATTACC
*
18561835 ATTATTGTTGCTACTATTCTT
1 ATTATT-TTGCTACTATTATT
**
18561856 ATTATCTTTTTTACTATTATT
1 ATTAT-TTTGCTACTATTATT
18561877 ATTATT
1 ATTATT
18561883 ATTATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.62
Consensus pattern (20 bp):
ATTATTTTGCTACTATTATT
Found at i:18561876 original size:3 final size:3
Alignment explanation
Indices: 18561870--18562097 Score: 103
Period size: 3 Copynumber: 77.7 Consensus size: 3
18561860 TCTTTTTTAC
* ** *
18561870 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TCC TAT TAA TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* ** * * * *
18561917 T-T TAC TGC TAA TATT TAT TAT CAT TAT TAT TAC TAT TA- TAT TTT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * ** * *
18561961 TAC TAC CAT TAC GGT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* ** * * *
18562009 TAT TAC TAT TAT GT-T TAT TGC TAT TAC TAC TAT TAT TA- TAT TGT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
18562053 TAG TAT CAC TAT TAT GT-T T-T TAT TAT TA- TAT TAT TTT TAC TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18562096 TA
1 TA
18562098 CTCTTTAAAT
Statistics
Matches: 163, Mismatches: 53, Indels: 18
0.70 0.23 0.08
Matches are distributed among these distances:
2 14 0.09
3 145 0.89
4 4 0.02
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:18561979 original size:44 final size:42
Alignment explanation
Indices: 18561887--18562003 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 42
18561877 ATTATTATTA
* * * *
18561887 TTATTATCATTATTATTCCTATTAATATTTTTTACTGCTAATAT
1 TTATTATCATTATTATTACTATT-ATA-TTTTTACTACCAATAG
*
18561931 TTATTATCATTATTATTACTATTATATTTTTACTACCATTACGG
1 TTATTATCATTATTATTACTATTATATTTTTACTACCAATA--G
* *
18561975 TTATTATTATTATTATTATTATTAT-TTTT
1 TTATTATCATTATTATTACTATTATATTTT
18562004 ATTTTTATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 12 0.19
43 7 0.11
44 45 0.70
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (42 bp):
TTATTATCATTATTATTACTATTATATTTTTACTACCAATAG
Found at i:18579917 original size:13 final size:13
Alignment explanation
Indices: 18579899--18579927 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
18579889 GGTTGTTTAT
18579899 TAAACTAATTAAC
1 TAAACTAATTAAC
18579912 TAAACTAATTAAC
1 TAAACTAATTAAC
18579925 TAA
1 TAA
18579928 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:18593603 original size:69 final size:69
Alignment explanation
Indices: 18593481--18593908 Score: 428
Period size: 69 Copynumber: 6.2 Consensus size: 69
18593471 ATCACTTGCA
* * * * * * *
18593481 AACCTTGATTTTACAATTGAAAGAGCTTTGCTCTCGCTAATTGTATTGAAGGTCGCGGCTCTTGG
1 AACCTTGATTTTACAACTG--GGAGCTTTACTCTCGCTAACTGTGTTGGAGGTCGCGGCTCTTCG
*
18593546 CCTGTG
64 CCTGCG
* * * * * *
18593552 GACCTTGATTTTACAACTGGGAGCTTTGCTCTCACTAACTGTGTTAGAGGTCGCGACTCTTCACC
1 AACCTTGATTTTACAACTGGGAGCTTTACTCTCGCTAACTGTGTTGGAGGTCGCGGCTCTTCGCC
*
18593617 TACG
66 TGCG
* * * * *
18593621 AACCTTGATTTTACAGCTGGGAGCTTTGCTCTCGCTAAGTGTGTTGGAGGTCGCGACTCTTTGCC
1 AACCTTGATTTTACAACTGGGAGCTTTACTCTCGCTAACTGTGTTGGAGGTCGCGGCTCTTCGCC
18593686 TGCG
66 TGCG
* * * * *
18593690 AACCTTGATTTTACAACTGGGAGCTGTACTTTTGCT-ACTTGGGTTGGAGGTCGTGGCTCTTCGC
1 AACCTTGATTTTACAACTGGGAGCTTTACTCTCGCTAAC-TGTGTTGGAGGTCGCGGCTCTTCGC
* *
18593754 TTACG
65 CTGCG
* * * * * * *
18593759 AATCTTAATTTTATAACTAGGAACTTTACTCTCGCTAACTGTGTTGGAGGTCGCAGCTCTTCACC
1 AACCTTGATTTTACAACTGGGAGCTTTACTCTCGCTAACTGTGTTGGAGGTCGCGGCTCTTCGCC
18593824 TGCG
66 TGCG
* ** * * **
18593828 AACCTTGATTTTACAACTGAGAGCTTTACTCTTACTAACTGTGTTAGAGGTTGCAACTCTTC-CC
1 AACCTTGATTTTACAACTGGGAGCTTTACTCTCGCTAACTGTGTTGGAGGTCGCGGCTCTTCGCC
18593892 TTGCG
66 -TGCG
*
18593897 AACCTCGATTTT
1 AACCTTGATTTT
18593909 CTAAACGACA
Statistics
Matches: 295, Mismatches: 59, Indels: 8
0.81 0.16 0.02
Matches are distributed among these distances:
68 3 0.01
69 273 0.93
70 2 0.01
71 17 0.06
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (69 bp):
AACCTTGATTTTACAACTGGGAGCTTTACTCTCGCTAACTGTGTTGGAGGTCGCGGCTCTTCGCC
TGCG
Found at i:18593908 original size:138 final size:137
Alignment explanation
Indices: 18593481--18593908 Score: 473
Period size: 138 Copynumber: 3.1 Consensus size: 137
18593471 ATCACTTGCA
* * * * * * *
18593481 AACCTTGATTTTACAATTGAAAGAGCTTTGCTCTCGCTAATTGTATTGAAGGTCGCGGCTCTTGG
1 AACCTTGATTTTACAACT--AGGAACTTTGCTCTCGCTAACTGTGTTGGAGGTCGC-GCTCTTCG
* * * *
18593546 CCTGTGGACCTTGATTTTACAACTGGGAGCTTTGCTCTCACTAACTGTGTTAGAGGTCGCGACTC
63 CCTGCGAACCTTGATTTTACAACTGGGAGCTTTACTCTTACTAACTGTGTTAGAGGTCGCGACTC
18593611 TTCACC-TACG
128 TTC-CCTTACG
* * * * *
18593621 AACCTTGATTTTACAGCTGGGAGCTTTGCTCTCGCTAAGTGTGTTGGAGGTCGCGACTCTTTGCC
1 AACCTTGATTTTACAACTAGGAACTTTGCTCTCGCTAACTGTGTTGGAGGTCGCG-CTCTTCGCC
* * * * * * *
18593686 TGCGAACCTTGATTTTACAACTGGGAGCTGTACTTTTGCT-ACTTGGGTTGGAGGTCGTGGCTCT
65 TGCGAACCTTGATTTTACAACTGGGAGCTTTACTCTTACTAAC-TGTGTTAGAGGTCGCGACTCT
*
18593750 TCGCTTACG
129 TCCCTTACG
* * * * *
18593759 AATCTTAATTTTATAACTAGGAACTTTACTCTCGCTAACTGTGTTGGAGGTCGCAGCTCTTCACC
1 AACCTTGATTTTACAACTAGGAACTTTGCTCTCGCTAACTGTGTTGGAGGTCGC-GCTCTTCGCC
* * *
18593824 TGCGAACCTTGATTTTACAACTGAGAGCTTTACTCTTACTAACTGTGTTAGAGGTTGCAACTCTT
