Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold205
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: 1179939
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.30
Warning! 53951 characters in sequence are not A, C, G, or T
File 3 of 7
Found at i:327981 original size:16 final size:17
Alignment explanation
Indices: 327951--327992 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
327941 TTTTTTGCTA
327951 TTTCGATTCTTTTTTTG
1 TTTCGATTCTTTTTTTG
327968 TTTCGATT-TTTTTTTG
1 TTTCGATTCTTTTTTTG
*
327984 TTTTGATTC
1 TTTCGATTC
327993 CTCTCTTGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.07, C:0.10, G:0.12, T:0.71
Consensus pattern (17 bp):
TTTCGATTCTTTTTTTG
Found at i:328044 original size:13 final size:13
Alignment explanation
Indices: 328028--328052 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
328018 TTTTTTCCCC
328028 TCTTTTTTTTCTT
1 TCTTTTTTTTCTT
328041 TCTTTTTTTTCT
1 TCTTTTTTTTCT
328053 CTTCCACAAC
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TCTTTTTTTTCTT
Found at i:328817 original size:33 final size:29
Alignment explanation
Indices: 328740--328836 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 29
328730 GGCTCTCTTT
328740 TTTTTTATTTGATTTT-TTTATTATATATA
1 TTTTTTATTT-ATTTTATTTATTATATATA
*
328769 -TTTTTATATATTTTTATTTAATTATGATTATA
1 TTTTTTATTTA-TTTTATTT-ATTAT-A-TATA
*
328801 TTTTTTAATTTATTTTATTTTATT-T-TAAA
1 TTTTTT-ATTTATTTTA-TTTATTATATATA
328830 TTTTTTA
1 TTTTTTA
328837 AAAATAACCT
Statistics
Matches: 57, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
27 1 0.02
28 13 0.23
29 12 0.21
30 5 0.09
31 1 0.02
32 5 0.09
33 13 0.23
34 7 0.12
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (29 bp):
TTTTTTATTTATTTTATTTATTATATATA
Found at i:328823 original size:24 final size:23
Alignment explanation
Indices: 328770--328823 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
328760 TTATATATAT
328770 TTTTATATATTTTTATTTAATTA
1 TTTTATATATTTTTATTTAATTA
* *
328793 TGATTATAT-TTTTTAATTTATTTTA
1 T-TTTATATATTTTT-ATTTA-ATTA
328818 TTTTAT
1 TTTTAT
328824 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 6 0.24
24 15 0.60
25 4 0.16
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTATATATTTTTATTTAATTA
Found at i:331198 original size:20 final size:21
Alignment explanation
Indices: 331173--331221 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
331163 GGCATAATGC
*
331173 ATCGATACAATTCT-TCATGT
1 ATCGATACAATTCTCCCATGT
*
331193 ATCGATAC-ATTGTCCCATGT
1 ATCGATACAATTCTCCCATGT
331213 ATCGATACA
1 ATCGATACA
331222 TTTCATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (21 bp):
ATCGATACAATTCTCCCATGT
Found at i:331330 original size:19 final size:19
Alignment explanation
Indices: 331250--331333 Score: 72
Period size: 19 Copynumber: 4.7 Consensus size: 19
331240 CTGCCACTTT
* *
331250 CATGTATCAATACAATTGAG
1 CATGTATCGATACAA-TGAA
*
331270 TATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
331289 CATGTGTTGATACAAT---
1 CATGTATCGATACAATGAA
331305 -A--TATCGATACAATGAA
1 CATGTATCGATACAATGAA
331321 CATGTATCGATAC
1 CATGTATCGATAC
331334 TTTCTAGGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
13 10 0.20
15 1 0.02
17 1 0.02
19 25 0.50
20 13 0.26
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:333653 original size:20 final size:20
Alignment explanation
Indices: 333611--333657 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
333601 TTTGTTCATG
* *
333611 ATTTTGATGAAAAACGGATA
1 ATTTTGATGAAAAACGAAGA
* *
333631 ATTTTGATGTAAAATGAAGA
1 ATTTTGATGAAAAACGAAGA
333651 ATTTTGA
1 ATTTTGA
333658 AACGGATTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (20 bp):
ATTTTGATGAAAAACGAAGA
Found at i:334107 original size:140 final size:140
Alignment explanation
Indices: 333855--334133 Score: 531
Period size: 140 Copynumber: 2.0 Consensus size: 140
333845 TACATTTTGA
333855 AAAATTTCTAAAATTTTGGCAAAAGTTAGTATTGATTTTCATCCTATCAATCCTAATTCAAATCA
1 AAAATTTCTAAAATTTTGGCAAAAGTTAGTATTGATTTTCATCCTATCAATCCTAATTCAAATCA
* * *
333920 AACAAGCAAACATTCATTCATCAACGAGAAGAACAATAAATTCACATACAATTAAACACATTTCA
66 AACAAACAAACATTCATTCATAAACAAGAAGAACAATAAATTCACATACAATTAAACACATTTCA
333985 ACAACAAATC
131 ACAACAAATC
333995 AAAATTTCTAAAATTTTGGCAAAAGTTAGTATTGATTTTCATCCTATCAATCCTAATTCAAATCA
1 AAAATTTCTAAAATTTTGGCAAAAGTTAGTATTGATTTTCATCCTATCAATCCTAATTCAAATCA
334060 AACAAACAAACATTCATTCATAAACAAGAAGAACAATAAATTCACATACAATTAAACACATTTCA
66 AACAAACAAACATTCATTCATAAACAAGAAGAACAATAAATTCACATACAATTAAACACATTTCA
334125 ACAACAAAT
131 ACAACAAAT
334134 AATCCAAAAA
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 136 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.29
Consensus pattern (140 bp):
AAAATTTCTAAAATTTTGGCAAAAGTTAGTATTGATTTTCATCCTATCAATCCTAATTCAAATCA
AACAAACAAACATTCATTCATAAACAAGAAGAACAATAAATTCACATACAATTAAACACATTTCA
ACAACAAATC
Found at i:335251 original size:19 final size:20
Alignment explanation
Indices: 335208--335258 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
335198 TACAAGCCAA
**
335208 TGTATCGATACATTTTTTGG
1 TGTATCGATACATACTTTGG
335228 TGTATCGATACATACTTT-G
1 TGTATCGATACATACTTTGG
*
335247 TGTATCGGTACA
1 TGTATCGATACA
335259 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATACTTTGG
Found at i:335363 original size:20 final size:20
Alignment explanation
Indices: 335310--335365 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
335300 ACATCTTTTT
* *
335310 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGAAA
335330 CATGTATCGATACTTTGAAA
1 CATGTATCGATACTTTGAAA
**
335350 TGTGTATCGATACTTT
1 CATGTATCGATACTTT
335366 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGAAA
Found at i:337810 original size:13 final size:13
Alignment explanation
Indices: 337792--337830 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
337782 ATAATCCCCC
* *
337792 TGTATCGATATAG
1 TGTATCGATACAA
337805 TGTATCGATACAA
1 TGTATCGATACAA
337818 TGTATCGATACAA
1 TGTATCGATACAA
337831 AGAAAGATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:344028 original size:13 final size:13
Alignment explanation
Indices: 344010--344035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
344000 CATTTTTTGG
344010 TGTATCGATACAT
1 TGTATCGATACAT
344023 TGTATCGATACAT
1 TGTATCGATACAT
344036 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:344032 original size:33 final size:32
Alignment explanation
Indices: 343990--344053 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
343980 TACCAGCCAA
**
343990 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTT-GTGTATCGATACAT
*
344023 TGTATCGATACATACTTTGTGTATCTATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
344054 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.44
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:348320 original size:12 final size:12
Alignment explanation
Indices: 348303--348335 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
348293 TGCAAGTCAA
348303 CTTCATCATTAT
1 CTTCATCATTAT
348315 CTTCATCATTAT
1 CTTCATCATTAT
348327 CTTCATCAT
1 CTTCATCAT
348336 CTTTGATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCATCATTAT
Found at i:351541 original size:57 final size:56
Alignment explanation
Indices: 351470--351586 Score: 139
Period size: 57 Copynumber: 2.1 Consensus size: 56
351460 AGACAATTTA
* * * *
351470 TCTTAAGATATGTCTACTTT-GCACATTATCCTTGATAAAACCA-GCTTATCTATATTG
1 TCTTAACACATGTCTACTTTAG-ACATTAT-CTTGATAAAACAATG-TTATCCATATTG
* *
351527 TCTTAACACATGTCTACTTTAGACATTATCTTGTTAACACAATGTTATCCATATTG
1 TCTTAACACATGTCTACTTTAGACATTATCTTGATAAAACAATGTTATCCATATTG
351583 TCTT
1 TCTT
351587 TAATAAGACA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
56 25 0.48
57 26 0.50
58 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (56 bp):
TCTTAACACATGTCTACTTTAGACATTATCTTGATAAAACAATGTTATCCATATTG
Found at i:351638 original size:28 final size:28
Alignment explanation
Indices: 351571--351673 Score: 118
Period size: 28 Copynumber: 3.6 Consensus size: 28
351561 TAACACAATG
* *
351571 TTATCCATATTGTCTTTAATAAGACAAGC
1 TTATCCATATTATC-TTAATAAAACAAGC
* * *
351600 TTATCCGTATTATCTTAGTAATACAAGC
1 TTATCCATATTATCTTAATAAAACAAGC
* *
351628 TTATCAATATTGTCTTAATAAAACAAGC
1 TTATCCATATTATCTTAATAAAACAAGC
351656 TTA-CCGATATTATCTTAA
1 TTATCC-ATATTATCTTAA
351674 CACATATCTA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
27 1 0.02
28 49 0.79
29 12 0.19
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (28 bp):
TTATCCATATTATCTTAATAAAACAAGC
Found at i:352379 original size:19 final size:18
Alignment explanation
Indices: 352354--352482 Score: 117
Period size: 19 Copynumber: 7.8 Consensus size: 18
352344 ATTTCAACAA
352354 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
352372 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
352388 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
352404 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
352420 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
352436 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
352452 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
352468 TTTTGTATCGATACA
1 -TTTGTATCGATACA
352483 ATGTATCGCT
Statistics
Matches: 92, Mismatches: 0, Indels: 37
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.36
15 6 0.07
17 6 0.07
18 1 0.01
19 46 0.50
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:352393 original size:13 final size:13
Alignment explanation
Indices: 352375--352463 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
352365 ACATAAGTGT
352375 TGTATCGATACAA
1 TGTATCGATACAA
352388 TGTATCGATACATAA
1 TGTATCGATAC--AA
352403 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
352420 TGTATCGATACATAA
1 TGTATCGATAC--AA
352435 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
352452 TGTATCGATACA
1 TGTATCGATACA
352464 TAAGTTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:352393 original size:32 final size:32
Alignment explanation
Indices: 352356--352490 Score: 261
Period size: 32 Copynumber: 4.2 Consensus size: 32
352346 TTCAACAATT
352356 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
352388 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
352420 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
352452 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
352484 TGTATCG
1 TGTATCG
352491 CTACGAAGCT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 102 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:352553 original size:13 final size:13
Alignment explanation
Indices: 352535--352559 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
352525 ATTACTCAAA
352535 TGTATCGATACAT
1 TGTATCGATACAT
352548 TGTATCGATACA
1 TGTATCGATACA
352560 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:352608 original size:52 final size:52
Alignment explanation
Indices: 352568--352696 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
352558 CACTGATCTT
352568 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
352620 TGTATCGATACATACAGGCAAATTTGCCCAGATTTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
352672 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
352697 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:356797 original size:98 final size:97
Alignment explanation
Indices: 356629--356864 Score: 316
Period size: 98 Copynumber: 2.4 Consensus size: 97
356619 TTTATTTATC
* *** **
356629 GGGGATACTTCAA-CCTCATTTTTAAACTTGCCAAGATTTAAGTCTTATTTTTTCTTAAATTGTC
1 GGGGATACTCCAACCCT-ATTTTTAAACTCATCAAGATTTAAGTCTTATTTTTAATTAAATTGTC
**
356693 ATCATCAGGGATACTCCAA-CCCATTCTTTTGA
65 ATCATCAGGGATACTCCAACCCCATTCTTTCAA
* * *
356725 GGGGATAC-CCTAACCTTATTTTTAAAAGTCATCAAGATTTAAGTCTTCGTTTTTAATTAAATTG
1 GGGGATACTCC-AACCCTATTTTT-AAACTCATCAAGATTTAAGTCTT-ATTTTTAATTAAATTG
356789 TCATCATCAGGGATACTCCAACCCCATTCTTTCAA
63 TCATCATCAGGGATACTCCAACCCCATTCTTTCAA
356824 GGGGATACTCCAACCCTATTTTTAAACTCATCAAGATTTAA
1 GGGGATACTCCAACCCTATTTTTAAACTCATCAAGATTTAA
356865 ATTCTATTTT
Statistics
Matches: 121, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
95 1 0.01
96 16 0.13
97 21 0.17
98 51 0.42
99 30 0.25
100 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (97 bp):
GGGGATACTCCAACCCTATTTTTAAACTCATCAAGATTTAAGTCTTATTTTTAATTAAATTGTCA
TCATCAGGGATACTCCAACCCCATTCTTTCAA
Found at i:357285 original size:21 final size:21
Alignment explanation
Indices: 357248--357287 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