65 TGCGAACCTTGATTTTACAACTGGGAGCTTTACTCTTACTAACTGTGTTAGAGGTCGCGACTCTT
*
18593889 CCCTTGCG
130 CCCTTACG
*
18593897 AACCTCGATTTT
1 AACCTTGATTTT
18593909 CTAAACGACA
Statistics
Matches: 238, Mismatches: 45, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
137 4 0.02
138 215 0.90
139 3 0.01
140 16 0.07
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (137 bp):
AACCTTGATTTTACAACTAGGAACTTTGCTCTCGCTAACTGTGTTGGAGGTCGCGCTCTTCGCCT
GCGAACCTTGATTTTACAACTGGGAGCTTTACTCTTACTAACTGTGTTAGAGGTCGCGACTCTTC
CCTTACG
Found at i:18596067 original size:21 final size:21
Alignment explanation
Indices: 18596031--18596090 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
18596021 ATGAGAGTTA
* * * *
18596031 AACGGAAACCCGTAAGGGTTG
1 AACGAAAACCCATAAGAGCTG
* *
18596052 AACGAAAGCTCATAAGAGCTG
1 AACGAAAACCCATAAGAGCTG
18596073 AACGAAAACCCATAAGAG
1 AACGAAAACCCATAAGAG
18596091 TTAAACTGAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (21 bp):
AACGAAAACCCATAAGAGCTG
Found at i:18596123 original size:42 final size:42
Alignment explanation
Indices: 18596010--18596123 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 42
18596000 CCGAAGGCTG
* * * * *
18596010 AACTGAAGCTCATGAGAGTTAAACGGAAACCCGTAAGGGTTG
1 AACTGAAGCTCATAAGAGTTAAACGAAAACCCATAAGAGTTA
* *
18596052 AAC-GAAAGCTCATAAGAGCTGAACGAAAACCCATAAGAGTTA
1 AACTG-AAGCTCATAAGAGTTAAACGAAAACCCATAAGAGTTA
* * *
18596094 AACTGAAGTTCAAAAGAGTTAAACAAAAAC
1 AACTGAAGCTCATAAGAGTTAAACGAAAAC
18596124 TGAAACTCAT
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
41 1 0.02
42 56 0.97
43 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (42 bp):
AACTGAAGCTCATAAGAGTTAAACGAAAACCCATAAGAGTTA
Found at i:18596124 original size:27 final size:27
Alignment explanation
Indices: 18596093--18596145 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
18596083 CATAAGAGTT
**
18596093 AAACTGAAGTTCAAAAGAGTTAAACAA
1 AAACTGAAACTCAAAAGAGTTAAACAA
* *
18596120 AAACTGAAACTCATATGAGTTAAACA
1 AAACTGAAACTCAAAAGAGTTAAACA
18596146 GAAGCTCGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (27 bp):
AAACTGAAACTCAAAAGAGTTAAACAA
Found at i:18596248 original size:24 final size:24
Alignment explanation
Indices: 18596220--18596266 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
18596210 TACTTGGGTA
18596220 ATTTACCATCAATTCATACTTTGT
1 ATTTACCATCAATTCATACTTTGT
** *
18596244 ATTTACTGTCAATTCATCCTTTG
1 ATTTACCATCAATTCATACTTTG
18596267 CCACAGAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (24 bp):
ATTTACCATCAATTCATACTTTGT
Found at i:18596356 original size:18 final size:18
Alignment explanation
Indices: 18596320--18596357 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
18596310 CATTTAATTC
18596320 AATTTTATAATTTAACAAT
1 AATTTTAT-ATTTAACAAT
18596339 AATTTTAT-TTTCAACAAT
1 AATTTTATATTT-AACAAT
18596357 A
1 A
18596358 GATATGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 7 0.39
19 8 0.44
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTTATATTTAACAAT
Found at i:18602517 original size:2 final size:2
Alignment explanation
Indices: 18602510--18602554 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
18602500 AACCCTCCTT
18602510 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18602552 TC T
1 TC T
18602555 TTCATTTCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:18602878 original size:34 final size:37
Alignment explanation
Indices: 18602839--18602911 Score: 98
Period size: 40 Copynumber: 2.0 Consensus size: 37
18602829 TAATGGAACC
18602839 TCAAAATAT-A-A-CTTTTGTTGAATCTTCATGCTTA
1 TCAAAATATAATACCTTTTGTTGAATCTTCATGCTTA
18602873 TCAAAATATAAAAATACCTTTTGTTGAATCTTCATGCTT
1 TCAAAATAT---AATACCTTTTGTTGAATCTTCATGCTT
18602912 TTGTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
34 9 0.27
38 1 0.03
39 1 0.03
40 22 0.67
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (37 bp):
TCAAAATATAATACCTTTTGTTGAATCTTCATGCTTA
Found at i:18606596 original size:17 final size:17
Alignment explanation
Indices: 18606573--18606606 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18606563 TATAATGTAA
*
18606573 AAAAAAAGGATAAACATT
1 AAAAAATGGA-AAACATT
18606591 AAAAAATGGAAAACAT
1 AAAAAATGGAAAACAT
18606607 AGATATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.68, C:0.06, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAAAATGGAAAACATT
Found at i:18609252 original size:45 final size:45
Alignment explanation
Indices: 18608949--18609246 Score: 251
Period size: 45 Copynumber: 6.7 Consensus size: 45
18608939 CTACCATGGT
* *
18608949 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGTCAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAAC
* * * * * * *
18608993 AAGTTTTATCTCCCTGAGGTTGCAGTGAAGCAAATTGAAGAA-AGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAAATAAC
* * * * * * *
18609038 AAGTCTTATCTCTCTAAAGTTGCAGTGGAGCAAACTGAAGATAAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAAC
* * * * * * *
18609083 GAGTCTTATCTCACTGAAGTTGCAGTGGAACAGATTGAAGATAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAAC
* * * * ** *
18609128 CAATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATTAAAGCT-AT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAAC
* * * *
18609172 AAACCTTATCACACTGAAGTTGCAGTGGAGCAGGTTAAAAATAAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAAC
*
18609217 AAATCTTATCTCCCTGAGGTTGCAGTGGAG
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAG
18609247 TAGGTTGAAG
Statistics
Matches: 200, Mismatches: 50, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
44 66 0.33
45 132 0.66
46 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (45 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAAC
Found at i:18609283 original size:44 final size:45
Alignment explanation
Indices: 18609185--18609284 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 45
18609175 CCTTATCACA
** *
18609185 CTGAAGTTGCAGTGGAGCAGGTTAAAAATAACAAATCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGGTTAAAAATAACAAATCCAATATCC
* * * * *
18609230 CTGAGGTTGCAGTGGAGTAGGTT-GAAGTTACAAATCCAATATCC
1 CTGAAGTTGCAGTGGAGCAGGTTAAAAATAACAAATCCAATATCC
*
18609274 TTGAAGTTGCA
1 CTGAAGTTGCA
18609285 ATTGTAATGA
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
44 24 0.53
45 21 0.47
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (45 bp):
CTGAAGTTGCAGTGGAGCAGGTTAAAAATAACAAATCCAATATCC
Found at i:18609581 original size:3 final size:3
Alignment explanation
Indices: 18609575--18609619 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
18609565 ATCTAAGATT
*
18609575 TTA TTA TTA TTA TTAA TTA TTA GTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18609620 ATTTTAAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:18609725 original size:23 final size:24
Alignment explanation
Indices: 18609699--18609757 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
18609689 ATAATGACAA
*
18609699 TTGTAATAAAA-ATATC-GGTACAT
1 TTGTAATAAAAGATA-CAGGTACAC
*
18609722 TTGTAATAAATAGATACATGTACAC
1 TTGTAATAAA-AGATACAGGTACAC
18609747 TTGTAATAAAA
1 TTGTAATAAAA
18609758 TAGTTAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 10 0.32
24 3 0.10
25 18 0.58
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (24 bp):
TTGTAATAAAAGATACAGGTACAC
Found at i:18612140 original size:45 final size:45
Alignment explanation
Indices: 18612076--18612241 Score: 188
Period size: 45 Copynumber: 3.6 Consensus size: 45
18612066 TGAGGCCACA
*
18612076 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATAGCG
* ** * *
18612121 AATCTTATTTCCCTAAAGTTGCAGTGGAATAGATTAAAGCTACAAGTCACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAG--A-TAG---CG
* *
18612172 AATCTTATCTCCCTAAAGTTGCAGTCGAGCAAATTAAAGATAGCG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATAGCG
* *
18612217 AATCTTATTTCCCTGAAGTTGCAGT
1 AATCTTATCTCCCTAAAGTTGCAGT
18612242 AGAATAGATT
Statistics
Matches: 100, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
45 59 0.59
47 1 0.01
48 4 0.04
49 1 0.01
51 35 0.35
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (45 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATAGCG
Found at i:18612202 original size:96 final size:96
Alignment explanation
Indices: 18612072--18612468 Score: 346
Period size: 96 Copynumber: 4.1 Consensus size: 96
18612062 AGATTGAGGC
* *
18612072 CACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCGAATCTTATTTCCCTAA
1 CACAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAGATAGCGAATCTTATTTCCCTAA
*
18612137 AGTTGCAGTGGAATAGATTAAAGCTACAAGT
66 AGTTGCAGTAGAATAGATTAAAGCTACAAGT
* * *
18612168 CACAAATCTTATCTCCCTAAAGTTGCAGTCGAGCAAATTAAAGATAGCGAATCTTATTTCCCTGA
1 CACAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAGATAGCGAATCTTATTTCCCTAA
*
18612233 AGTTGCAGTAGAATAGATTAGAGCTACAAGT
66 AGTTGCAGTAGAATAGATTAAAGCTACAAGT
* * * * * * * * *
18612264 TACAAATCCTATAC-CTCTAAAGCTGCAGTAG-GTCGGATCAAATCTACTATGGTGAATCTTATC
1 CACAAATCTTAT-CTCCCTAAAGTTGCAGTAGAG-CAGATTAAA--GA-TA--GCGAATCTTATT
* **
18612327 TCCTTAAAGTTGCAGTAGAGCAGATTAAAG-TCACAAGT
59 TCCCTAAAGTTGCAGTAGAATAGATTAAAGCT-ACAAGT
* * * * * * * *
18612365 ------T-TCATTTCCCTGAAGTTGCAATAGAGTAGATAAAAGATAGCAAATCTTATTTCCCTGA
1 CACAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAGATAGCGAATCTTATTTCCCTAA
* * * **
18612423 AGTTGTAGTGGAACAAGATTAAAGCTACAAAC
66 AGTTGCAGTAGAA-TAGATTAAAGCTACAAGT
*
18612455 CACAAATATTATCT
1 CACAAATCTTATCT
18612469 TACTGAAGTT
Statistics
Matches: 236, Mismatches: 46, Indels: 37
0.74 0.14 0.12
Matches are distributed among these distances:
89 24 0.10
90 13 0.06
91 3 0.01
92 1 0.00
94 21 0.09
95 3 0.01
96 121 0.51
97 5 0.02
98 1 0.00
99 2 0.01
100 1 0.00
101 41 0.17
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (96 bp):
CACAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAGATAGCGAATCTTATTTCCCTAA
AGTTGCAGTAGAATAGATTAAAGCTACAAGT
Found at i:18620918 original size:29 final size:29
Alignment explanation
Indices: 18620874--18620940 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
18620864 GCCTTTGTTA
* *
18620874 GACAATAGTTCGAGGTTGAGTCTATGCTT
1 GACAATAGTTCGAGGTTGAATATATGCTT
** *
18620903 GACAATAGTTTTAGGTTGAATATGTGCTT
1 GACAATAGTTCGAGGTTGAATATATGCTT
18620932 GACAATAGT
1 GACAATAGT