357238 GGGTATCTCT
*
357248 CTAGTTTTTAACATAAAATAC
1 CTAGTTTTCAACATAAAATAC
357269 CTAGTTTTCAA-AGTAAAAT
1 CTAGTTTTCAACA-TAAAAT
357288 CCATAGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (21 bp):
CTAGTTTTCAACATAAAATAC
Found at i:362482 original size:12 final size:12
Alignment explanation
Indices: 362462--362492 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
362452 AAATCTTTAC
362462 AAAAA-ACAAAA
1 AAAAACACAAAA
362473 AAAAACACAAAA
1 AAAAACACAAAA
362485 AAAAACAC
1 AAAAACAC
362493 TTATTCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAACACAAAA
Found at i:377464 original size:12 final size:12
Alignment explanation
Indices: 377441--377475 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
377431 ACCTTCTCTT
377441 AAAA-AAAA-AA
1 AAAACAAAACAA
377451 AAAACAAAACAA
1 AAAACAAAACAA
377463 AAAACAAAACAA
1 AAAACAAAACAA
377475 A
1 A
377476 GAAAAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.17
11 4 0.17
12 15 0.65
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAACAAAACAA
Found at i:377466 original size:17 final size:16
Alignment explanation
Indices: 377441--377481 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
377431 ACCTTCTCTT
377441 AAAAAAAAAAAAAACA
1 AAAAAAAAAAAAAACA
*
377457 AAACAAAAAACAAAACA
1 AAA-AAAAAAAAAAACA
377474 AAGAAAAA
1 AA-AAAAA
377482 GATAGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 18 0.82
18 1 0.05
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAACA
Found at i:378633 original size:63 final size:61
Alignment explanation
Indices: 378465--379192 Score: 423
Period size: 58 Copynumber: 12.3 Consensus size: 61
378455 CCTTCCGCTT
* * * * **
378465 TTTAGCCCTCAAAGAGCAGGATGCC-TTTC-CTTTTAAAGCCAACACAAGTTGGTTGCATT
1 TTTAGTCCTCAAAAAGCAGGATGCCTTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
378524 TTTCAG-CCTC-AAAAGCA-GACGCTTTTTCT-TTTTAAAGCCCACACAAGTTGGTGGAACC
1 TTT-AGTCCTCAAAAAGCAGGATGCCTTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACC
378582 TTTAGTCCTCAAAAAGCAGGATGCCTTTTCTACGTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTTAGTCCTCAAAAAGCAGGATGCCTTTTCT-C-TTTTAAAGCCCACACAAGTTGGTGGCACC
378645 TTTAGTCCTCAAAGAGAGCAGGATG-C----CT-TTTTAAA-CCCACACAAGTTGGTGGCA-C
1 TTTAGTCCTCAAA-A-AGCAGGATGCCTTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
378700 TTCCCAGTCCTC-AAGAGCAGGACGCCTTCTC-CTTTT-AAG-CCACACAAGTTTGTGGCA-C
1 TT--TAGTCCTCAAAAAGCAGGATGCCTTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * *
378758 TTCCTAGTCTTCAAATAGCAGGA---C---GC-CTTTTAAAG-CCACACAAGTTGGTGGCAAC
1 TT--TAGTCCTCAAAAAGCAGGATGCCTTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
378813 TTCCCCAGTCTTTCAAAGAGAGGCAGGACG-C-TTCCTCCTTTAAAGCCCACACAAGTTGGTGGC
1 TT---TAGTC-CTCAAA-A-A-GCAGGATGCCTTTTCTCTTTTAAAGCCCACACAAGTTGGTGGC
378876 A-C
59 ACC
* *
378878 TTCCTGGTCCTCAAAGAA-CAGGATG------C-CTTTTAAAGCCC-CACAAGTTGGTGGCA-T
1 TT--TAGTCCTCAAA-AAGCAGGATGCCTTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
378932 TTTCCAGCCCTCAAAGAGCGGGATGCC-TTTCT-TTTAAAAGCCCACCCAAGTTGGTGGCACCC
1 TTT--AGTCCTCAAAAAGCAGGATGCCTTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCA-CC
** *
378994 TTTAGTCC-C-AAAAGCAGGAT-TTTTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTAGTCCTCAAAAAGCAGGATGCCTTTTCTCTTTT-AAAGCCCACACAAGTTGGTGGCACC
* * *
379053 -TTAGTCCCTTCAAAGAGTAGGATGCCTTTT-TCTTTTTCAAAGCCACACACAATTTGGTGGCAC
1 TTTAGT-CC-TCAAAAAGCAGGATGCCTTTTCTC-TTTT-AAAGCC-CACACAAGTTGGTGGCAC
379116 C
61 C
* * * **
379117 TTTCAGTCCCCAAAGAGCAGGA--CC----CT-TTTCAAAGCCCACACAAGTTGG-GGCATTT
1 TTT-AGTCCTCAAAAAGCAGGATGCCTTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCA-CC
*
379172 TTTAGTCCTCAAAGAGCAGGA
1 TTTAGTCCTCAAAAAGCAGGA
379193 CACCTTTCAA
Statistics
Matches: 552, Mismatches: 57, Indels: 125
0.75 0.08 0.17
Matches are distributed among these distances:
52 1 0.00
53 7 0.01
54 80 0.14
55 32 0.06
56 35 0.06
57 29 0.05
58 89 0.16
59 49 0.09
60 66 0.12
61 1 0.00
62 18 0.03
63 63 0.11
64 37 0.07
65 24 0.04
66 21 0.04
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (61 bp):
TTTAGTCCTCAAAAAGCAGGATGCCTTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:378745 original size:177 final size:178
Alignment explanation
Indices: 378465--378788 Score: 399
Period size: 178 Copynumber: 1.8 Consensus size: 178
378455 CCTTCCGCTT
* * **
378465 TTTAGCCCTCAAAGAGCAGGATGCCTTTCCTTTTAAAGCCAACACAAGTTGGTTGCATTTTTCAG
1 TTTAGCCCTCAAAGAGCAGGATGCC-TT-CTTTTAAAGCCAACACAAGTTGGTGGCACTTCCCAG
* * *
378530 CCTCAAAAGCAGACGCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGAACCTT-TAGTCCTCAA
64 CCTCAAAAGCAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGAA-CTTCTAGTCCTCAA
*
378594 AAAGCAGGATGCCTTTTCTACGTTTTAAAGCCCACACAAGTTGGTGGCACC
128 AAAGCAGGACGCCTTTTCTACGTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
378645 TTTAGTCCTCAAAGAGAGCAGGATGCC-T-TTTTAAA-CCCACACAAGTTGGTGGCACTTCCCAG
1 TTTAGCCCTC-AA-AGAGCAGGATGCCTTCTTTTAAAGCCAACACAAGTTGGTGGCACTTCCCAG
* * * *
378707 TCCTCAAGAGCAGGACGCCTTCTCCTTTT-AAG-CCACACAAGTTTGTGGCACTTCCTAGTCTTC
64 -CCTCAAAAGCA-GACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGAACTT-CTAGTCCTC
*
378770 AAATAGCAGGACGCCTTTT
126 AAAAAGCAGGACGCCTTTT
378789 AAAGCCACAC
Statistics
Matches: 123, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
176 3 0.02
177 38 0.31
178 44 0.36
179 13 0.11
180 10 0.08
181 2 0.02
182 13 0.11
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (178 bp):
TTTAGCCCTCAAAGAGCAGGATGCCTTCTTTTAAAGCCAACACAAGTTGGTGGCACTTCCCAGCC
TCAAAAGCAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGAACTTCTAGTCCTCAAAAA
GCAGGACGCCTTTTCTACGTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:378802 original size:54 final size:54
Alignment explanation
Indices: 378616--379504 Score: 439
Period size: 54 Copynumber: 15.9 Consensus size: 54
378606 CTTTTCTACG
*
378616 TTTTAAAGCCCACACAAGTTGGTGGCACCTT--TAGTCCTCAAAGAGAGCAGGATGCC
1 TTTTAAAG-CCACACAAGTTGGTGGCA-CTTCCTAGTCCTC-AA-AGAGCAGGACGCC
* *
378672 TTTTTAAACCCACACAAGTTGGTGGCACTTCCCAGTCCTC-AAGAGCAGGACGCCTTC
1 -TTTTAAAGCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG-C--C
* * * *
378729 TCCTTTTAAGCCACACAAGTTTGTGGCACTTCCTAGTCTTCAAATAGCAGGACGCC
1 T--TTTAAAGCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCC
* *
378785 TTTTAAAGCCACACAAGTTGGTGGCAACTTCCCCAGTCTTTCAAAGAGAGGCAGGACGCTTCC
1 TTTTAAAGCCACACAAGTTGGTGGC-ACTT-CCTAGTC-CTC-AA-AGA-GCAGGACG---CC
* * *
378848 TCCTTTAAAGCCCACACAAGTTGGTGGCACTTCCTGGTCCTCAAAGAACAGGATGCC
1 T--TTTAAAG-CCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCC
* * * * *
378905 TTTTAAAGCCCCACAAGTTGGTGGCATTTTCC-AGCCCTCAAAGAGCGGGATGCCTTTC
1 TTTTAAAGCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACG-C---C
* ***
378963 TTTTAAAAGCCCACCCAAGTTGGTGGCAC--CCTTTAGTCC-CAAA-AGCAGGATTTTTTTTTC
1 TTTT-AAAG-CCACACAAGTTGGTGGCACTTCC--TAGTCCTCAAAGAGCAGGA------CGCC
* * *
379023 TTTTCAAAGCCCACACAAGTTGGTGGCAC--CTTAGTCCCTTCAAAGAGTAGGATGCCTTTTTC
1 TTTT-AAAG-CCACACAAGTTGGTGGCACTTCCTAGT-CC-TCAAAGAGCAGGACG-C-----C
* * *
379085 TTTTTCAAAGCCACACACAATTTGGTGGCACCTTTC-AGTCCCCAAAGAGCAGGAC-CC
1 -TTTT-AAAG-C-CACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGCC
* ** *
379142 TTTTCAAAGCCCACACAAGTTGG-GGCATTTTTTAGTCCTCAAAGAGCAGGACACC
1 TTTT-AAAG-CCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCC
* *
379197 TTTCAAAGCCCACACAAGTTGGTGG------C-A-TCCTCAAAGAGCAGGACACC
1 TTTTAAAG-CCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCC
* *
379244 TTTCAAAGCCCACACAAGTTTGGTGG------C-A-TCCTCAAAGAGCAGGACACC
1 TTTTAAAG-CCACACAAG-TTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCC
* * * * *
379292 TCTTAAAGCCCACACAAGTTGGTGGAACCTTTC-AGTCCCCAAAGAGCAGGACACC
1 TTTTAAAG-CCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGCC
* * * *
379347 -TTCAAAGCCCACACAAGTTGGTGGCATTTCC-AGTCCTCAAAGAGTAGGAC-AC
1 TTTTAAAG-CCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCC
* * * * *
379399 TAGCTAAAAGCCCACACAAGTTGGT-ACACCTTTC-AGTCCTTAAAGAGCAGGACGCC
1 T--TTTAAAG-CCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGCC
* * * **
379455 -TTCAAAGCCCACACGAGTTGGGGTGCACTTTTTAGTCCTC-AAGAGCAGGA
1 TTTTAAAG-CCACACAAGTTGGTG-GCACTTCCTAGTCCTCAAAGAGCAGGA
379505 TACACTTTAT
Statistics
Matches: 686, Mismatches: 75, Indels: 145
0.76 0.08 0.16
Matches are distributed among these distances:
47 45 0.07
48 46 0.07
52 1 0.00
53 41 0.06
54 146 0.21
55 106 0.15
56 40 0.06
57 24 0.03
58 51 0.07
59 23 0.03
60 63 0.09
61 7 0.01
62 10 0.01
63 16 0.02
64 33 0.05
65 14 0.02
66 20 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (54 bp):
TTTTAAAGCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCC
Found at i:378880 original size:120 final size:114
Alignment explanation
Indices: 378553--379504 Score: 474
Period size: 120 Copynumber: 8.4 Consensus size: 114
378543 CGCTTTTTCT
* * *
378553 TTTTAAAGCCCACACAAGTTGGTGG-AACCTT--TAGTCCTCAAAAAGCAGGATGCCTTTTCTAC
1 TTTTAAAG-CCACACAAGTTGGTGGCAA-CTTCCCAGTCCTC-AAGAGCAGGACGCC--TTCT-C
*
378615 GTTTTAAAGCCCACACAAGTTGGTGGCACCTT--TAGTCCTCAAAGAGAGCAGGATGCC
60 -CTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTC-AA-AGAGCAGGATGCC
* *
378672 TTTTTAAACCCACACAAGTTGGTGGC-ACTTCCCAGTCCTCAAGAGCAGGACGCCTTCTCCTTTT
1 -TTTTAAAGCCACACAAGTTGGTGGCAACTTCCCAGTCCTCAAGAGCAGGACGCCTTCTCCTTTA
* * * *
378736 AAG-CCACACAAGTTTGTGGCACTTCCTAGTCTTCAAATAGCAGGACGCC
65 AAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATGCC
*
378785 TTTTAAAGCCACACAAGTTGGTGGCAACTTCCCCAGTCTTTCAAAGAGAGGCAGGACG-CTTCCT
1 TTTTAAAGCCACACAAGTTGGTGGCAACTT-CCCAGTC-CTC--A-AGA-GCAGGACGCCTT-CT
* *
378849 CCTTTAAAGCCCACACAAGTTGGTGGCACTTCCTGGTCCTCAAAGAACAGGATGCC
59 CCTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATGCC
* * * * * * *
378905 TTTTAAAGCCCCACAAGTTGGTGGC-ATTTTCCAGCCCTCAAAGAGCGGGATGCCTT-TCTTTTA
1 TTTTAAAGCCACACAAGTTGGTGGCAACTTCCCAGTCCTC-AAGAGCAGGACGCCTTCTCCTTT-
* **
378968 AAAGCCCACCCAAGTTGGTGGCAC--CCTTTAGTCC-CAAA-AGCAGGATTTTTTTTTC
64 AAAGCCCACACAAGTTGGTGGCACTTCC--TAGTCCTCAAAGAGCAGGA------TGCC
* * * *
379023 TTTTCAAAGCCCACACAAGTTGGTGGCACCTT---AGTCCCTTCAAAGAGTAGGATGCCTTTTTC
1 TTTT-AAAG-CCACACAAGTTGGTGGCAACTTCCCAGT-CC-TC-AAGAGCAGGACGCC-TTCTC
* * * * *
379085 TTTTTCAAAGCCACACACAATTTGGTGGCACCTTTC-AGTCCCCAAAGAGCAGGA-CCC
60 -CTTT-AAAGCC-CACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGATGCC
* *** *
379142 TTTTCAAAGCCCACACAAGTTGG-GGC-ATTTTTTAGTCCTCAAAGAGCAGGACACCTT-T-C--
1 TTTT-AAAG-CCACACAAGTTGGTGGCAACTTCCCAGTCCTC-AAGAGCAGGACGCCTTCTCCTT
**
379201 -AAAGCCCACACAAGTTGGTGG------C-A-TCCTCAAAGAGCAGGACACC
63 TAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATGCC
* * *
379244 TTTCAAAGCCCACACAAGTTTGGTGGC-A--T-CC--T-C-AAAGAGCAGGAC-AC--CT-C-TT
1 TTTTAAAG-CCACACAAG-TTGGTGGCAACTTCCCAGTCCTCAAGAGCAGGACGCCTTCTCCTTT
* * * **
379296 AAAGCCCACACAAGTTGGTGGAACCTTTC-AGTCCCCAAAGAGCAGGACACC
64 AAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGATGCC
* * * * ** *
379347 -TTCAAAGCCCACACAAGTTGGTGGC-A-TTTCCAGTCCTCAAAGAGTAGGAC-AC-T-AGC-TA
1 TTTTAAAG-CCACACAAGTTGGTGGCAACTTCCCAGTCCTC-AAGAGCAGGACGCCTTCTCCTTT
* * * *
379405 AAAGCCCACACAAGTTGGT-ACACCTTTC-AGTCCTTAAAGAGCAGGACGCC
64 AAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGATGCC
* * * ***
379455 -TTCAAAGCCCACACGAGTTGGGGTGC-ACTTTTTAGTCCTCAAGAGCAGGA
1 TTTTAAAG-CCACACAAGTTGGTG-GCAACTTCCCAGTCCTCAAGAGCAGGA
379505 TACACTTTAT
Statistics
Matches: 693, Mismatches: 73, Indels: 143
0.76 0.08 0.16
Matches are distributed among these distances:
93 2 0.00
94 1 0.00
95 32 0.05
97 1 0.00
98 1 0.00
101 39 0.06
102 31 0.04
103 25 0.04
105 1 0.00
106 1 0.00
108 59 0.09
109 47 0.07
110 16 0.02
112 32 0.05
113 27 0.04
114 60 0.09
115 21 0.03
116 4 0.01
117 11 0.02
118 39 0.06
119 82 0.12
120 112 0.16
121 4 0.01
122 2 0.00
123 10 0.01
124 20 0.03
125 5 0.01
126 7 0.01
127 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (114 bp):
TTTTAAAGCCACACAAGTTGGTGGCAACTTCCCAGTCCTCAAGAGCAGGACGCCTTCTCCTTTAA
AGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATGCC
Found at i:379131 original size:64 final size:62
Alignment explanation
Indices: 378465--379192 Score: 432
Period size: 54 Copynumber: 12.4 Consensus size: 62
378455 CCTTCCGCTT
* * * **
378465 TTTAG-CCCTCAAAGAGCAGGATGCC-TTTCCTTTT-AAAGCCAACACAAGTTGGTTGCATT
1 TTTAGTCCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
* * *
378524 TTTCAG--CCTCAAA-AGCA-GACG-CTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGAACC
1 TTT-AGTCCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
*
378582 TTTAGT-CCTCAAAAAGCAGGATGCCTTTTCTACGTTTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTTAGTCCCTCAAAGAGCAGGATGCCTTTT-T-C-TTTTCAAAGCCCACACAAGTTGGTGGCACC
378645 TTTAGT-CCTCAAAGAGAGCAGGATGCC----T-TTTT-AAA-CCCACACAAGTTGGTGGCA-C
1 TTTAGTCCCTC-AA-AGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
* * * * *
378700 TTCCCAGT-CCTC-AAGAGCAGGACGCCTTCTCCTTTT--AAG-CCACACAAGTTTGTGGCA-C
1 TT--TAGTCCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
* * * *
378758 TTCCTAGT-CTTCAAATAGCAGGACG-C-----CTTTT-AAAG-CCACACAAGTTGGTGGCAAC
1 TT--TAGTCCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
* ** * ** *
378813 TTCCCCAGTCTTTCAAAGAG-AGGCAGGACGCTTCCTCCTTT-AAAGCCCACACAAGTTGGTGGC
1 TT---TAGTCCCTCAAAGAGCAGG-ATG-C-CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGC
378876 A-C
60 ACC
* * *
378878 TTCCTGGT-CCTCAAAGAACAGGATG-C-----CTTTT-AAAGCCC-CACAAGTTGGTGGCA-T
1 TT--TAGTCCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
* * *
378932 TTTCCAG-CCCTCAAAGAGCGGGATGCC--TTTCTTTTAAAAGCCCACCCAAGTTGGTGGCACCC
1 TTT--AGTCCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-CC
***
378994 TTTAGT-CC-CAAA-AGCAGGATTTTTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTAGTCCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
* *
379053 -TTAGTCCCTTCAAAGAGTAGGATGCCTTTTTCTTTTTCAAAGCCACACACAATTTGGTGGCACC
1 TTTAGTCCC-TCAAAGAGCAGGATGCCTTTTTC-TTTTCAAAGCC-CACACAAGTTGGTGGCACC
**
379117 TTTCAGTCCC-CAAAGAGCAGGA--CC-----CTTTTCAAAGCCCACACAAGTTGG-GGCATTT
1 TTT-AGTCCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-CC
379172 TTTAGT-CCTCAAAGAGCAGGA
1 TTTAGTCCCTCAAAGAGCAGGA
379193 CACCTTTCAA
Statistics
Matches: 558, Mismatches: 51, Indels: 125
0.76 0.07 0.17
Matches are distributed among these distances:
52 1 0.00
53 7 0.01
54 84 0.15
55 33 0.06
56 39 0.07
57 38 0.07
58 82 0.15
59 44 0.08
60 56 0.10
61 9 0.02
62 19 0.03
63 55 0.10
64 42 0.08
65 25 0.04
66 24 0.04
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (62 bp):
TTTAGTCCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
Found at i:379199 original size:55 final size:55
Alignment explanation
Indices: 379087--379504 Score: 429
Period size: 55 Copynumber: 7.9 Consensus size: 55
379077 CCTTTTTCTT
* *
379087 TTTCAAAGCCACACACAATTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGAC-CC
1 TTTCAAAGCC-CACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACC
** *
379142 TTTTCAAAGCCCACACAAGTTGG-GGCATTTTTTAGTCCTCAAAGAGCAGGACACC
1 -TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACC
379197 TTTCAAAGCCCACACAAGTTGGTGG-------CA-TCCTCAAAGAGCAGGACACC
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACC
379244 TTTCAAAGCCCACACAAGTTTGGTGG-------CA-TCCTCAAAGAGCAGGACACC
1 TTTCAAAGCCCACACAAG-TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACC
* *
379292 TCTT-AAAGCCCACACAAGTTGGTGGAACCTTTCAGTCCCCAAAGAGCAGGACACC
1 T-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACC
*
379347 -TTCAAAGCCCACACAAGTTGGTGGCA--TTTCCAGTCCTCAAAGAGTAGGACA-C
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACACC
* * * * *
379399 TAGCTAAAAGCCCACACAAGTTGGT-ACACCTTTCAGTCCTTAAAGAGCAGGACGCC
1 T--TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACC
* * * *
379455 -TTCAAAGCCCACACGAGTTGGGGTGCACTTTTTAGTCCTC-AAGAGCAGGA
1 TTTCAAAGCCCACACAAGTTGGTG-GCACCTTTCAGTCCTCAAAGAGCAGGA
379505 TACACTTTAT
Statistics
Matches: 316, Mismatches: 24, Indels: 46
0.82 0.06 0.12
Matches are distributed among these distances:
47 45 0.14
48 45 0.14
49 2 0.01
52 4 0.01
53 39 0.12
54 83 0.26
55 84 0.27
56 14 0.04
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (55 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACC
Found at i:379286 original size:48 final size:47
Alignment explanation
Indices: 379177--379373 Score: 281
Period size: 47 Copynumber: 4.0 Consensus size: 47
379167 CATTTTTTAG
379177 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
379224 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTTGGTGGCA
1 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAG-TTGGTGGCA
379272 TCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGAACCTTTCA
1 TCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGG-------CA
*
379326 GTCCCCAAAGAGCAGGACACC-TTCAAAGCCCACACAAGTTGGTGGCA
1 -TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
379373 T
1 T
379374 TTCCAGTCCT
Statistics
Matches: 138, Mismatches: 1, Indels: 23
0.85 0.01 0.14
Matches are distributed among these distances:
46 1 0.01
47 47 0.34
48 44 0.32
49 2 0.01
53 2 0.01
54 23 0.17
55 19 0.14
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (47 bp):
TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:379307 original size:95 final size:95
Alignment explanation
Indices: 379119--379373 Score: 295
Period size: 101 Copynumber: 2.5 Consensus size: 95
379109 GTGGCACCTT
379119 TCAGTCCCCAAAGAGCAGGAC-CCTTTTCAAAGCCCACACAAGTTGG-GGCATTTTTTAGTCCTC
1 TCAGTCCCCAAAGAGCAGGACACC--TTCAAAGCCCACACAAGTTGGTGGC-------A-TCCTC
379182 AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG
56 AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG
*
379222 -CA-TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTTGGTGGCATCCTCAAAGAGCA
1 TCAGTCCCCAAAGAGCAGGACACC-TTCAAAGCCCACACAAG-TTGGTGGCATCCTCAAAGAGCA
379285 GGACACCTCTT-AAAGCCCACACAAGTTGGTGG
64 GGACACCT-TTCAAAGCCCACACAAGTTGGTGG
379317 AACCTTTCAGTCCCCAAAGAGCAGGACACCTTCAAAGCCCACACAAGTTGGTGGCAT
1 ------TCAGTCCCCAAAGAGCAGGACACCTTCAAAGCCCACACAAGTTGGTGGCAT
379374 TTCCAGTCCT
Statistics
Matches: 138, Mismatches: 2, Indels: 26
0.83 0.01 0.16
Matches are distributed among these distances:
95 42 0.30
96 3 0.02
101 44 0.32
102 27 0.20
103 22 0.16
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (95 bp):
TCAGTCCCCAAAGAGCAGGACACCTTCAAAGCCCACACAAGTTGGTGGCATCCTCAAAGAGCAGG
ACACCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:380949 original size:12 final size:13
Alignment explanation
Indices: 380932--380965 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
380922 ATCCTTTAGC
380932 AAAAAACCAA-AA
1 AAAAAACCAACAA
380944 AAAAAACACAACAA
1 AAAAAAC-CAACAA
380958 AAAAAACC
1 AAAAAACC
380966 TATCCATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 4 0.20
14 9 0.45
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACCAACAA
Found at i:382813 original size:48 final size:52
Alignment explanation
Indices: 382728--382855 Score: 147
Period size: 53 Copynumber: 2.5 Consensus size: 52
382718 GAGTTTCTCA
* * * * *
382728 TTCTCCACAAACGGGGATATTTCCAACTCCGATTTTATT-AAAAACA-CAATT
1 TTCTTCACAATCGGGGATA-CTCCAACTCCGAATTTATTAAAAAACACCAAGT
* *
382779 TTC-T-ATAATCGGGGATACTCCAACTCTGAATTTATTCAAAAAACACCAAGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGAATTTATT-AAAAAACACCAAGT
382830 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
382856 CCCCGTTATC
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
48 16 0.25
49 11 0.17
50 7 0.11
51 10 0.16
52 1 0.02
53 19 0.30
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (52 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGAATTTATTAAAAAACACCAAGT
Found at i:382912 original size:27 final size:26
Alignment explanation
Indices: 382839--382912 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
382829 TTTCTTCACA
382839 ATCGGGGATACTCCAACCCCCGTTATC
1 ATCGGGGATACTCCAA-CCCCGTTATC
382866 ATCGGGGATAC-CCAACCCCGTTAT-
1 ATCGGGGATACTCCAACCCCGTTATC
*
382890 TTCCGAGGGATACTCCAACCCCG
1 AT-CG-GGGATACTCCAACCCCG
382913 ACTTTTTTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
24 1 0.02
25 11 0.26
26 11 0.26
27 20 0.47
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.20
Consensus pattern (26 bp):
ATCGGGGATACTCCAACCCCGTTATC
Found at i:383078 original size:53 final size:53
Alignment explanation
Indices: 382978--383116 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 53
382968 GTTATTAGCT
* * *
382978 AAAACACTAATTTTTTTTACATCGGGGATACTCCCAACCCTGGTTTATTTTC-
1 AAAACACCAATTTTTTTTACATCGGGGATACTCCCAACCCTGATTTATTTCCA
383030 AAAACACCAATGTTTTCGTTTA-ATCGGGGATACT-CCAACTCC-GATTTATTTCCA
1 AAAACACCAAT-TTTT--TTTACATCGGGGATACTCCCAAC-CCTGATTTATTTCCA
* *
383084 AAAACACC-ATTTTTTTCACAATCGAGGATACTC
1 AAAACACCAATTTTTTTTAC-ATCGGGGATACTC
383117 ACCTCATTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
50 3 0.04
52 25 0.34
53 20 0.27
54 22 0.30
55 4 0.05
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.35
Consensus pattern (53 bp):
AAAACACCAATTTTTTTTACATCGGGGATACTCCCAACCCTGATTTATTTCCA
Found at i:388799 original size:75 final size:73
Alignment explanation
Indices: 388653--389382 Score: 291
Period size: 71 Copynumber: 10.2 Consensus size: 73
388643 AAAAGCAGCA
* * * * *
388653 TTTTTTTTAACTACCACAAAGC-CTACTCAAGTTGTTGGCACCTATCTACCTCTAGTCCTCAAAG
1 TTTTCTTTACCTACCACAAAGCAC-ACACAAGTGGGTGGCACCTATCTACCTCTAGTCCTCAAAG
388717 AGCAAGATG
65 AGCAAGATG
* * * *
388726 TTTTTTTTTCTTACCTACCATAAAGCACACACAAGTGGGT-GCACCTATCTACCTTTAGT-TTCA
1 ---TTTTCT-TTACCTACCACAAAGCACACACAAGTGGGTGGCACCTATCTACCTCTAGTCCTCA
388789 AAGAGCAAGATG
62 AAGAGCAAGATG
* * * *
388801 TTTTCTTTACCTACCACAAAGCTCATACAAGTTGGTGGCA-CTATCTACCTCTAATTCC-CAAAG
1 TTTTCTTTACCTACCACAAAGCACACACAAGTGGGTGGCACCTATCTACCTCT-AGTCCTCAAAG
* *
388864 AGCAGGACATT
65 AGCA--AGATG
* * * * *
388875 TTTTC-TTACGTATCACAAAACCCACACAAGCT-GGTGGCACCTATCTACCTC-AGTCCTTAAA-
1 TTTTCTTTACCTACCACAAAGCACACACAAG-TGGGTGGCACCTATCTACCTCTAGTCCTCAAAG
*
388936 AGCAAGATA
65 AGCAAGATG
* * * * * *
388945 TTTTTTCTTACGTA-CACATAAGTC-CACATAAGCT-GGT--CACTTATCTACCTCCAGTGCTCG
1 TTTTCT-TTACCTACCACA-AAG-CACACACAAG-TGGGTGGCACCTATCTACCTCTAGTCCTC-
* *
389005 AGAGAG-TAGAATG
61 AAAGAGCAAG-ATG
*** * * *** * *
389018 CTTTT-TCTTAAAAACC-CAAAGCCCACATAAACCGGTGGTACCTATCTACCT-TAGT-CACAAA
1 -TTTTCT-TTACCTACCACAAAGCACACACAAGTGGGTGGCACCTATCTACCTCTAGTCCTCAAA
**
389079 GAGCTGGATG
64 GAGCAAGATG
* * * * * *
389089 -TTT-ATTA--T--GATAAAGCGCACA-TAGCT-GGTGGCACCTATCTACCT-TAGTCTTCAAAG
1 TTTTCTTTACCTACCACAAAGCACACACAAG-TGGGTGGCACCTATCTACCTCTAGTCCTCAAAG
*
389145 AGCATGATG
65 AGCAAGATG
* ** * * *
389154 CTTTT-TTTACCT-CCTACAAAGCTCACA-AAGTTAGTGGCACC-A-CTGCCTCTAGTCTTTAAA
1 -TTTTCTTTACCTACC-ACAAAGCACACACAAGTGGGTGGCACCTATCTACCTCTAGTCCTCAAA
* **
389214 GAGCAGGACAC
64 GAGCAAGA-TG
* * * * * *
389225 TTTT-TTTGCCTACCATAGAGC-CACA-TAGTTGGT-GCACCTATCTACCTCTACTCCTCAAAGA
1 TTTTCTTTACCTACCACAAAGCACACACAAGTGGGTGGCACCTATCTACCTCTAGTCCTCAAAGA
*
389286 GCAAAATG
66 GCAAGATG
* * * * * * *
389294 TTTTTTCTTACCT-CTATAAAGCCCACATAAACT-AGTGGCACCTATCTACCTCTAGT-CTCAAA
1 TTTTCT-TTACCTACCACAAAGCACACA-CAAGTGGGTGGCACCTATCTACCTCTAGTCCTCAAA
* *
389356 GAGTAGGATG
64 GAGCAAGATG
*
389366 CTATTC-TTACCTACCAC
1 -TTTTCTTTACCTACCAC
389383 CACATAAGTG
Statistics
Matches: 509, Mismatches: 97, Indels: 100
0.72 0.14 0.14
Matches are distributed among these distances:
64 22 0.04
65 21 0.04
67 6 0.01
68 8 0.02
69 24 0.05
70 82 0.16
71 92 0.18
72 86 0.17
73 69 0.14
74 36 0.07
75 15 0.03
76 24 0.05
77 23 0.05
78 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (73 bp):
TTTTCTTTACCTACCACAAAGCACACACAAGTGGGTGGCACCTATCTACCTCTAGTCCTCAAAGA
GCAAGATG
Found at i:388904 original size:73 final size:74
Alignment explanation
Indices: 388652--389453 Score: 389
Period size: 72 Copynumber: 11.3 Consensus size: 74
388642 AAAAAGCAGC
* * *
388652 ATTTTTT-TTAACTACCACAAAGC-CTACTCAAGTTGTTGGCACCTATCTACCTCTAGTCCTCAA
1 ATTTTTTCTTACCTACCACAAAGCAC-ACACAAGTTGGTGGCACCTATCTACCTCTAGTCCTCAA
*
388715 AGAGCAAGATGTT
65 AGAGC-AG--GAT
* * * * *
388728 TTTTTTTCTTACCTACCATAAAGCACACACAAGTGGGT-GCACCTATCTACCTTTAGT-TTCAAA
1 ATTTTTTCTTACCTACCACAAAGCACACACAAGTTGGTGGCACCTATCTACCTCTAGTCCTCAAA
*
388791 GAGCAAGAT
66 GAGCAGGAT
* * * * *
388800 GTTTTCT-TTACCTACCACAAAGCTCATACAAGTTGGTGGCA-CTATCTACCTCTAATTCC-CAA
1 ATTTTTTCTTACCTACCACAAAGCACACACAAGTTGGTGGCACCTATCTACCTCT-AGTCCTCAA
*
388862 AGAGCAGGAC
65 AGAGCAGGAT
* * * * * *
388872 ATTTTTTCTTACGTATCACAAAACCCACACAAGCTGGTGGCACCTATCTACCTC-AGTCCTTAAA
1 ATTTTTTCTTACCTACCACAAAGCACACACAAGTTGGTGGCACCTATCTACCTCTAGTCCTCAAA
*
388936 -AGCAAGAT
66 GAGCAGGAT
* * * * * *
388944 ATTTTTTCTTACGTA-CACATAAGTC-CACATAAGCTGGT--CACTTATCTACCTCCAGTGCTCG
1 ATTTTTTCTTACCTACCACA-AAG-CACACACAAGTTGGTGGCACCTATCTACCTCTAGTCCTC-
* * *
389005 AGAGAGTAGAAT
63 AAAGAGCAGGAT
** *** * * *** * *
389017 GCTTTTTCTTAAAAACC-CAAAGCCCACATAAACCGGTGGTACCTATCTACCT-TAGT-CACAAA