18620941 GCATCTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.36
Consensus pattern (29 bp):
GACAATAGTTCGAGGTTGAATATATGCTT
Found at i:18625184 original size:11 final size:11
Alignment explanation
Indices: 18625168--18625202 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
18625158 ATTTTGAACT
18625168 TCCCACATGTG
1 TCCCACATGTG
18625179 TCCCACATGTG
1 TCCCACATGTG
* *
18625190 TCTCACATATG
1 TCCCACATGTG
18625201 TC
1 TC
18625203 TAGTAAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.31
Consensus pattern (11 bp):
TCCCACATGTG
Found at i:18636327 original size:48 final size:48
Alignment explanation
Indices: 18636162--18636320 Score: 246
Period size: 48 Copynumber: 3.3 Consensus size: 48
18636152 ATCCTGTATA
* * * *
18636162 GCATCGGCATTGTTACGTGAGCCAGTGTAAGACCATGTTTGGGACATA
1 GCATCGACATTGTTACATGAGCCAGTGTAAGACCATGTCTGGGACATG
* * *
18636210 GCATCGACATTGTTACATGAGCCAATGTAAGACCATGTCTAGAACATG
1 GCATCGACATTGTTACATGAGCCAGTGTAAGACCATGTCTGGGACATG
*
18636258 GCATCGGCATTGTTACATGAGCCAGTGTAAGACCATGTCTGGGACATG
1 GCATCGACATTGTTACATGAGCCAGTGTAAGACCATGTCTGGGACATG
18636306 GCATCGACATTGTTA
1 GCATCGACATTGTTA
18636321 TGTGAGCGGC
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 99 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (48 bp):
GCATCGACATTGTTACATGAGCCAGTGTAAGACCATGTCTGGGACATG
Found at i:18636339 original size:23 final size:23
Alignment explanation
Indices: 18636305--18636350 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
18636295 TCTGGGACAT
18636305 GGCATCGACATTGTTATGTGAGC
1 GGCATCGACATTGTTATGTGAGC
*
18636328 GGCATCGGCATTGTTATGTGAGC
1 GGCATCGACATTGTTATGTGAGC
18636351 CAGTGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (23 bp):
GGCATCGACATTGTTATGTGAGC
Found at i:18636350 original size:71 final size:71
Alignment explanation
Indices: 18636257--18636397 Score: 219
Period size: 71 Copynumber: 2.0 Consensus size: 71
18636247 TCTAGAACAT
*
18636257 GGCATCGGCATTGTTACATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGTTAT
1 GGCATCGGCATTGTTACATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATGGTTAT
*
18636322 GTGAGC
66 CTGAGC
** ** *
18636328 GGCATCGGCATTGTTATGTGAGCCAGTGTAAGATTATGTCTGGGACATGGCATCGGCATGGTTAT
1 GGCATCGGCATTGTTACATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATGGTTAT
18636393 CTGAG
66 CTGAG
18636398 TCAGTGTAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (71 bp):
GGCATCGGCATTGTTACATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATGGTTAT
CTGAGC
Found at i:18636360 original size:119 final size:119
Alignment explanation
Indices: 18636210--18636430 Score: 336
Period size: 119 Copynumber: 1.9 Consensus size: 119
18636200 TTGGGACATA
*
18636210 GCATCGACATTGTTACATGAGCCAATGTAAGACCATGTCTAGAACATGGCATCGGCATTGTTA-C
1 GCATCGACATTGTTACATGAGCCAATGTAAGACCATGTCTAGAACATGGCATCGGCATGGTTATC
18636274 ATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGTTATGTGAGCG
66 -TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGTTATGTGAGCG
* ** * ** * *
18636329 GCATCGGCATTGTTATGTGAGCCAGTGTAAGATTATGTCTGGGACATGGCATCGGCATGGTTATC
1 GCATCGACATTGTTACATGAGCCAATGTAAGACCATGTCTAGAACATGGCATCGGCATGGTTATC
*
18636394 TGAGTCAGTGTAAGACCATGTCTGGGACATGGCATCG
66 TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
18636431 GCATGAGGCA
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
119 90 0.99
120 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (119 bp):
GCATCGACATTGTTACATGAGCCAATGTAAGACCATGTCTAGAACATGGCATCGGCATGGTTATC
TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGTTATGTGAGCG
Found at i:18636384 original size:48 final size:48
Alignment explanation
Indices: 18636328--18636435 Score: 171
Period size: 48 Copynumber: 2.2 Consensus size: 48
18636318 TTATGTGAGC
* * **
18636328 GGCATCGGCATTGTTATGTGAGCCAGTGTAAGATTATGTCTGGGACAT
1 GGCATCGGCATGGTTATCTGAGCCAGTGTAAGACCATGTCTGGGACAT
*
18636376 GGCATCGGCATGGTTATCTGAGTCAGTGTAAGACCATGTCTGGGACAT
1 GGCATCGGCATGGTTATCTGAGCCAGTGTAAGACCATGTCTGGGACAT
18636424 GGCATCGGCATG
1 GGCATCGGCATG
18636436 AGGCATCGTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (48 bp):
GGCATCGGCATGGTTATCTGAGCCAGTGTAAGACCATGTCTGGGACAT
Found at i:18639936 original size:39 final size:39
Alignment explanation
Indices: 18639890--18640063 Score: 231
Period size: 39 Copynumber: 4.5 Consensus size: 39
18639880 ATTCACTTTT
* * *
18639890 AAGCATATACCACATTACACATATAATCAAATAATATTC
1 AAGCATATATCACAATACACATATAATCAAATAACATTC
* * *
18639929 AAACATATATCACAATACACGTATAATCACATAACATTC
1 AAGCATATATCACAATACACATATAATCAAATAACATTC
* * * *
18639968 AAGCATATATCATAATACTCATATAATCACATAACTTTC
1 AAGCATATATCACAATACACATATAATCAAATAACATTC
* *
18640007 AAGCATATATCACAATACTCATATAATCAAATAACATTT
1 AAGCATATATCACAATACACATATAATCAAATAACATTC
*
18640046 AAGCATATATCATAATAC
1 AAGCATATATCACAATAC
18640064 TCAAAAACAT
Statistics
Matches: 119, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 119 1.00
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.29
Consensus pattern (39 bp):
AAGCATATATCACAATACACATATAATCAAATAACATTC
Found at i:18639979 original size:22 final size:22
Alignment explanation