1 ATTTTTTCTTACCTACCACAAAGCACACACAAGTTGGTGGCACCTATCTACCTCTAGTCCTCAAA
*
389079 GAGCTGG--
66 GAGCAGGAT
* * * * * * * *
389086 A-TGTTTATTA--T--GATAAAGCGCACA-TAGCTGGTGGCACCTATCTACCT-TAGTCTTCAAA
1 ATTTTTTCTTACCTACCACAAAGCACACACAAGTTGGTGGCACCTATCTACCTCTAGTCCTCAAA
*
389144 GAGCATGAT
66 GAGCAGGAT
** * * * * *
389153 GCTTTTT-TTACCT-CCTACAAAGCTCACA-AAGTTAGTGGCACC-A-CTGCCTCTAGTCTTTAA
1 ATTTTTTCTTACCTACC-ACAAAGCACACACAAGTTGGTGGCACCTATCTACCTCTAGTCCTCAA
*
389213 AGAGCAGGAC
65 AGAGCAGGAT
* * * * * *
389223 ACTTTTT-TTGCCTACCATAGAGC-CACA-TAGTTGGT-GCACCTATCTACCTCTACTCCTCAAA
1 ATTTTTTCTTACCTACCACAAAGCACACACAAGTTGGTGGCACCTATCTACCTCTAGTCCTCAAA
**
389284 GAGCAAAAT
66 GAGCAGGAT
* * * * * ** *
389293 GTTTTTTCTTACCT-CTATAAAGCCCACATAAACTAGTGGCACCTATCTACCTCTAGT-CTCAAA
1 ATTTTTTCTTACCTACCACAAAGCACACACAAGTTGGTGGCACCTATCTACCTCTAGTCCTCAAA
*
389356 GAGTAGGAT
66 GAGCAGGAT
** * * * * * *
389365 -GCTATTCTTACCTA-C-C--A-C-CACATAAG-TGGTGGCACTTATCTGCCTCTAATTCTCAAA
1 ATTTTTTCTTACCTACCACAAAGCACACACAAGTTGGTGGCACCTATCTACCTCTAGTCCTCAAA
* *
389422 GAGCATGAC
66 GAGCAGGAT
* *
389431 A-TTTTTCTTACCGACCGCAAAGC
1 ATTTTTTCTTACCTACCACAAAGC
389454 CTACAAAAGT
Statistics
Matches: 558, Mismatches: 126, Indels: 89
0.72 0.16 0.12
Matches are distributed among these distances:
64 23 0.04
65 38 0.07
66 29 0.05
67 5 0.01
68 18 0.03
69 17 0.03
70 80 0.14
71 96 0.17
72 101 0.18
73 70 0.13
74 24 0.04
75 9 0.02
76 24 0.04
77 23 0.04
78 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (74 bp):
ATTTTTTCTTACCTACCACAAAGCACACACAAGTTGGTGGCACCTATCTACCTCTAGTCCTCAAA
GAGCAGGAT
Found at i:389273 original size:70 final size:72
Alignment explanation
Indices: 389100--389363 Score: 220
Period size: 70 Copynumber: 3.7 Consensus size: 72
389090 TTATTATGAT
* * * **
389100 AAAGCGCACATAGCTGGTGGCACCTATCTACCT-TAGTCTTCAAAGAGCATGATGCTTTTTTTAC
1 AAAGCTCACATAGTTGGTGGCACCTATCTACCTCTAGTCTTCAAAGAGCAGGACACTTTTTTTAC
389164 CTCCTAC
66 CTCCTAC
* * * * *
389171 AAAGCTCACAAAGTTAGTGGCACC-A-CTGCCTCTAGTCTTTAAAGAGCAGGACACTTTTTTTGC
1 AAAGCTCACATAGTTGGTGGCACCTATCTACCTCTAGTCTTCAAAGAGCAGGACACTTTTTTTAC
*
389234 CTACC-AT
66 CT-CCTAC
* * * ** ***
389241 AGAGC-CACATAGTTGGT-GCACCTATCTACCTCTACTCCTCAAAGAGCAAAATGTTTTTTCTTA
1 AAAGCTCACATAGTTGGTGGCACCTATCTACCTCTAGTCTTCAAAGAGCAGGACACTTTTT-TTA
*
389304 CCT-CTAT
65 CCTCCTAC
* ** * *
389311 AAAGCCCACATAAACTAGTGGCACCTATCTACCTCTAGTC-TCAAAGAGTAGGA
1 AAAGCTCACAT-AGTTGGTGGCACCTATCTACCTCTAGTCTTCAAAGAGCAGGA
389364 TGCTATTCTT
Statistics
Matches: 152, Mismatches: 32, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
68 5 0.03
69 17 0.11
70 65 0.43
71 32 0.21
72 14 0.09
73 19 0.12
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (72 bp):
AAAGCTCACATAGTTGGTGGCACCTATCTACCTCTAGTCTTCAAAGAGCAGGACACTTTTTTTAC
CTCCTAC
Found at i:448407 original size:31 final size:31
Alignment explanation
Indices: 448326--448432 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 31
448316 TTAGCGCTAC
* * *
448326 ATTGTATCGACTACAAAACTTATGTAATCGATACC
1 ATTGTATCGA-TACAACACCTA-GT-ATCGATA-A
448361 ATTGTA-CGA-ACAACACCTAGTATCGATAA
1 ATTGTATCGATACAACACCTAGTATCGATAA
448390 ATTGTATCGATACAACACTTCT-GTA-CGATAA
1 ATTGTATCGATACAACAC--CTAGTATCGATAA
448421 CATTGCTATCGA
1 -ATTG-TATCGA
448433 GAAAAACTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
29 6 0.10
30 10 0.16
31 15 0.24
32 15 0.24
33 8 0.13
34 3 0.05
35 6 0.10
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (31 bp):
ATTGTATCGATACAACACCTAGTATCGATAA
Found at i:448443 original size:32 final size:31
Alignment explanation
Indices: 448384--448446 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
448374 CACCTAGTAT
* *
448384 CGATAAATTGTATCGATACAACACTTCTGTA
1 CGATAAATTGTATCGAGACAAAACTTCTGTA
448415 CGATAACATTGCTATCGAGA-AAAACTTCTGTA
1 CGATAA-ATTG-TATCGAGACAAAACTTCTGTA
448447 TTCGATTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 6 0.21
32 15 0.54
33 7 0.25
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (31 bp):
CGATAAATTGTATCGAGACAAAACTTCTGTA
Found at i:456471 original size:74 final size:74
Alignment explanation
Indices: 456183--457091 Score: 665
Period size: 73 Copynumber: 12.6 Consensus size: 74
456173 AGGTTAATGT
* * **
456183 GGTGCCTCGAGCTTATGTGGGCTTTGA-GGTAGGTAA-AAAAATA-AGTCCAACTCTTTGTA-GA
1 GGTGCCACCAGCTTATGTGGGCTTT-ATGGTAGGTAAGAAAAA-ACA-TCCTGCTCTTTG-AGGA
*
456244 CTA-AGGTAAATA
62 CTAGAGGTAGATA
* * * ** * ** * * *
456256 GGTGCCACCAACTTTTGTAGGCTTTGCGGTCGGTAAG-AAAAATGTCATGCTCTTTGAGAATTAG
1 GGTGCCACCAGCTTATGTGGGCTTTATGGTAGGTAAGAAAAAACATCCTGCTCTTTGAGGACTAG
*
456320 AGGCAGATA
66 AGGTAGATA
* * * *
456329 AGTGCCACCAGCTTATGT-GG-----TGGTAGGTAAG-AATAGCATCCTACTCTTTGAGGACTAG
1 GGTGCCACCAGCTTATGTGGGCTTTATGGTAGGTAAGAAAAAACATCCTGCTCTTTGAGGACTAG
456387 AGGTAGATA
66 AGGTAGATA
* * * ** *
456396 GGTGCCACTAGTTTATGTGGGCTTTATAGTAGGTAAGAAAAAACATTTTGCTCTTTGAGGAGTAG
1 GGTGCCACCAGCTTATGTGGGCTTTATGGTAGGTAAGAAAAAACATCCTGCTCTTTGAGGACTAG
456461 AGGTAGATA
66 AGGTAGATA
* * * * *** * *
456470 GGTGCCACCAACTTATGTGGACTCTATGGTAGGCAA-AAAAAGTGTCCTGCTCTTTAAAGACTAG
1 GGTGCCACCAGCTTATGTGGGCTTTATGGTAGGTAAGAAAAAACATCCTGCTCTTTGAGGACTAG
*
456534 AGGCAGATA
66 AGGTAGATA
* * * * * * *
456543 GGTGCCACTAACTTATGTGAGCTTTGTAGG-AGGT-A-AAAAAGCATCATGCTCTTTGAAGACTA
1 GGTGCCACCAGCTTATGTGGGCTTTAT-GGTAGGTAAGAAAAAACATCCTGCTCTTTGAGGACTA
*
456605 AAGGTAGATA
65 GAGGTAGATA
* * * *
456615 GGTGCCACCAGCTTATGTGCGCTTTAT--CA--T---AATAAACATCCAGCTCTTTGTA-GACTA
1 GGTGCCACCAGCTTATGTGGGCTTTATGGTAGGTAAGAAAAAACATCCTGCTCTTTG-AGGACTA
456672 -AGGTAGATA
65 GAGGTAGATA
* * * ** ** * * * * * *
456681 GGTACCACCGGTTTATGTGGGCTTTGGGGTTTGTAAGAAAAAGCATTCTACTCTCTGAGCACTGG
1 GGTGCCACCAGCTTATGTGGGCTTTATGGTAGGTAAGAAAAAACATCCTGCTCTTTGAGGACTAG
456746 AGGTAGATA
66 AGGTAGATA
* * * * * * *
456755 AGTGCCACCAGCTTATGTGGACTTTATGGTACGTAAGAAAAAATATCTTGCTTTTTAAGGACTAG
1 GGTGCCACCAGCTTATGTGGGCTTTATGGTAGGTAAGAAAAAACATCCTGCTCTTTGAGGACTAG
456820 AGGTAGATA
66 AGGTAGATA
* * * * * ** *
456829 GGTGCCACCAGCTTGTGTGGGTTTTGTGATACGTAAGAAAAAATGTCCTGCTCTTTG-GGAATTA
1 GGTGCCACCAGCTTATGTGGGCTTTATGGTAGGTAAGAAAAAACATCCTGCTCTTTGAGG-ACTA
456893 GAGGTAGATA
65 GAGGTAGATA
* * * * * * * ** *
456903 -GTGCCACCAACTTGTATGAGCTTTGTGGTAGGTAA-AGAAAACATCTTGCTCTTTGAAAACTAA
1 GGTGCCACCAGCTTATGTGGGCTTTATGGTAGGTAAGAAAAAACATCCTGCTCTTTGAGGACTAG
456966 AGGTAGATA
66 AGGTAGATA
* * *
456975 GGTGCCACCAGCTTGTGTGTGCTTTATGGTAGGTAAGAAAAAAACATCTTGCTCTTTGAGGACTA
1 GGTGCCACCAGCTTATGTGGGCTTTATGGTAGGTAAG-AAAAAACATCCTGCTCTTTGAGGACTA
457040 GAGGTAGATA
65 GAGGTAGATA
* * * * *
457050 GGTGCCAACAACTTGA-GTAGGCTTTGTGGTAGTTAA-AAAAAA
1 GGTGCCACCAGCTT-ATGTGGGCTTTATGGTAGGTAAGAAAAAA
457092 TGTCATGCTT
Statistics
Matches: 656, Mismatches: 150, Indels: 60
0.76 0.17 0.07
Matches are distributed among these distances:
66 30 0.05
67 72 0.11
68 4 0.01
70 2 0.00
71 1 0.00
72 99 0.15
73 202 0.31
74 185 0.28
75 61 0.09
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (74 bp):
GGTGCCACCAGCTTATGTGGGCTTTATGGTAGGTAAGAAAAAACATCCTGCTCTTTGAGGACTAG
AGGTAGATA
Found at i:456541 original size:214 final size:216
Alignment explanation
Indices: 456247--456641 Score: 487
Period size: 214 Copynumber: 1.8 Consensus size: 216
456237 TTGTAGACTA
* * * * * *
456247 AGGTAAATAGGTGCCACCAACTTTTGTAGGCTTTGCGGTCGGTAAGAAAAATGTCATGCTCTTTG
1 AGGTAAATAGGTGCCACCAACTTATGTAGGCTCTACGGTAGGCAAGAAAAATGTCATGCTCTTTA
* * * * *
456312 AGAATTAGAGGCAGATAAGTGCCACCAGCTTATGTG-G-TG-GTAGGTAAGAATAGCATCCTACT
66 AGAACTAGAGGCAGATAAGTGCCACCAACTTATGTGAGTTGAGGAGGTAA-AAAAGCATCATACT
* * * * *
456374 CTTTGAGGACTAGAGGTAGATAGGTGCCACTAGTTTATGTGGGCTTTATAGTAGGTAAGAAAAAA
130 CTTTGAAGACTAAAGGTAGATAGGTGCCACCAGCTTATGTGCGCTTTATAGTAGGTAAGAAAAAA
456439 CATTTTGCTCTTTGAGGAGTAG
195 CATTTTGCTCTTTGAGGAGTAG
* * *
456461 AGGTAGATAGGTGCCACCAACTTATGT-GGACTCTATGGTAGGCAA-AAAAAGTGTCCTGCTCTT
1 AGGTAAATAGGTGCCACCAACTTATGTAGG-CTCTACGGTAGGCAAGAAAAA-TGTCATGCTCTT
* *
456524 TAA-AGACTAGAGGCAGATAGGTGCCACTAACTTATGTGAGCTTTGTAGGAGGTAAAAAAGCATC
64 TAAGA-ACTAGAGGCAGATAAGTGCCACCAACTTATGTGAG--TTG-AGGAGGTAAAAAAGCATC
*
456588 ATGCTCTTTGAAGACTAAAGGTAGATAGGTGCCACCAGCTTATGTGCGCTTTAT
125 ATACTCTTTGAAGACTAAAGGTAGATAGGTGCCACCAGCTTATGTGCGCTTTAT
456642 CATAATAAAC
Statistics
Matches: 150, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
213 8 0.05
214 77 0.51
215 1 0.01
218 2 0.01
219 55 0.37
220 7 0.05
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (216 bp):
AGGTAAATAGGTGCCACCAACTTATGTAGGCTCTACGGTAGGCAAGAAAAATGTCATGCTCTTTA
AGAACTAGAGGCAGATAAGTGCCACCAACTTATGTGAGTTGAGGAGGTAAAAAAGCATCATACTC
TTTGAAGACTAAAGGTAGATAGGTGCCACCAGCTTATGTGCGCTTTATAGTAGGTAAGAAAAAAC
ATTTTGCTCTTTGAGGAGTAG
Found at i:456823 original size:359 final size:359
Alignment explanation
Indices: 456355--457001 Score: 888
Period size: 359 Copynumber: 1.8 Consensus size: 359
456345 GTGGTGGTAG
* * * * * * *
456355 GTAAGAATAGCATCCTACTCTTTGAGGACTAGAGGTAGATAGGTGCCACTAGTTTATGTGGGCTT
1 GTAAGAAAAGCATCCTACTCTCTGAGCACTAGAGGTAGATAAGTGCCACCAGCTTATGTGGACTT
* * * *
456420 TATAGTAGGTAAGAAAAAACATTTTGCTCTTTGAGGAGTAGAGGTAGATAGGTGCCACCAACTTA
66 TATAGTACGTAAGAAAAAACATCTTGCTCTTTAAGGACTAGAGGTAGATAGGTGCCACCAACTTA
* * *
456485 TGTGGACTCTATGGTAGGCAA-AAAAAGTGTCCTGCTCTTTAA-AGACTAGAGGCAGATAGGTGC
131 TGTGGACTCTATGATACGCAAGAAAAAATGTCCTGCTCTTTAAGA-ACTAGAGGCAGATA-GTGC
* * * *
456548 CACTAACTTATGTGAGCTTTGTAGG-AGGTAAA-AAAGCATCATGCTCTTTGAAGACTAAAGGTA
194 CACCAACTTATATGAGCTTTGT-GGTAGGTAAAGAAAACATCATGCTCTTTGAAAACTAAAGGTA
456611 GATAGGTGCCACCAGCTTATGTGCGCTTTATCATAATAAACATCCAGCTCTTTGTAGACTAAGGT
258 GATAGGTGCCACCAGCTTATGTGCGCTTTATCATAATAAACATCCAGCTCTTTGTAGACTAAGGT
456676 AGATAGGTACCACCGGTTTATGTGGGCTTTGGGGTTT
323 AGATAGGTACCACCGGTTTATGTGGGCTTTGGGGTTT
* *
456713 GTAAGAAAAAGCATTCTACTCTCTGAGCACTGGAGGTAGATAAGTGCCACCAGCTTATGTGGACT
1 GTAAG-AAAAGCATCCTACTCTCTGAGCACTAGAGGTAGATAAGTGCCACCAGCTTATGTGGACT
* * * *
456778 TTATGGTACGTAAGAAAAAATATCTTGCTTTTTAAGGACTAGAGGTAGATAGGTGCCACCAGCTT
65 TTATAGTACGTAAGAAAAAACATCTTGCTCTTTAAGGACTAGAGGTAGATAGGTGCCACCAACTT
* ** * * * ** * *
456843 GTGTGGGTTTTGTGATACGTAAGAAAAAATGTCCTGCTCTTTGGGAATTAGAGGTAGATAGTGCC
130 ATGTGGACTCTATGATACGCAAGAAAAAATGTCCTGCTCTTTAAGAACTAGAGGCAGATAGTGCC
* *
456908 ACCAACTTGTATGAGCTTTGTGGTAGGTAAAGAAAACATCTTGCTCTTTGAAAACTAAAGGTAGA
195 ACCAACTTATATGAGCTTTGTGGTAGGTAAAGAAAACATCATGCTCTTTGAAAACTAAAGGTAGA
* *
456973 TAGGTGCCACCAGCTTGTGTGTGCTTTAT
260 TAGGTGCCACCAGCTTATGTGCGCTTTAT
457002 GGTAGGTAAG
Statistics
Matches: 246, Mismatches: 38, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
358 7 0.03
359 151 0.61
360 87 0.35
361 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (359 bp):
GTAAGAAAAGCATCCTACTCTCTGAGCACTAGAGGTAGATAAGTGCCACCAGCTTATGTGGACTT
TATAGTACGTAAGAAAAAACATCTTGCTCTTTAAGGACTAGAGGTAGATAGGTGCCACCAACTTA
TGTGGACTCTATGATACGCAAGAAAAAATGTCCTGCTCTTTAAGAACTAGAGGCAGATAGTGCCA
CCAACTTATATGAGCTTTGTGGTAGGTAAAGAAAACATCATGCTCTTTGAAAACTAAAGGTAGAT
AGGTGCCACCAGCTTATGTGCGCTTTATCATAATAAACATCCAGCTCTTTGTAGACTAAGGTAGA
TAGGTACCACCGGTTTATGTGGGCTTTGGGGTTT
Found at i:456929 original size:73 final size:72
Alignment explanation
Indices: 456745--457092 Score: 346
Period size: 74 Copynumber: 4.7 Consensus size: 72
456735 CTGAGCACTG
* * *
456745 GAGGTAGATAAGTGCCACCAGCTTATGTGGACTTTATGGTACGTAAGAAAAAATATCTTGCTTTT
1 GAGGTAGATAGGTGCCACCAGCTTGTGTGG-CTTTATGGTACGTAAGAAAAAATATCTTGCTCTT
*
456810 TAAGGACTA
65 T-GGGACTA
* * *
456819 GAGGTAGATAGGTGCCACCAGCTTGTGTGGGTTT-TGTGATACGTAAGAAAAAATGTCCTGCTCT
1 GAGGTAGATAGGTGCCACCAGCTTGTGTGGCTTTATG-G-TACGTAAGAAAAAATATCTTGCTCT
*
456883 TTGGGAATTA
64 TTGGG-ACTA
* * * * * *
456893 GAGGTAGATA-GTGCCACCAACTTGTATGAGCTTTGTGGTAGGTAA-AGAAAACATCTTGCTCTT
1 GAGGTAGATAGGTGCCACCAGCTTGTGTG-GCTTTATGGTACGTAAGAAAAAATATCTTGCTCTT
**
456956 TGAAAACTA
65 TG-GGACTA
* * *
456965 AAGGTAGATAGGTGCCACCAGCTTGTGTGTGCTTTATGGTAGGTAAGAAAAAAACATCTTGCTCT
1 GAGGTAGATAGGTGCCACCAGCTTGTGTG-GCTTTATGGTACGTAAG-AAAAAATATCTTGCTCT
457030 TTGAGGACTA
64 TTG-GGACTA
* * * *
457040 GAGGTAGATAGGTGCCAACAACTTGAGTAGGCTTTGTGGTA-GTTAA-AAAAAAT
1 GAGGTAGATAGGTGCCACCAGCTTGTGT-GGCTTTATGGTACG-TAAGAAAAAAT
457093 GTCATGCTTT
Statistics
Matches: 230, Mismatches: 33, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
72 30 0.13
73 65 0.28
74 71 0.31
75 63 0.27
76 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (72 bp):
GAGGTAGATAGGTGCCACCAGCTTGTGTGGCTTTATGGTACGTAAGAAAAAATATCTTGCTCTTT
GGGACTA
Found at i:458537 original size:69 final size:69
Alignment explanation
Indices: 458421--458559 Score: 197