Indices: 18639954--18640020 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 22
18639944 TACACGTATA
18639954 ATCACATAACATTCAAGCATAT
1 ATCACATAACATTCAAGCATAT
* * *
18639976 AT--CATAATACTC-A-TATA-
1 ATCACATAACATTCAAGCATAT
*
18639993 ATCACATAACTTTCAAGCATAT
1 ATCACATAACATTCAAGCATAT
18640015 ATCACA
1 ATCACA
18640021 ATACTCATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
17 2 0.06
18 3 0.09
19 8 0.24
20 9 0.27
21 3 0.09
22 8 0.24
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (22 bp):
ATCACATAACATTCAAGCATAT
Found at i:18640008 original size:78 final size:78
Alignment explanation
Indices: 18639867--18640066 Score: 258
Period size: 78 Copynumber: 2.5 Consensus size: 78
18639857 TAGTTCATTT
* * * * * *
18639867 ACATGATAATCACATTCACTTTTAAGCATATACCACATTACACATATAATCAAATAATATTCAAA
1 ACAT-ATAATCACA-TAACATTTAAGCATATATCATAATACTCATATAATCAAATAATATTCAAA
18639932 CATATATCACAATAC
64 CATATATCACAATAC
* * * *
18639947 ACGTATAATCACATAACATTCAAGCATATATCATAATACTCATATAATCACATAACT-TTCAAGC
1 ACATATAATCACATAACATTTAAGCATATATCATAATACTCATATAATCAAATAA-TATTCAAAC
18640011 ATATATCACAATAC
65 ATATATCACAATAC
* *
18640025 TCATATAATCAAATAACATTTAAGCATATATCATAATACTCA
1 ACATATAATCACATAACATTTAAGCATATATCATAATACTCA
18640067 AAAACATGTT
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
78 92 0.88
79 10 0.10
80 3 0.03
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.30
Consensus pattern (78 bp):
ACATATAATCACATAACATTTAAGCATATATCATAATACTCATATAATCAAATAATATTCAAACA
TATATCACAATAC
Found at i:18642916 original size:51 final size:51
Alignment explanation
Indices: 18642857--18642961 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
18642847 CCTTTCTCAT
18642857 TGTTTGCAAAATGTCCCACTATTGTTGTCCTATTTGGCTATTCATGTTTAA
1 TGTTTGCAAAATGTCCCACTATTGTTGTCCTATTTGGCTATTCATGTTTAA
*
18642908 TGTTTGCAAAATGTCCCACTATTGTTGTCCTATTTGGCTATTCGTGTTTAA
1 TGTTTGCAAAATGTCCCACTATTGTTGTCCTATTTGGCTATTCATGTTTAA
18642959 TGT
1 TGT
18642962 CCCAGCAGAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (51 bp):
TGTTTGCAAAATGTCCCACTATTGTTGTCCTATTTGGCTATTCATGTTTAA
Found at i:18647889 original size:5 final size:6
Alignment explanation
Indices: 18647842--18647895 Score: 53
Period size: 5 Copynumber: 9.7 Consensus size: 6
18647832 CTTAATCACT
* * *
18647842 TTAATA TTAA-A TTAATA -TAATA TTTATC TAAATA TT-ATA TTAAT-
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
18647886 TTAATA TTAA
1 TTAATA TTAA
18647896 ATCTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
5 20 0.53
6 18 0.47
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:18647908 original size:33 final size:33
Alignment explanation
Indices: 18647845--18647908 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
18647835 AATCACTTTA
* *
18647845 ATATTAAATTAATATAATATTTATCTAAATATT
1 ATATTAAATTAATATAATATCTATCAAAATATT
*
18647878 ATATTAATTTAATATTAA-ATCTATCAAAATA
1 ATATTAAATTAATA-TAATATCTATCAAAATA
18647909 ATATTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (33 bp):
ATATTAAATTAATATAATATCTATCAAAATATT
Found at i:18649170 original size:11 final size:12
Alignment explanation
Indices: 18649141--18649173 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
18649131 ATGTCAAGTG
18649141 AATTAATTCACA
1 AATTAATTCACA
*
18649153 GATTAATTCA-A
1 AATTAATTCACA
18649164 AATTAATTCA
1 AATTAATTCA
18649174 TCTTGAGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (12 bp):
AATTAATTCACA
Found at i:18658837 original size:23 final size:22
Alignment explanation
Indices: 18658811--18658853 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
18658801 CGATATACAA
*
18658811 ATTAAGGAATTATTAAAAAAATG
1 ATTAA-GAATTAATAAAAAAATG
*
18658834 ATTAATAATTAATAAAAAAA
1 ATTAAGAATTAATAAAAAAA
18658854 ACTAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (22 bp):
ATTAAGAATTAATAAAAAAATG
Found at i:18661617 original size:17 final size:17
Alignment explanation
Indices: 18661586--18661626 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
18661576 CTTTTATCTT
*
18661586 TATTTATAATGAATT-A
1 TATTCATAATGAATTCA
18661602 TATTCATAATTGAATTCA
1 TATTCATAA-TGAATTCA
18661620 -ATTCATA
1 TATTCATA
18661627 TATACGAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 13 0.59
18 1 0.05
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (17 bp):
TATTCATAATGAATTCA
Found at i:18664331 original size:12 final size:12
Alignment explanation
Indices: 18664314--18664360 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
18664304 TGGGAGTAAA
18664314 GTTTTATATTTG
1 GTTTTATATTTG
*
18664326 GTTTTATATGTTAAA
1 GTTTTATAT-TT--G
18664341 GTTTTATATTTG
1 GTTTTATATTTG
18664353 GTTTTATA
1 GTTTTATA
18664361 AGTTAATGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 17 0.57
13 2 0.07
14 2 0.07
15 9 0.30
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (12 bp):
GTTTTATATTTG
Found at i:18664344 original size:27 final size:27
Alignment explanation
Indices: 18664310--18664366 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
18664300 TTAGTGGGAG
*
18664310 TAAAGTTTTATATTTGGTTTTATATGT
1 TAAAGTTTTATATTTGGTTTTATAAGT
18664337 TAAAGTTTTATATTTGGTTTTATAAGT
1 TAAAGTTTTATATTTGGTTTTATAAGT