Period size: 69 Copynumber: 2.0 Consensus size: 69
458411 ATGGATTGGG
*
458421 AGAATTTGTTTGAGCACCAAATCACTTTTTCAAAACTAACAAAAATGAATCCTCTTATCATGGGC
1 AGAATTTGTTTGAGCACCAAATCACCTTTTCAAAACTAACAAAAATGAATCCTCTTATCATGGGC
458486 TCTT
66 TCTT
* * * * ** * *
458490 AGAATTTGTTTGAGCACTAAGTCACCTTTTCAACACTAACAAGAATGAATTTTCTTGTCATGGTC
1 AGAATTTGTTTGAGCACCAAATCACCTTTTCAAAACTAACAAAAATGAATCCTCTTATCATGGGC
458555 TCTT
66 TCTT
458559 A
1 A
458560 CCATGTGCTT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (69 bp):
AGAATTTGTTTGAGCACCAAATCACCTTTTCAAAACTAACAAAAATGAATCCTCTTATCATGGGC
TCTT
Found at i:462745 original size:28 final size:28
Alignment explanation
Indices: 462686--462759 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
462676 ATAAAGCCGG
*** * *
462686 GGTTGGAGTATCCCCTCGGAAGTAACGG
1 GGTTGGAGTATCCCCGATGAAATAACGA
*
462714 GGTTGGAGTATCCCCGATGAAATAATGA
1 GGTTGGAGTATCCCCGATGAAATAACGA
*
462742 GGTTGGAGTATCCTCGAT
1 GGTTGGAGTATCCCCGAT
462760 TGTGAAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGATGAAATAACGA
Found at i:462812 original size:52 final size:51
Alignment explanation
Indices: 462743--463131 Score: 254
Period size: 53 Copynumber: 7.4 Consensus size: 51
462733 AAATAATGAG
*
462743 GTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGGAAATAAAATCGGA
** * * *
462795 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCAGG-
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAATC-GGA
* * * * ** *
462847 GTTGGAGTATCCCCGATTGTAAAAAAAATTAGTGTTTTAGCAATAAACCCGGG
1 GTTGGAGTATCCCCGATTGT--GAAAAATTGGTGTTTTGGAAATAAAATCGGA
* *** * *
462900 GTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAA-AAAAGTCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAA-TCGGA
* * *** * * *
462951 GTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTGT-T-TTGGA-AATAAAATCGGA
*
463006 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGTG--TTTTGGAAATAAAATCGGA
* * *
463060 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGGAAATAAAATCGGA
* *
463111 GTTGGAATATCCCCGTTTGTG
1 GTTGGAGTATCCCCGATTGTG
463132 GAGAATTGAG
Statistics
Matches: 259, Mismatches: 52, Indels: 52
0.71 0.14 0.14
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
50 3 0.01
51 67 0.26
52 53 0.20
53 71 0.27
54 25 0.10
55 20 0.08
56 2 0.01
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:462936 original size:104 final size:104
Alignment explanation
Indices: 462742--462964 Score: 245
Period size: 104 Copynumber: 2.1 Consensus size: 104
462732 GAAATAATGA
* * * * *
462742 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTAAAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTGGAGTATCC
* *** *
462807 CCGATTAAAGGAAAATTGGTGTTTT-GAAAATAAAACCAG
66 CCGATTAAAGAAAAATCAATATTTTGGAAAA-AAAACCAG
* * *
462846 GGTTGGAGTATCCCCGATTGTAAAAAAAATTAGTG-TTTTAGCAATAAACCCGGGGTTGGAGTAT
1 GGTTGGAGTATCCCCGATTGT--AAAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTGGAGTAT
* ** *
462910 CCCCGATT-ATGAAAAATCAATATTTTGGAAAAAAAGTCGG
64 CCCCGATTAAAGAAAAATCAATATTTTGGAAAAAAAACCAG
462950 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
462965 TCGGAAATAA
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
104 52 0.53
105 37 0.37
106 10 0.10
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (104 bp):
GGTTGGAGTATCCCCGATTGTAAAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTGGAGTATCC
CCGATTAAAGAAAAATCAATATTTTGGAAAAAAAACCAG
Found at i:463010 original size:27 final size:28
Alignment explanation
Indices: 462947--463022 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
462937 GAAAAAAAGT
***
462947 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
462975 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
463002 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
463023 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:463102 original size:264 final size:264
Alignment explanation
Indices: 462632--463130 Score: 806
Period size: 264 Copynumber: 1.9 Consensus size: 264
462622 TCGAAAATAA
* * *
462632 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGGAAAAAAAGCCGGGGTTGGAGTAT
* * *
462697 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAATGAGGTTGGAGTATCCTCGATTG
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTG
* *
462762 TGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
131 TGAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGT
*
462827 GTTTTGAAAATAAAACCAGG-GTTGGAGTATCCCCGATTGTAAAAAAAATTAGTGTTTTAGCAAT
196 GTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTAAAAAAAATTAGTGTTTTAGCAAT
462891 AAACC
260 AAACC
* *
462896 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAAAAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGGAAAAAAAGCCGGGGTTGGAGTAT
* *
462961 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGATTG
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTG
*
463025 TGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTATA-GAAAATTA
131 TGAA-AAATTGGTG-TTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTA
* *
463089 GTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGTTTGT
194 GTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGT
463131 GGAGAATTGA
Statistics
Matches: 216, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
263 30 0.14
264 147 0.68
265 39 0.18
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (264 bp):
CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGGAAAAAAAGCCGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTG
TGAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGT
GTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTAAAAAAAATTAGTGTTTTAGCAATA
AACC
Found at i:464948 original size:11 final size:11
Alignment explanation
Indices: 464932--464965 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
464922 CAATGGAATA
464932 GTGTTTTTTTT
1 GTGTTTTTTTT
464943 GTGTTTTTTTT
1 GTGTTTTTTTT
* *
464954 TTGGTTTTTTT
1 GTGTTTTTTTT
464965 G
1 G
464966 CTAAAGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (11 bp):
GTGTTTTTTTT
Found at i:465515 original size:13 final size:13
Alignment explanation
Indices: 465497--465522 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
465487 ACAAAGATCC
465497 ATGTATCGATACA
1 ATGTATCGATACA
465510 ATGTATCGATACA
1 ATGTATCGATACA
465523 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:465518 original size:33 final size:33
Alignment explanation
Indices: 465476--465542 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
465466 AAAATTCCCA
***
465476 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
465509 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
465542 A
1 A
465543 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:465649 original size:21 final size:20
Alignment explanation
Indices: 465623--465699 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 20
465613 GTTGGGACCT
*
465623 TGTATCGATACATTTGTATAA
1 TGTATCGATACA-TTCTATAA
* *
465644 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTA-TAA
465665 TGTATCGATACATTCTATAAA
1 TGTATCGATACATTCTAT-AA
465686 TGTATCGATACATT
1 TGTATCGATACATT
465700 TGGATAATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTCTATAA
Found at i:466416 original size:119 final size:116
Alignment explanation
Indices: 466208--466419 Score: 252
Period size: 119 Copynumber: 1.8 Consensus size: 116
466198 GGGTGTCCAC
** * * *
466208 TTTTCAAGGACAAAGGAAAAGAGAATGAAATGGGTCTTGCTCCTTGAAGACCAAGGAAGAGAAGA
1 TTTTCAAGGACAAAGGAAAAGAGAATGAAATACGTCCTGCTCCTTGAAGACAAAAGAAGAGAAGA
466273 AAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACATCCCA
66 AAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACATCCCA
* *
466324 TTTTCCAAGGACAAAGGAAAAAGGGAAATGAAATACGTCCTGCT-CTCTGAGGACAAAAGAA-AG
1 TTTT-CAAGGACAAAGG-AAAAGAG-AATGAAATACGTCCTGCTCCT-TGAAGACAAAAGAAGAG
* *
466387 AGGAAAA-TAAAGTGTATCCTGC-TCTTTGAGGAC
62 AAGAAAAGGAAAGTG--TCCTGCTTC-TTGAGGAC
466420 TAAAAAGTGC
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
116 4 0.05
117 18 0.22
118 18 0.22
119 40 0.50
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (116 bp):
TTTTCAAGGACAAAGGAAAAGAGAATGAAATACGTCCTGCTCCTTGAAGACAAAAGAAGAGAAGA
AAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACATCCCA
Found at i:466489 original size:55 final size:55
Alignment explanation
Indices: 466403--467413 Score: 912
Period size: 55 Copynumber: 18.0 Consensus size: 55
466393 ATAAAGTGTA
* * *
466403 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
466458 TCCTGCTCTTTAAGGACTGAAAGGTGTCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* * *
466513 TCCTACTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
466568 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
*
466623 TCCTGCTCTTTGA-G---G--A--TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
466670 TCCTGCTCTTTGA-G---G--A--TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* ** *
466717 TCCTGCTCTTTGAGGACTAAAAAATGCCCCCAACTTGTGTGGGCTTTGAAAAGG-G
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGGCG
* *
466772 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* * *
466833 TCCTACTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAACA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* *
466893 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* * * * *
466952 TCCCGCTCTTTGAGGGCTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
467007 TCCTGTTCTTTGAGGACCAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGA-CTGAAAGGTGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCG
* * *
467068 TCCTGCTCTTTGAAGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
467123 TCCTGCTATTTGAAGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCG
* * *
467184 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
467239 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCG
*
467299 TCCTGCTTTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-----G---AAAGGCG
* * * *
467361 TCCTGCTCTTTGAGGACTGGAAA-ATGCAACCAACTTGTGTTGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
467414 AAAAGGCATC
Statistics
Matches: 841, Mismatches: 63, Indels: 104
0.83 0.06 0.10
Matches are distributed among these distances:
47 88 0.10
48 3 0.00
49 1 0.00
51 1 0.00
53 3 0.00
54 33 0.04
55 342 0.41
56 14 0.02
59 18 0.02
60 168 0.20
61 116 0.14
62 24 0.03
63 21 0.02
64 9 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:466661 original size:47 final size:47
Alignment explanation
Indices: 466592--466783 Score: 271
Period size: 47 Copynumber: 3.9 Consensus size: 47
466582 GACTGAAAGG
466592 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGA
466639 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGA
466686 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTAAAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGG--------A
*
466741 TGCCCCCAACTTGTGTGGGCTTTGAAAAGG-GTCCTGCTCTTTG
1 TGCCACCAACTTGTGTGGGCTTTG-AAAGGTGTCCTGCTCTTTG
466784 GGGACTGAAA
Statistics
Matches: 134, Mismatches: 1, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
47 90 0.67
48 2 0.01
55 37 0.28
56 5 0.04
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (47 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGA
Found at i:466785 original size:204 final size:212
Alignment explanation
Indices: 466424--467344 Score: 887
Period size: 204 Copynumber: 4.1 Consensus size: 212
466414 GAGGACTAAA
* * *
466424 AAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTAAGGACTGAAAGGTGTCACC
1 AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTT-A-GA--GGAA-GTGCCACC
* * *
466489 AACTTGTGTGGGCTTTA-AGAGGTGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGT
61 AACTTGTGTGGGCTTTAGAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGT
* ** *
466553 GGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AA
126 GGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAA
*
466617 G-AGGTGTCCTGCTCTTTGAGG
191 GAAGGCGTCCTGCTCTTTGAGG
*
466638 -A-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTT-GAGG-A-TGCCACCAACTT
1 AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTAGAGGAAGTGCCACCAACTT
* ** *
466698 GTGTGGGCTTT-GAAAGGTGTCCTGCTCTTTGAGGACTAAAAAATGCCCCCAACTTGTGTGGGCT
66 GTGTGGGCTTTAGAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCT
* *
466762 TTGAAAAGG-GTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
131 TT-AAAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAAG-
* * *