18664364 TAA
1 TAA
18664367 TGACATACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (27 bp):
TAAAGTTTTATATTTGGTTTTATAAGT
Found at i:18667050 original size:3 final size:3
Alignment explanation
Indices: 18667042--18667091 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
18667032 AGATATTTAC
18667042 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TTA TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
18667089 TTA
1 TTA
18667092 ATTGAGATAG
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:18669141 original size:28 final size:28
Alignment explanation
Indices: 18669101--18669155 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
18669091 ATGAAAATAG
18669101 CTTTAAAATGGTCAAAATCATATTTTCA
1 CTTTAAAATGGTCAAAATCATATTTTCA
18669129 CTTTAAAATGGTCAAAATCATATTTTC
1 CTTTAAAATGGTCAAAATCATATTTTC
18669156 TCACGGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (28 bp):
CTTTAAAATGGTCAAAATCATATTTTCA
Found at i:18673057 original size:23 final size:23
Alignment explanation
Indices: 18673027--18673073 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
18673017 ATTGAAAGAG
18673027 TTAATACTCCAAGAGGCACATGA
1 TTAATACTCCAAGAGGCACATGA
18673050 TTAATACTCCAAGAGGCACATGA
1 TTAATACTCCAAGAGGCACATGA
18673073 T
1 T
18673074 GGTTCATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (23 bp):
TTAATACTCCAAGAGGCACATGA
Found at i:18675959 original size:37 final size:38
Alignment explanation
Indices: 18675909--18676005 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 38
18675899 CGGATAGATT
18675909 CGATGAGGCGTTGGTCGCCAC-TTTGCTTCG-ACTTAGC
1 CGATGAGGCGTTGGTCGCCACTTTTGCTTCGAAC-TAGC
** ** *
18675946 CGATGAGATGTTGGTCATCACTTATTTGCTTCGAACTATC
1 CGATGAGGCGTTGGTCGCCAC-T-TTTGCTTCGAACTAGC
18675986 CGATGAGGCGTTGGTCGCCA
1 CGATGAGGCGTTGGTCGCCA
18676006 TTCTGGTGTG
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 17 0.36
40 28 0.60
41 2 0.04
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.31
Consensus pattern (38 bp):
CGATGAGGCGTTGGTCGCCACTTTTGCTTCGAACTAGC
Found at i:18676365 original size:13 final size:13
Alignment explanation
Indices: 18676338--18676374 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
18676328 AGATAGTTTG
*
18676338 GTATGAATTTATAT
1 GTATG-ATTTGTAT
18676352 GTATGATTTGTAT
1 GTATGATTTGTAT
18676365 GTATGATTTG
1 GTATGATTTG
18676375 CTAATTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (13 bp):
GTATGATTTGTAT
Found at i:18680442 original size:15 final size:15
Alignment explanation
Indices: 18680422--18680478 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
18680412 AATGTTACCA
18680422 CCACCACCACCATAG
1 CCACCACCACCATAG
*
18680437 CCACCACCTCCATAG
1 CCACCACCACCATAG
** * *
18680452 TTACCACCCCCGTAG
1 CCACCACCACCATAG
18680467 CCACCACCACCA
1 CCACCACCACCA
18680479 CCATAGCTGC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.28, C:0.54, G:0.07, T:0.11
Consensus pattern (15 bp):
CCACCACCACCATAG
Found at i:18680442 original size:18 final size:18
Alignment explanation
Indices: 18680419--18680485 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 18
18680409 TCCAATGTTA
18680419 CCACCACCACCACCATAG
1 CCACCACCACCACCATAG
*
18680437 ---CCACCACCTCCATAG
1 CCACCACCACCACCATAG
** *
18680452 TTACCA-C-CC-CCGTAG
1 CCACCACCACCACCATAG
18680467 CCACCACCACCACCATAG
1 CCACCACCACCACCATAG
18680485 C
1 C
18680486 TGCCAGCACC
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
15 23 0.61
16 3 0.08
17 3 0.08
18 9 0.24
ACGTcount: A:0.28, C:0.54, G:0.07, T:0.10
Consensus pattern (18 bp):
CCACCACCACCACCATAG
Found at i:18683003 original size:19 final size:21
Alignment explanation
Indices: 18682970--18683010 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
18682960 TAAATTATTT
*
18682970 ATTTATATAATTTAAACATAA
1 ATTTATATAATTTAAAAATAA
18682991 ATTTATAT-A-TTAAAAATAA
1 ATTTATATAATTTAAAAATAA
18683010 A
1 A
18683011 AATATCACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 1 0.05
21 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTATATAATTTAAAAATAA
Found at i:18684890 original size:5 final size:5
Alignment explanation
Indices: 18684880--18684906 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
18684870 AAGATATTAT
18684880 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
18684907 ATTAAATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:18685465 original size:29 final size:29
Alignment explanation
Indices: 18685433--18685554 Score: 88
Period size: 29 Copynumber: 4.2 Consensus size: 29
18685423 ATTATTCCTA
*
18685433 TTATTTTTATGTTTCTATTTATATTTATT
1 TTATTTTTATATTTCTATTTATATTTATT
* * * * *
18685462 TTATTATTCTAATACTA-TTATTATTTATC
1 TTATTTTTATATTTCTATTTA-TATTTATT
* * *
18685491 TAATTTTTAT-TTATCTATTTATATTTCTA
1 TTATTTTTATATT-TCTATTTATATTTATT
* * *
18685520 CTATTATTATATTTCTATTTAT-TATATTT
1 TTATTTTTATATTTCTATTTATATTTA-TT
18685549 TTATTT
1 TTATTT
18685555 CTATTTGTAT
Statistics
Matches: 67, Mismatches: 21, Indels: 10
0.68 0.21 0.10
Matches are distributed among these distances:
28 6 0.09
29 56 0.84
30 5 0.07
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (29 bp):
TTATTTTTATATTTCTATTTATATTTATT