466826 AAAAGCATCCTACTCTTTGAGG
192 -AAGGCGTCCTGCTCTTTGAGG
* *
466848 ACTAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAACATCCTGCTCTTT-GAGGACTA
1 ----AA-GTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCGTCCTGCTCTTTAGAGG----
* * * *
466912 AAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGGCTGGAAAAT
51 AA-GTGCCACCAACTTGTGTGGGCTTT---AG-AAAGGCGTCCTGCTCTTTGAGGACTGGAAAAT
* * *
466977 GCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGTTCTTTGAGGACCAGGAA-GTGCCACCAAC
111 GCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGA-CTGAAAGGTGCCACCAAC
467041 TTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTCTTTGAAGACTGGG
175 TTGTGTGGGCTTT--AA--AGAAGGCGTCCTGCTCTTT---GA---GG
* *
467089 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTATTTGAAGACTAGGAAGTGCCACC
1 AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTT--AG---AGGAAGTGCCACC
* *
467154 AACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACT
61 AACTTGTGTGGGCTTT---A-GA-AAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACT
467219 TGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCT
121 TGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCT
* *
467283 TTAAAAGGAAAAGGCATCCTGCTTTTTGAGG
186 TT-AAA-G--AAGGCGTCCTGCTCTTTGAGG
467314 ACTAAAGGTGCCACCAACTTGTGTGGGCTTT
1 ----AA-GTGCCACCAACTTGTGTGGGCTTT
467345 AAAAAGAAAA
Statistics
Matches: 598, Mismatches: 49, Indels: 104
0.80 0.07 0.14
Matches are distributed among these distances:
204 119 0.20
205 5 0.01
206 1 0.00
207 4 0.01
209 2 0.00
210 16 0.03
212 40 0.07
213 1 0.00
215 1 0.00
217 24 0.04
218 4 0.01
223 15 0.03
225 2 0.00
228 4 0.01
229 3 0.01
230 62 0.10
231 68 0.11
232 74 0.12
233 1 0.00
234 7 0.01
235 106 0.18
236 31 0.05
237 4 0.01
238 2 0.00
241 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (212 bp):
AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTAGAGGAAGTGCCACCAACTT
GTGTGGGCTTTAGAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCT
TTAAAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAGG
CGTCCTGCTCTTTGAGG
Found at i:467105 original size:116 final size:118
Alignment explanation
Indices: 466686--467436 Score: 839
Period size: 116 Copynumber: 6.4 Consensus size: 118
466676 TCTTTGAGGA
** ** *
466686 TGCCACCAACTTGTGTGGGCTTT-----G-AAAGGTGTCCTGCTCTTTGAGGACTAAAAAATGCC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGGAAAGTGCC
* * * * * *
466745 CCCAACTTGTGTGGGCTTTGAAAAGG-GTCCTGCTCTTTGGGGA-CTGAAAGG
66 ACCAACTTGTGTGGGCTTTAAAAAGGCATCCTGCTCTTTGAGGACCAGGAAGG
* *
466796 TGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAAAGCATCCTACTCTTTGAGGACT--AAAGGTG
1 TGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGGAAA-GTG
** *
466858 CCACCAACTTGTGTGGGCTTTGAAAAGAAAAAACATCCTGCTCTTTGAGGACTA--AAGG
64 CCACCAACTTGTGTGGGCTTT----A-AAAAGGCATCCTGCTCTTTGAGGACCAGGAAGG
* * * *
466916 TGCCACCAACTTGGGTGGGCTTTAAAA-GAAAAGGCATCCCGCTCTTTGAGGGCTGGAAAATGCC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGGAAAGTGCC
*
466980 ACCAACTTGTGTGGGCTTT-AAAAGGCATCCTGTTCTTTGAGGACCAGGAA-G
66 ACCAACTTGTGTGGGCTTTAAAAAGGCATCCTGCTCTTTGAGGACCAGGAAGG
* * * *
467031 TGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTCTTTGAAGACTGGGAAGTGCC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGGAAAGTGCC
* * * *
467096 ACCAACTTGTGTGGGCTTT-AAAAGGCGTCCTGCTATTTGAAGACTAGGAA-G
66 ACCAACTTGTGTGGGCTTTAAAAAGGCATCCTGCTCTTTGAGGACCAGGAAGG
* * *
467147 TGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTCTTTGAGGACTGGGAAGTGCC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGGAAAGTGCC
*
467212 ACCAACTTGTGTGGGCTTT-AAAAGGCATCCTGCTCTTTGAGGACTA--AAGG
66 ACCAACTTGTGTGGGCTTTAAAAAGGCATCCTGCTCTTTGAGGACCAGGAAGG
*
467262 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTTTTTGAGGACT--AAAGGTGC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGGAAA-GTGC
* * **
467325 CACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCGTCCTGCTCTTTGAGGA-CTGGAAAA
65 CACCAACTTGTGTGGGCTTT-------AAAAAGGCATCCTGCTCTTTGAGGACCAGGAAGG
* *
467385 TGCAACCAACTTGTGTTGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGG
467437 GCTAAAAAGC
Statistics
Matches: 558, Mismatches: 52, Indels: 49
0.85 0.08 0.07
Matches are distributed among these distances:
110 23 0.04
113 2 0.00
114 52 0.09
115 103 0.18
116 206 0.37
119 27 0.05
120 53 0.09
121 18 0.03
122 23 0.04
123 51 0.09
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (118 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGGAAAGTGCC
ACCAACTTGTGTGGGCTTTAAAAAGGCATCCTGCTCTTTGAGGACCAGGAAGG
Found at i:468445 original size:12 final size:12
Alignment explanation
Indices: 468428--468462 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
468418 TCTCTTTTTC
468428 TTTGTTTTGTTT
1 TTTGTTTTGTTT
468440 TTTGTTTTGTTT
1 TTTGTTTTGTTT
468452 TTT-TTTT-TTT
1 TTTGTTTTGTTT
468462 T
1 T
468463 AAGAGAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.17
11 4 0.17
12 15 0.65
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (12 bp):
TTTGTTTTGTTT
Found at i:468448 original size:17 final size:15
Alignment explanation
Indices: 468422--468462 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
468412 CTTTTCTCTC
*
468422 TTTTTCTTTGTTTTGT
1 TTTTTTTTTGTTTT-T
468438 TTTTTGTTTTGTTTTT
1 TTTTT-TTTTGTTTTT
468454 TTTTTTTTT
1 TTTTTTTTT
468463 AAGAGAAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 11 0.48
17 8 0.35
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTGTTTTT
Found at i:480991 original size:77 final size:78
Alignment explanation
Indices: 480864--481056 Score: 201
Period size: 79 Copynumber: 2.5 Consensus size: 78
480854 ACGGGGTTGG
* * * * ** * * *
480864 AGTATTCCCTTGAAAATAACGGGGCTGGAGTATCTCCGGTTGTGAGAAATCGATGA-TT-AAAAA
1 AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAAT-ATTTGAAAAA
*
480927 AAAATCGGAATTGA
65 AAAACCGGAATTGA
* *
480941 AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGAGAAT
1 AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATA-TTTGAAAAA
* ** *
481006 AAAGCCGGGGTTGG
65 AAAACCGGAATTGA
*
481020 AGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCC
1 AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
481057 GATGAAATAA
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
76 1 0.01
77 45 0.47
78 2 0.02
79 48 0.50
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (78 bp):
AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTGAAAAAA
AAACCGGAATTGA
Found at i:481044 original size:28 final size:27
Alignment explanation
Indices: 481011--481082 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 27
481001 AGAATAAAGC
481011 CGGGGTTGGAGTATCCCC-TCGAAAGTAA
1 CGGGGTTGGAGTATCCCCAT-GAAA-TAA
481039 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCC-ATGAAATAA
*
481067 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
481083 TCGATTGTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCATGAAATAA
Found at i:481254 original size:104 final size:104
Alignment explanation
Indices: 481070--481292 Score: 245
Period size: 104 Copynumber: 2.1 Consensus size: 104
481060 GAAATAACGA
* * * * *
481070 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCA
1 GGTTGGAGTATCCCCGATTGTAAAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTGGAGTATCA
* *** *
481135 CCGATTAAAGGAAAATTGGTGTTTTAAAAATAAAACCGG
66 CCGATTAAAGAAAAATCAATATTTTAAAAATAAAACCGG
*
481174 GGTTGGAGTATCCCCGATTGTAAAAAAAATTAGTG-TTTTAGCAATAAAACC-GAGGTTGGAGTA
1 GGTTGGAGTATCCCCGATTGT--AAAAAATTAGTGTTTTTAGAAATAAAACCGGA-GTTGGAGTA
* * ** **
481237 TCCCCGATT-ATGAAAAATCAATATTTTGGAAATAAAGTCGG
63 TCACCGATTAAAGAAAAATCAATATTTTAAAAATAAAACCGG
481278 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
481293 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
104 59 0.60
105 30 0.30
106 10 0.10
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.30
Consensus pattern (104 bp):
GGTTGGAGTATCCCCGATTGTAAAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTGGAGTATCA
CCGATTAAAGAAAAATCAATATTTTAAAAATAAAACCGG
Found at i:481281 original size:264 final size:264
Alignment explanation
Indices: 480963--481456 Score: 823
Period size: 264 Copynumber: 1.9 Consensus size: 264
480953 AAAATAACGG
480963 GGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGAGAATAAAGCCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGAGAATAAAGCCGGGGTTGGAGTATCCC
* *
481028 CTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGA
66 CTCGAAAATAACGGGGTTGGAGTATCCCCGATG-AATAACGAGGTTGGAGTATCCCCGATTGTGA
*
481093 A-AAATTGGTG-TTTTTGGAAATAAAATCGGAGTTGGAGTATCACCGATTAAAGGAAAATTGGTG
130 ACAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCACCGATTAAA-GAAAATTAGTG
* *
481156 TTTTAAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTAAAAAAAATTAGTGTTTTAGCAATAA
194 TTTTAAAAATAAAACCGGAGTTGGAATATCCCCGATTGTAAAAAAAATTAGTGTTTTAGCAATAA
481221 AACCGA
259 AACCGA
* *
481227 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTG-GAAATAAAGTCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGAG-AATAAAGCCGGGGTTGGAGTATCC
* *
481291 CCTCGAAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGA
65 CCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAATAACGAGGTTGGAGTATCCCCGATTGTGA
* *
481356 ACAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTAGTGT
130 ACAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCACCGATTAAAGAAAATTAGTGT
* *
481421 TTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
195 TTTAAAAATAAAACCGGAGTTGGAATATCCCCGATT
481457 ATGGAGAATT
Statistics
Matches: 214, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
263 30 0.14
264 145 0.68
265 39 0.18
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (264 bp):
GGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGAGAATAAAGCCGGGGTTGGAGTATCCC
CTCGAAAATAACGGGGTTGGAGTATCCCCGATGAATAACGAGGTTGGAGTATCCCCGATTGTGAA
CAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCACCGATTAAAGAAAATTAGTGTT
TTAAAAATAAAACCGGAGTTGGAATATCCCCGATTGTAAAAAAAATTAGTGTTTTAGCAATAAAA
CCGA
Found at i:481338 original size:27 final size:27
Alignment explanation
Indices: 481275--481350 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
481265 GAAATAAAGT
481275 CGGGGTTGGAGTATCCCCTCGA-AAATAA
1 CGGGGTTGGAGTAT-CCC-CGATAAATAA
* *
481303 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATAAATAA
481330 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
481351 TGTGAACAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 3 0.07
27 28 0.62
28 14 0.31
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATAAATAA
Found at i:481438 original size:51 final size:51
Alignment explanation
Indices: 481071--481458 Score: 216
Period size: 53 Copynumber: 7.4 Consensus size: 51
481061 AAATAACGAG
* * * *
481071 GTTGGAGTATCCTCGATTGT-GAAAAATTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAG-AAAATTAGTG-TTTTGAAAATAAAATCGGA
* * * * * *
481123 GTTGGAGTATCACCGATTAAAGGAAAATTGGTGTTTTAAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGA
* * * *
481175 GTTGGAGTATCCCCGATTGTAAAAAAAATTAGTGTTTT-AGCAATAAAA-CCGA
1 GTTGGAGTATCCCCGA-T-TATAGAAAATTAGTGTTTTGA-AAATAAAATCGGA
* * * * * *
481227 GGTTGGAGTATCCCCGATTAT-GAAAAATCAATATTTTGGAAATAAAGTCGGG
1 -GTTGGAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATCGGA
** *** * *** ** * *
481279 GTTGGAGTATCCCCTCGAAAATA-ACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTAT-CCC-CGATTATAGA--AAATT--AGTGT-TTTGAAAATAAAATCGGA
* * *
481334 GTTGGAGTATCCCCGATTGT-GAACAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAG-A-AAATTAGTG--TTTTGAAAATAAAATCGGA
481388 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
*
481439 GTTGGAATATCCCCGATTAT
1 GTTGGAGTATCCCCGATTAT
481459 GGAGAATTGA
Statistics
Matches: 252, Mismatches: 60, Indels: 49
0.70 0.17 0.14
Matches are distributed among these distances:
51 68 0.27
52 59 0.23
53 69 0.27
54 33 0.13
55 15 0.06
56 5 0.02
57 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:483258 original size:12 final size:12
Alignment explanation
Indices: 483241--483272 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
483231 CAATGGAATA
483241 GTGTTTTTTTTT
1 GTGTTTTTTTTT
483253 GTGTTTTTTTTT
1 GTGTTTTTTTTT
483265 GT-TTTTTT
1 GTGTTTTTT
483273 GCTAAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (12 bp):
GTGTTTTTTTTT
Found at i:483823 original size:13 final size:13
Alignment explanation
Indices: 483805--483830 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
483795 AAAAAGATCC
483805 ATGTATCGATACA
1 ATGTATCGATACA
483818 ATGTATCGATACA
1 ATGTATCGATACA
483831 TTTCCTTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:486585 original size:103 final size:103
Alignment explanation
Indices: 486444--486703 Score: 283
Period size: 104 Copynumber: 2.5 Consensus size: 103
486434 AAAATAAGGC
* * * *
486444 TAGAGTATCCCCTCAAAGA-AGTGAGATTGGAGTATCCCCAAAGATAAAATTATGAAAATATTTA
1 TAGAATATCCCCTCAAA-ATAGTGGGGTTGGAGTTTCCCCAAAGATAAAATTATGAAAATATTTA
*
486508 GAAACAAATAGAAAATTTAAGTTTTTTTAAAGAACAGGGT
65 GAAACAAAAAGAAAATTTAA-TTTTTTTAAAGAACAGGGT
* * *** * * * *
486548 T-GTAGTAT-CCTTTGGAGTAGTGGGGTTGGAGTTTCCCCAAAGTTGAAGATGATGAAAATATTT
1 TAG-AATATCCCCTCAAAATAGTGGGGTTGGAGTTTCCCCAAAGAT-AAAATTATGAAAATATTT
* * * * **
486611 AGGAACAAAAAGTAAATTTCATTTTTTTTAAGAATGGGGT
64 AGAAACAAAAAGAAAATTTAATTTTTTTAAAGAACAGGGT
486651 TAGAATATCCCCTCAAAATAGTGGGGTTGGAGTTTCCCCAAAGATAAAATTAT
1 TAGAATATCCCCTCAAAATAGTGGGGTTGGAGTTTCCCCAAAGATAAAATTAT
486704 ATGAAAAGAA
Statistics
Matches: 124, Mismatches: 27, Indels: 11
0.77 0.17 0.07
Matches are distributed among these distances:
103 54 0.44
104 70 0.56
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Consensus pattern (103 bp):
TAGAATATCCCCTCAAAATAGTGGGGTTGGAGTTTCCCCAAAGATAAAATTATGAAAATATTTAG
AAACAAAAAGAAAATTTAATTTTTTTAAAGAACAGGGT
Found at i:488696 original size:21 final size:21
Alignment explanation
Indices: 488653--488698 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
488643 GGAAATCTCT
** *
488653 TTTTTCTCTCTTTTTTTCTTC
1 TTTTTCTCTCTTTTCCTCCTC
*
488674 TTTTTCTTTCTTTTCCTCCTC
1 TTTTTCTCTCTTTTCCTCCTC
488695 TTTT
1 TTTT
488699 AGCTGAGCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTCTCTCTTTTCCTCCTC
Found at i:495341 original size:20 final size:20
Alignment explanation
Indices: 495316--495369 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
495306 GTTTGTGACA
* **
495316 ATGTATCGATACAATTTTTC
1 ATGTATCGATACAATGTACC
495336 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
495356 ATGTATCGATACAA
1 ATGTATCGATACAA
495370 ACCGTGGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:497927 original size:26 final size:26
Alignment explanation
Indices: 497891--497947 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
497881 ATAGTAACCC
497891 ATGTATCAATACATTGTATCGATATA
1 ATGTATCAATACATTGTATCGATATA
*
497917 ATGTATTAATACATTGTATCGATATA
1 ATGTATCAATACATTGTATCGATATA
497943 ATGTA
1 ATGTA
497948 CCGATACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (26 bp):
ATGTATCAATACATTGTATCGATATA
Found at i:497947 original size:13 final size:13
Alignment explanation
Indices: 497891--497956 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
497881 ATAGTAACCC
*
497891 ATGTATCAATACA
1 ATGTATCGATACA
* *
497904 TTGTATCGATATA
1 ATGTATCGATACA
**
497917 ATGTATTAATACA
1 ATGTATCGATACA
* *
497930 TTGTATCGATATA
1 ATGTATCGATACA
*
497943 ATGTACCGATACA
1 ATGTATCGATACA
497956 A
1 A
497957 AGAACATTGT
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:497954 original size:26 final size:26
Alignment explanation
Indices: 497891--497955 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
497881 ATAGTAACCC
*
497891 ATGTATCAATACATTGTATCGATATA
1 ATGTACCAATACATTGTATCGATATA
**
497917 ATGTATTAATACATTGTATCGATATA
1 ATGTACCAATACATTGTATCGATATA
*
497943 ATGTACCGATACA
1 ATGTACCAATACA
497956 AAGAACATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (26 bp):
ATGTACCAATACATTGTATCGATATA
Found at i:505049 original size:79 final size:79
Alignment explanation
Indices: 504900--505071 Score: 204
Period size: 79 Copynumber: 2.2 Consensus size: 79
504890 GAGTACTTCA
* * * *
504900 ACCCCATTTTTACTTCCAAAACATCTAATTTTTCATCTTCGGGATACTCCAACCCCACCACTTTT
1 ACCCCATTTTTACTTCCAAAACATCAAATTTTTCATCTTAGGGATACTCCAACCCCACCACTCTC
*
504965 GAAGGGATAGTCCC
66 CAAGGGATAGTCCC
* * *
504979 ACCCTATTTTTACTTCCACAACATCAAATTTTTCATCTCTAGGGATA-TGCCTACCCCACCA-TC
1 ACCCCATTTTTACTTCCAAAACATCAAATTTTTCATCT-TAGGGATACT-CCAACCCCACCACTC
* * *
505042 TCCAAGGGGATACTTCA
64 TCCAA-GGGATAGTCCC
505059 ACCCCATTTTTAC
1 ACCCCATTTTTAC
505072 ACTAAAATTT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
79 40 0.51
80 38 0.49
ACGTcount: A:0.27, C:0.32, G:0.09, T:0.32
Consensus pattern (79 bp):
ACCCCATTTTTACTTCCAAAACATCAAATTTTTCATCTTAGGGATACTCCAACCCCACCACTCTC
CAAGGGATAGTCCC
Found at i:508373 original size:32 final size:32
Alignment explanation
Indices: 508331--508405 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
508321 AACAGTAAAT
* * *
508331 GTATCGATACATAAGTGTTGTATCGATTCAAC
1 GTATCAATACATAAGTATTGTATCGATACAAC
*
508363 GTATCAATACATAAGTATTGTATCGATACAAT
1 GTATCAATACATAAGTATTGTATCGATACAAC
*
508395 GTATCACTACA
1 GTATCAATACA
508406 AAGCTACTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (32 bp):
GTATCAATACATAAGTATTGTATCGATACAAC
Found at i:508447 original size:20 final size:20
Alignment explanation
Indices: 508422--508476 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
508412 CTGCCAAGGA
* *
508422 AATGTATCGATATATTATTC
1 AATGTATCGATACATCATTC
508442 AATGTATCGATACATCATTC
1 AATGTATCGATACATCATTC
508462 AATGTATCGATACAT
1 AATGTATCGATACAT
508477 GCAGGCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATCATTC
Found at i:512514 original size:7 final size:7
Alignment explanation
Indices: 512502--512546 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
512492 GGATAAAATC
*
512502 ATAGATA
1 ATAGATT
512509 ATAGATT
1 ATAGATT
*
512516 ATAAATT
1 ATAGATT
*
512523 ATAAATT
1 ATAGATT
512530 ATAGATT
1 ATAGATT
512537 ATAGATT
1 ATAGATT
512544 ATA
1 ATA
512547 ATAAAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (7 bp):
ATAGATT
Found at i:512532 original size:14 final size:14
Alignment explanation
Indices: 512513--512563 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
512503 TAGATAATAG
512513 ATTATAAATTATAA
1 ATTATAAATTATAA
* *
512527 ATTATAGATTATAG
1 ATTATAAATTATAA
512541 ATTAT-AA-TA-AA
1 ATTATAAATTATAA
*
512552 AATATAAATTAT
1 ATTATAAATTAT
512564 TTACTTTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
11 5 0.17
12 4 0.14
13 3 0.10
14 17 0.59
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (14 bp):
ATTATAAATTATAA
Found at i:512916 original size:20 final size:19
Alignment explanation
Indices: 512881--512920 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
512871 TTATATCAGA
512881 TATTTAATTTTAAAATTATT
1 TATTTAATTTTAAAA-TATT
512901 TATTTAATATTT-AAATATT
1 TATTTAAT-TTTAAAATATT
512920 T
1 T
512921 TCCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 11 0.58
21 3 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTAATTTTAAAATATT
Found at i:513266 original size:16 final size:15
Alignment explanation
Indices: 513248--513288 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
513238 TTCAAATTTT
*
513248 TTTTTAATTTGAGTC
1 TTTTTAATTTGAATC
513263 TTTTTAGATTTGAATC
1 TTTTTA-ATTTGAATC
513279 TTTTTAATTT
1 TTTTTAATTT
513289 TAATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (15 bp):
TTTTTAATTTGAATC
Found at i:513739 original size:34 final size:35
Alignment explanation
Indices: 513701--513767 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
513691 CCTTACAACA
513701 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
513735 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
513768 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:514245 original size:13 final size:13
Alignment explanation
Indices: 514227--514252 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
514217 CAAATTTTTG
514227 TGTATCGATACAT
1 TGTATCGATACAT
514240 TGTATCGATACAT
1 TGTATCGATACAT
514253 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:514267 original size:32 final size:33
Alignment explanation
Indices: 514207--514270 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
514197 TACAAGCCAA
* *
514207 TGTATCGATACAAATTTTTGTGTATCGATACAT
1 TGTATCGATACAAATCTTGGTGTATCGATACAT
*
514240 TGTATCGATACATA-CTTGGTGTATCGATACA
1 TGTATCGATACAAATCTTGGTGTATCGATACA
514271 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAAATCTTGGTGTATCGATACAT
Found at i:516429 original size:23 final size:24
Alignment explanation
Indices: 516384--516430 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
516374 CAAAGGATTG
*
516384 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
516408 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
516431 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:519050 original size:34 final size:35
Alignment explanation
Indices: 519012--519078 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
519002 CCTTACAACA
519012 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
*
519046 CTATCTTTTTCAAATGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
519079 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.34
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:519556 original size:13 final size:13
Alignment explanation
Indices: 519538--519563 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
519528 CAAATTTTTG
519538 TGTATCGATACAT
1 TGTATCGATACAT
519551 TGTATCGATACAT
1 TGTATCGATACAT
519564 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:519578 original size:32 final size:33
Alignment explanation
Indices: 519518--519581 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
519508 TACAAGCCAA
* *
519518 TGTATCGATACAAATTTTTGTGTATCGATACAT
1 TGTATCGATACAAATCTTGGTGTATCGATACAT
*
519551 TGTATCGATACATA-CTTGGTGTATCGATACA
1 TGTATCGATACAAATCTTGGTGTATCGATACA
519582 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAAATCTTGGTGTATCGATACAT
Found at i:521580 original size:20 final size:21
Alignment explanation
Indices: 521555--521593 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
521545 ATTGTTTCTA
*
521555 TATTTATGT-TTTTTAATGCT
1 TATTTATGTAGTTTTAATGCT
521575 TATTTATGTAGTTTTAATG
1 TATTTATGTAGTTTTAATG
521594 ATTTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.62
Consensus pattern (21 bp):
TATTTATGTAGTTTTAATGCT
Found at i:521845 original size:22 final size:23
Alignment explanation
Indices: 521806--521851 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
521796 TTTCTTTAAA
*
521806 AAATTATTTATTTTTTAAAATTT
1 AAATCATTTATTTTTTAAAATTT
521829 AAATCATTTA-TTTTTAAAATTT
1 AAATCATTTATTTTTTAAAATTT
521851 A
1 A
521852 TTGTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATCATTTATTTTTTAAAATTT
Found at i:527740 original size:17 final size:19
Alignment explanation
Indices: 527712--527746 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
527702 TAGTGGGGTG
527712 TAAAAGATATTTT-AATTT
1 TAAAAGATATTTTCAATTT
527730 TAAAA-ATATTTTCAATT
1 TAAAAGATATTTTCAATT
527747 CTAATTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (19 bp):
TAAAAGATATTTTCAATTT
Found at i:532920 original size:61 final size:61
Alignment explanation
Indices: 532844--532961 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 61
532834 TTTCTCCCAC
* * *
532844 TTGAAGTGGAATTAATTTGAGACCTAAAATTTATATCAACTATCTTGCAAATTGGATCCAG
1 TTGAAGCGGAATTAATTTGAGACCTAAAATTTAAATCAACTATCTTGCAAATGGGATCCAG
*
532905 TTGAAGCGGAATTAATTTGAGGCCTAAAATTTAAATCAACTATCTTGCAAATGGGAT
1 TTGAAGCGGAATTAATTTGAGACCTAAAATTTAAATCAACTATCTTGCAAATGGGAT
532962 TAATAAAATC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (61 bp):
TTGAAGCGGAATTAATTTGAGACCTAAAATTTAAATCAACTATCTTGCAAATGGGATCCAG
Found at i:535089 original size:6 final size:6
Alignment explanation
Indices: 535078--535106 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
535068 GGTGATTAAT
535078 AAAAAG AAAAAG AAAAA- AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
535107 GAACTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:535098 original size:11 final size:12
Alignment explanation
Indices: 535078--535106 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
535068 GGTGATTAAT
535078 AAAAAGAAAAAG
1 AAAAAGAAAAAG
535090 AAAAA-AAAAAG
1 AAAAAGAAAAAG
535101 AAAAAG
1 AAAAAG
535107 GAACTTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:535697 original size:118 final size:119
Alignment explanation
Indices: 535480--535731 Score: 461
Period size: 122 Copynumber: 2.1 Consensus size: 119
535470 AAATATCAAA
535480 AATTTAATTGTAATGTCTAGGTAAAATCACTTGTGAGTAAATGTGGCATTATATATATATATATA
1 AATTTAATTGTAATGTCTAGGTAAAATCACTTGTGAGTAAATGTGGCATTATATATATATATATA
535545 TATATATACACGTGACACTGCTTAACAAAATATTAAAAATTTAAAAAGTCAAATAAT