Found at i:18685502 original size:15 final size:14
Alignment explanation
Indices: 18685434--18685544 Score: 68
Period size: 14 Copynumber: 7.6 Consensus size: 14
18685424 TTATTCCTAT
18685434 TATTTTTATGTT-TC
1 TATTTTTAT-TTATC
*
18685448 TATTTATATTTAT-
1 TATTTTTATTTATC
*
18685461 T-TTATTATTCTAATAC
1 TATTTTTATT-T-AT-C
*
18685477 TATTATTATTTATC
1 TATTTTTATTTATC
18685491 TAATTTTTATTTATC
1 T-ATTTTTATTTATC
* *
18685506 TATTTATATTTCTAC
1 TATTTTTATTTAT-C
*
18685521 TATTATTATATT-TC
1 TATTTTTAT-TTATC
18685535 TATTTATTAT
1 TATTT-TTAT
18685545 ATTTTTATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
12 6 0.08
13 4 0.05
14 28 0.36
15 28 0.36
16 4 0.05
17 8 0.10
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (14 bp):
TATTTTTATTTATC
Found at i:18685545 original size:15 final size:15
Alignment explanation
Indices: 18685509--18685554 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
18685499 ATTTATCTAT
18685509 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
18685526 TTATATTTCTATTTA
1 TTATATTTCTATTTA
*
18685541 TTATATTTTTATTT
1 TTATATTTCTATTT
18685555 CTATTTGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:18685560 original size:58 final size:57
Alignment explanation
Indices: 18685433--18685560 Score: 134
Period size: 58 Copynumber: 2.2 Consensus size: 57
18685423 ATTATTCCTA
** *
18685433 TTATTTTTATGTTTCTATTTATATTTATTTTATTATTCTAATACTATTATTATTTATC
1 TTATTTTTAT-TTTCTATTTATATTTATACTATTATTATAATACTATTATTATTTATC
* * * *
18685491 TAATTTTTATTTATCTATTTATATTTCTACTATTATTATATTTCTATTTATTATATT-T-
1 TTATTTTTATTT-TCTATTTATATTTATACTATTATTATAATACTA-TTATTAT-TTATC
*
18685549 TTATTTCTATTT
1 TTATTTTTATTT
18685561 GTATACTAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
57 2 0.03
58 46 0.79
59 8 0.14
60 2 0.03
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (57 bp):
TTATTTTTATTTTCTATTTATATTTATACTATTATTATAATACTATTATTATTTATC
Found at i:18685650 original size:24 final size:25
Alignment explanation
Indices: 18685620--18685680 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
18685610 ACTCTTGTTA
*
18685620 TTAACATTTTAT-TTATTTATTTATT
1 TTAACATTTTATGTTA-TTATCTATT
*
18685645 TT-ACATTTTTTGTTATTATCTATT
1 TTAACATTTTATGTTATTATCTATT
*
18685669 TTAACTTTTTAT
1 TTAACATTTTAT
18685681 ATAACGCTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 18 0.60
25 12 0.40
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.67
Consensus pattern (25 bp):
TTAACATTTTATGTTATTATCTATT
Found at i:18687100 original size:4 final size:4
Alignment explanation
Indices: 18687082--18687122 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
18687072 TATAGAAAGG
* *
18687082 TAAA GAAA T-AA TAAA TAAA TAAA TGAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
18687123 TAAAGAAGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:18687112 original size:16 final size:15
Alignment explanation
Indices: 18687082--18687126 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 15
18687072 TATAGAAAGG
*
18687082 TAAAGAAATAATAAA
1 TAAATAAATAATAAA
18687097 TAAATAAATGAATAAA
1 TAAATAAAT-AATAAA
18687113 TAAATAAAT-ATAAA
1 TAAATAAATAATAAA
18687127 GAAGACAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 5 0.18
15 8 0.29
16 15 0.54
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (15 bp):
TAAATAAATAATAAA
Found at i:18689930 original size:16 final size:17
Alignment explanation
Indices: 18689909--18689941 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18689899 AGCATCGTAC
*
18689909 ACGAAAA-AATGTTATT
1 ACGAAAACAAAGTTATT
18689925 ACGAAAACAAAGTTATT
1 ACGAAAACAAAGTTATT
18689942 TTACTACTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (17 bp):
ACGAAAACAAAGTTATT
Found at i:18698774 original size:58 final size:58
Alignment explanation
Indices: 18698652--18698820 Score: 295
Period size: 58 Copynumber: 2.9 Consensus size: 58
18698642 GTGCCCACTG
* *
18698652 ACCGATCTCGCACACATAGTGCTCGGTTGAA-GAACTCGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
18698709 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
* *
18698767 ACTGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTC
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTC
18698821 TAATCATTCG
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
57 30 0.28
58 77 0.72
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (58 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
Found at i:18698808 original size:29 final size:29
Alignment explanation
Indices: 18698659--18698817 Score: 121
Period size: 29 Copynumber: 5.5 Consensus size: 29
18698649 CTGACCGATC
* * *
18698659 TCGCACACATAGTGCTCGGTTGAA-GAAC
1 TCGCACACACAGTGCTCGGTTAAAGGAAT
** **
18698687 TCGCACACACAGTGCCTCAATT-ACCG-AT
1 TCGCACACACAGTG-CTCGGTTAAAGGAAT
*
18698715 CTCGCACACATAGTGCTCGGTTAAAGGAAT
1 -TCGCACACACAGTGCTCGGTTAAAGGAAT
** **
18698745 TCGCACACACAGTGCCTCAATT-ACTG-AT
1 TCGCACACACAGTG-CTCGGTTAAAGGAAT
*
18698773 CTCGCACACATAGTGCTCGGTTAAAGGAAT
1 -TCGCACACACAGTGCTCGGTTAAAGGAAT
*
18698803 TTGCACACACAGTGC
1 TCGCACACACAGTGC
18698818 CTCTAATCAT
Statistics
Matches: 100, Mismatches: 22, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
28 27 0.27
29 64 0.64
30 9 0.09
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (29 bp):
TCGCACACACAGTGCTCGGTTAAAGGAAT
Found at i:18699035 original size:43 final size:43
Alignment explanation
Indices: 18698986--18699281 Score: 450
Period size: 43 Copynumber: 6.9 Consensus size: 43
18698976 CACCAGCATT
*
18698986 AAGCCTGCTAGGCACGAAGACCCGAATACACATCACCGGCACG
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACG
* * * *
18699029 AAGCCTGCTAGGCACGAAAGCCTGAATACACATCACCGACACA
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACG
*
18699072 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACG
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACG
* *
18699115 AAGCCTGCTAGGCACGAAGGCCCAAATACACATCATCGGCACG
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACG
* * *
18699158 AAGCCTGCAAGGCATGAAGGCTCGAATACACATCAGCC-GCACG
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCA-CCGGCACG
*
18699201 AAGCCTGCTAGGCACGAAGGCCTGAATACACATCACCGGCACG
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACG
* *
18699244 CAGCCTGCTAGGCACGAAGGCTCGAATACACATCACCG
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCG
18699282 AGTTTCATGC
Statistics
Matches: 226, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
42 2 0.01
43 223 0.99
44 1 0.00
ACGTcount: A:0.32, C:0.33, G:0.24, T:0.11
Consensus pattern (43 bp):
AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACG
Found at i:18702913 original size:77 final size:77
Alignment explanation
Indices: 18702786--18702939 Score: 299
Period size: 77 Copynumber: 2.0 Consensus size: 77
18702776 TGGAATACGT
18702786 TATGAATACGGTCTAGATCTGGGGCTAACTCCAACTGATAAGTGATCGGTCCCACTCGCTTCAGA
1 TATGAATACGGTCTAGATCTGGGGCTAACTCCAACTGATAAGTGATCGGTCCCACTCGCTTCAGA
18702851 ATTAGATAAGGC
66 ATTAGATAAGGC
18702863 TATGAATACGGTCTAGATCTGGGGCTAACTCCAACTGATAAGTGATCGGTCCCACTCGCTTCAGA
1 TATGAATACGGTCTAGATCTGGGGCTAACTCCAACTGATAAGTGATCGGTCCCACTCGCTTCAGA
*
18702928 ATTAGATGAGGC
66 ATTAGATAAGGC
18702940 CCAATAAACC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (77 bp):
TATGAATACGGTCTAGATCTGGGGCTAACTCCAACTGATAAGTGATCGGTCCCACTCGCTTCAGA
ATTAGATAAGGC
Found at i:18719365 original size:33 final size:33
Alignment explanation
Indices: 18719323--18719389 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
18719313 TCTGATAAAT
*
18719323 TGAATTGAATTGAATTATTGTATAG-TTCGAAAA
1 TGAATTGAATTGAATTATTATATAGATT-GAAAA
18719356 TGAATTGAATTGAATTATTATATAGATTGAAAA
1 TGAATTGAATTGAATTATTATATAGATTGAAAA
18719389 T
1 T
18719390 TGGACCAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.42, C:0.01, G:0.16, T:0.40
Consensus pattern (33 bp):
TGAATTGAATTGAATTATTATATAGATTGAAAA
Found at i:18723147 original size:18 final size:19
Alignment explanation
Indices: 18723124--18723166 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
18723114 ATATATTCTC
18723124 ATTATTATCATT-ACTTTT
1 ATTATTATCATTAACTTTT
* *
18723142 ATTATTATTATTAATTTTT
1 ATTATTATCATTAACTTTT
18723161 ATTATT
1 ATTATT
18723167 TGACGTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTATTATCATTAACTTTT
Found at i:18732666 original size:25 final size:24
Alignment explanation
Indices: 18732631--18732681 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
18732621 CATACCGCAA
18732631 CTCTTTATGAGCATCCTGATATAGG
1 CTCTTTATGAGCATCCTGATAT-GG
* *
18732656 CTCTTTGTGAGCTTCCTGATATGG
1 CTCTTTATGAGCATCCTGATATGG
18732680 CT
1 CT
18732682 TACTTGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.39
Consensus pattern (24 bp):
CTCTTTATGAGCATCCTGATATGG
Found at i:18734701 original size:43 final size:43
Alignment explanation
Indices: 18734635--18734719 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
18734625 GCTGCTATAA
*
18734635 AACATGACATTTATCGGCATTTTTCCCACAAACGCCGCTAAAG
1 AACATGACATTTAGCGGCATTTTTCCCACAAACGCCGCTAAAG
* * *
18734678 AACATGACCTTTAGCGGCGTTTTTCCCACAAACGCTGCTAAA
1 AACATGACATTTAGCGGCATTTTTCCCACAAACGCCGCTAAA
18734720 ATTAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (43 bp):
AACATGACATTTAGCGGCATTTTTCCCACAAACGCCGCTAAAG
Found at i:18734987 original size:6 final size:6
Alignment explanation
Indices: 18734976--18735052 Score: 57
Period size: 6 Copynumber: 12.5 Consensus size: 6
18734966 CTTAAATATT
* *
18734976 AAAATA AAAATA AAAATA TAGAATCA AAAAT- AAAATA AATAATA AAAATT
1 AAAATA AAAATA AAAATA -AAAAT-A AAAATA AAAATA AA-AATA AAAATA
* * * * *
18735026 AGATTA AATATA AAGATA TAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
18735053 TACAGCAAGT
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
5 5 0.09
6 34 0.63
7 14 0.26
8 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.23
Consensus pattern (6 bp):
AAAATA
Found at i:18734994 original size:20 final size:20
Alignment explanation
Indices: 18734969--18735010 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
18734959 AAGTTATCTT
18734969 AAATATTAAAAT-AAAAATAA
1 AAATA-TAAAATCAAAAATAA
*
18734989 AAATATAGAATCAAAAATAA
1 AAATATAAAATCAAAAATAA
18735009 AA
1 AA
18735011 TAAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (20 bp):
AAATATAAAATCAAAAATAA
Done.