66 TATATAT--A-GTGACACTGCTTAACAAAATATTAAAAATTTAAAAAGTCAAATAAT
535602 AATTTAATTGTAATGTCTAGGTAAAATCACTTGTGAGTAAATGTGGCATTATATATATATATATA
1 AATTTAATTGTAATGTCTAGGTAAAATCACTTGTGAGTAAATGTGGCATTATATATATATATATA
*
535667 TATATAT-GTGACATTGCTTAACAAAATATTAAAAATTTAAAAAGTCAAATAAT
66 TATATATAGTGACACTGCTTAACAAAATATTAAAAATTTAAAAAGTCAAATAAT
535720 AATTTAATTGTA
1 AATTTAATTGTA
535732 CGGCTTTCAC
Statistics
Matches: 129, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
118 57 0.44
122 72 0.56
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (119 bp):
AATTTAATTGTAATGTCTAGGTAAAATCACTTGTGAGTAAATGTGGCATTATATATATATATATA
TATATATAGTGACACTGCTTAACAAAATATTAAAAATTTAAAAAGTCAAATAAT
Found at i:538503 original size:20 final size:20
Alignment explanation
Indices: 538478--538532 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
538468 CTACCAGTTT
* *
538478 CATGTATCTATACAATTGTA
1 CATGTATCGATACAATTGAA
538498 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
538517 CAAGTATCGATACAAT
1 CATGTATCGATACAAT
538533 GAATCAATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:545503 original size:15 final size:15
Alignment explanation
Indices: 545485--545519 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
545475 CGAGTCAACT
545485 TCATCATTATCATCA
1 TCATCATTATCATCA
*
545500 TCATCATTATCTTCA
1 TCATCATTATCATCA
545515 TCATC
1 TCATC
545520 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:547200 original size:20 final size:19
Alignment explanation
Indices: 547175--547230 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 19
547165 CTGCTAGTTT
* *
547175 CATGTATTGATACAATTATG
1 CATGTATTGATACAATGA-A
*
547195 CATGTATCGATACAATGAA
1 CATGTATTGATACAATGAA
*
547214 CATATATTGATACAATG
1 CATGTATTGATACAATG
547231 CATCGAGACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (19 bp):
CATGTATTGATACAATGAA
Found at i:547227 original size:19 final size:20
Alignment explanation
Indices: 547179--547230 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
547169 TAGTTTCATG
* * *
547179 TATTGATACAATTATGCATG
1 TATTGATACAATGATACATA
*
547199 TATCGATACAATGA-ACATA
1 TATTGATACAATGATACATA
547218 TATTGATACAATG
1 TATTGATACAATG
547231 CATCGAGACA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
TATTGATACAATGATACATA
Found at i:549720 original size:22 final size:21
Alignment explanation
Indices: 549695--549743 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
549685 AAAAATAAAT
549695 AAAACTAATATGAAATA-AACCA
1 AAAACTAAT-T-AAATATAACCA
* *
549717 AAAATTAATTAAATATAACTA
1 AAAACTAATTAAATATAACCA
549738 AAAACT
1 AAAACT
549744 CTACGACTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAACTAATTAAATATAACCA
Found at i:554237 original size:19 final size:20
Alignment explanation
Indices: 554213--554266 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
554203 ATCGTTACAT
554213 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTGTA
* *
554232 TGTATCGATACATTAACTGTT
1 TGTATCGATACA-AAACTGTA
554253 TGTATCGATACAAA
1 TGTATCGATACAAA
554267 TTGAAGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAAAACTGTA
Found at i:556007 original size:157 final size:156
Alignment explanation
Indices: 555673--556272 Score: 517
Period size: 150 Copynumber: 3.9 Consensus size: 156
555663 ATGAGGAAAG
* * * * * * * *
555673 GAACCTATCTCTAATACCCACCTTCGGCATAAAAGCGGACC-AGGTAACAACCTAAGACTCGATT
1 GAACCTAT-TCTAATGCCCACCTTTGGCATAAAAGTGGACCTCGGTGACAACCTAGGACTTGGTT
* *
555737 TTAAAAAATTACA-AAAATGCCCTTATGGG-A-ACCTTCGACATAAAAGTATC-CGATACCTCTA
65 CTAAAAAATTA-AGAAAATGCCCCTATGGGTATACCTTCGACATAAAAGTATCTCGATACC-CTA
* *
555798 AAGGACTTAAAAAGGATTTCAAAAGGGAT
128 AAAGACTTAAAAAGGATTACAAAAGGGAT
* *
555827 GAACCTATCCTAAATGCCCACCTTTGGCATAAAAGTGGACCTCGG-GACAACCTAGGACTTGGCT
1 GAACCTATTCT-AATGCCCACCTTTGGCATAAAAGTGGACCTCGGTGACAACCTAGGACTTGGTT
* *
555891 CTAAAAAATTAAGAAAATGCCCCATATGGGTATACCTTCGACATAAAAGTATCTCGGTAATCCTA
65 CTAAAAAATTAAGAAAATGCCCC-TATGGGTATACCTTCGACATAAAAGTATCTCGAT-ACCCTA
* *
555956 AAAGACTTAAAAA-GATTAGAGATA-GGAT
128 AAAGACTTAAAAAGGATTACA-AAAGGGAT
* * * *
555984 GAACCTATTCTAATTGCCCACCTTTAGCATAAAAGTAGA-CTCGGTGACAATCTAGGTCTTGGTT
1 GAACCTATTCTAA-TGCCCACCTTTGGCATAAAAGTGGACCTCGGTGACAACCTAGGACTTGGTT
* * * *
556048 CTAAAAAATTATGAAAATGCCCCTAT-GGTATACCTTCAACGTAAAAGTACCT-GATACCCTTAA
65 CTAAAAAATTAAGAAAATGCCCCTATGGGTATACCTTCGACATAAAAGTATCTCGATACCC-TAA
*
556111 AAGACTTAAAAAAGG-TT---TAA--GAT
129 AAGACTT-AAAAAGGATTACAAAAGGGAT
* * * ** * * * * *
556134 GAACCTATCCTAAATACCTACCTTTGGCATAAAA-TCAAACC-CGATGACGACCTAAGAGTTAGT
1 GAACCTATTCT-AATGCCCACCTTTGGCATAAAAGT-GGACCTCGGTGACAACCTAGGACTTGGT
* * * * *
556197 TCTAAAAAATTACA-AAAATGCCCTTA-GAGG-ATACTTTCGACGTAGAAGTA-CCCGATACCCC
64 TCTAAAAAATTA-AGAAAATGCCCCTATG-GGTATACCTTCGACATAAAAGTATCTCGATA-CCC
*
556258 TAAAGGACTTAAAAA
126 TAAAAGACTTAAAAA
556273 AGATGATAAA
Statistics
Matches: 373, Mismatches: 51, Indels: 49
0.79 0.11 0.10
Matches are distributed among these distances:
149 7 0.02
150 100 0.27
151 9 0.02
153 6 0.02
154 79 0.21
155 38 0.10
156 12 0.03
157 100 0.27
158 20 0.05
159 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (156 bp):
GAACCTATTCTAATGCCCACCTTTGGCATAAAAGTGGACCTCGGTGACAACCTAGGACTTGGTTC
TAAAAAATTAAGAAAATGCCCCTATGGGTATACCTTCGACATAAAAGTATCTCGATACCCTAAAA
GACTTAAAAAGGATTACAAAAGGGAT
Found at i:557589 original size:11 final size:11
Alignment explanation
Indices: 557573--557597 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
557563 ATGGATCATG
557573 AAGGCTAAATC
1 AAGGCTAAATC
557584 AAGGCTAAATC
1 AAGGCTAAATC
557595 AAG
1 AAG
557598 CATGAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (11 bp):
AAGGCTAAATC
Found at i:557928 original size:24 final size:24
Alignment explanation
Indices: 557879--557953 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
557869 GCTAGCTTAG
* *
557879 TTTTTCTATTATTTTTTAC-TTACT
1 TTTTTCTATT-TTTCTTACTTTTCT
557903 TTTTTCTATTTTTCTTACTTTTCT
1 TTTTTCTATTTTTCTTACTTTTCT
*
557927 TTCTCTCT-TTTTTC-T-CTTTT-T
1 TT-TTTCTATTTTTCTTACTTTTCT
557948 TTTTTC
1 TTTTTC
557954 GAGTTGATCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.07
21 3 0.07
22 5 0.11
23 8 0.18
24 22 0.49
25 4 0.09
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTCTATTTTTCTTACTTTTCT
Found at i:558826 original size:164 final size:161
Alignment explanation
Indices: 558475--558826 Score: 381
Period size: 164 Copynumber: 2.2 Consensus size: 161
558465 TAAATTTTTC
* *
558475 ATTTAATATGAATTAAATGATGATATTTGATGAATTTTAAAAATTAAAACAAGAAAAATCCCGCC
1 ATTTAATATGAATTAAATGATAATATTTGATGAATTTTAAAAATTAAAAAAAGAAAAATCCCGCC
* * *
558540 GAAAATATTTACAGAGTAGAAAACTTTGTATTTCGAAAATAAGGAAAATTAAAAAAAAATGAAAA
66 GAAAAAATTTACAGAGTAGAAAACTTCGTATTTCAAAAATAAGG-AAATTAAAAAAAAATGAAAA
* ** * *
558605 ATGAGTGAAAATGAGTGAATTTTTGAAAACTA
130 ATCAGTGAAAAAAAATGAATTTTTGAAAAATA
* *
558637 ATTTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAATAAAGAAAAATCTCC
1 ATTTAATATGAATTAAATGATAATATTTGATGAATTTTAAAAATT-AAAA-AAAGAAAAATC-CC
** * ** * *
558702 -TTGAAAAAATTTATAGAGTAGAAAACTTCGTATTTCAAAAATAAGG-GTTTCCAAAAAAAATTT
63 GCCGAAAAAATTTACAGAGTAGAAAACTTCGTATTTCAAAAATAAGGAAATT--AAAAAAAAATG
* * *
558765 AATAACTCA-TGAAATAAAAAT-AATTTTTTAAAAATG
126 AA-AAATCAGTGAAA-AAAAATGAATTTTTGAAAAATA
*
558801 ATTTGATAGTG-ATTAAATGATAATAT
1 ATTTAATA-TGAATTAAATGATAATAT
558827 GTGGAGAATT
Statistics
Matches: 157, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
162 44 0.28
163 4 0.03
164 98 0.62
165 11 0.07
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.32
Consensus pattern (161 bp):
ATTTAATATGAATTAAATGATAATATTTGATGAATTTTAAAAATTAAAAAAAGAAAAATCCCGCC
GAAAAAATTTACAGAGTAGAAAACTTCGTATTTCAAAAATAAGGAAATTAAAAAAAAATGAAAAA
TCAGTGAAAAAAAATGAATTTTTGAAAAATA
Found at i:567161 original size:97 final size:96
Alignment explanation
Indices: 567053--567234 Score: 265
Period size: 97 Copynumber: 1.9 Consensus size: 96
567043 TGACGATGAC
567053 AATTTAAGCAAAAATAAGACTTAAATCTTGACAAGTTTAAAAACGGAGTTAGAGTATCCTCTCGA
1 AATTTAAGCAAAAATAAGACTTAAATCTTGACAAGTTTAAAAACGGAGTTAGAGTATCCTCTCGA
567118 AATAATGGGATTGGAGTATCCCCAATGTTGAT
66 AA-AATGGGATTGGAGTATCCCCAATGTTGAT
* * * * * * * *
567150 AATTTAGGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATGGGGTTAGTGTATTCTCTTGG
1 AATTTAAGCAAAAATAAGACTTAAATCTTGACAAGTTTAAAAACGGAGTTAGAGTATCCTCTCGA
* *
567215 AAGATGGGGTTGGAGTATCC
66 AAAATGGGATTGGAGTATCC
567235 TCGATAAATA
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
96 16 0.21
97 59 0.79
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (96 bp):
AATTTAAGCAAAAATAAGACTTAAATCTTGACAAGTTTAAAAACGGAGTTAGAGTATCCTCTCGA
AAAATGGGATTGGAGTATCCCCAATGTTGAT
Found at i:569791 original size:20 final size:20
Alignment explanation
Indices: 569768--569827 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
569758 TAGTATTGAT
*
569768 ACATTCACTTATGTATCGAC
1 ACATTAACTTATGTATCGAC
* * *
569788 ACATTTACTTATGTTTCGAT
1 ACATTAACTTATGTATCGAC
*
569808 ACATTAACTTGTTGTATCGA
1 ACATTAACTT-ATGTATCGA
569828 TAAAAATTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 26 0.79
21 7 0.21
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (20 bp):
ACATTAACTTATGTATCGAC
Found at i:575308 original size:94 final size:94
Alignment explanation
Indices: 575138--575317 Score: 270
Period size: 94 Copynumber: 1.9 Consensus size: 94
575128 TTCAAGTTTG
* * * * *
575138 ATAAAAAATTTGAGCTGTGAATTTGGCATGAATTCTGGTGTGACAAAACATGTTGAAGCCAAACA
1 ATAAAAAATTTGAGCTATGAATTTGGCATGAATTATGGTGTGACAAAACATGCTCAAACCAAACA
*
575203 TTGAGTCAATGAACAAAGGCTCAAATCTA
66 TTAAGTCAATGAACAAAGGCTCAAATCTA
* *
575232 ATAAAAAATTTGAGCTATGAATTTGGTATGAATTATGGTGTGACAAAACATGCTCAAACTAAACA
1 ATAAAAAATTTGAGCTATGAATTTGGCATGAATTATGGTGTGACAAAACATGCTCAAACCAAACA
* *
575297 TTAAGTTAATGAGCAAAGGCT
66 TTAAGTCAATGAACAAAGGCT
575318 GAAAATAGCT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 76 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (94 bp):
ATAAAAAATTTGAGCTATGAATTTGGCATGAATTATGGTGTGACAAAACATGCTCAAACCAAACA
TTAAGTCAATGAACAAAGGCTCAAATCTA
Found at i:585754 original size:32 final size:32
Alignment explanation
Indices: 585717--585794 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
585707 ACATTATGCT
585717 TTGTATCGATACATTGTATCAAAACATGTTCA
1 TTGTATCGATACATTGTATCAAAACATGTTCA
585749 TTGTATCGATACATTGTATCAAAACATGTTCA
1 TTGTATCGATACATTGTATCAAAACATGTTCA
585781 TTGTATCGATACAT
1 TTGTATCGATACAT
585795 ACTTAATTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (32 bp):
TTGTATCGATACATTGTATCAAAACATGTTCA
Found at i:585794 original size:19 final size:19
Alignment explanation
Indices: 585728--585811 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 19
585718 TGTATCGATA
* *
585728 CATTGTATCAAAACATGTT
1 CATTGTATCGATACATGTT
585747 CATTGTATCGAT--A----
1 CATTGTATCGATACATGTT
* *
585760 CATTGTATCAAAACATGTT
1 CATTGTATCGATACATGTT
*
585779 CATTGTATCGATACATACTT
1 CATTGTATCGATACAT-GTT
*
585799 AATTGTATCGATA
1 CATTGTATCGATA
585812 TATGAAACTG
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
13 10 0.20
15 1 0.02
17 1 0.02
19 24 0.48
20 14 0.28
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATGTT
Found at i:585885 original size:20 final size:20
Alignment explanation
Indices: 585844--585888 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
585834 TTAAGTGAAA
*
585844 TGTATCGATACATGGGACAT
1 TGTATCGATACATGAGACAT
585864 TGTATCGATACATGAAGA-AT
1 TGTATCGATACATG-AGACAT
585884 TGTAT
1 TGTAT
585889 TAATACATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATGAGACAT
Found at i:593658 original size:15 final size:16
Alignment explanation
Indices: 593621--593658 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
593611 TTGGATGAGC
593621 GGATTACCGCAATAAA
1 GGATTACCGCAATAAA
593637 GGATTACCGCAATAAA
1 GGATTACCGCAATAAA
593653 -GATTAC
1 GGATTAC
593659 ATCCGACGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (16 bp):
GGATTACCGCAATAAA
Found at i:594355 original size:16 final size:16
Alignment explanation
Indices: 594334--594368 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
594324 CTTGGTTTTG
594334 ATATAACAAAGATTGA
1 ATATAACAAAGATTGA
594350 ATATAACAAAGATTGA
1 ATATAACAAAGATTGA
594366 ATA
1 ATA
594369 AAACCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (16 bp):
ATATAACAAAGATTGA
Found at i:594663 original size:33 final size:33
Alignment explanation
Indices: 594619--594697 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
594609 CATATCTAGA
594619 TGTATCAATACATTATGCTTTGTATTGATACAT
1 TGTATCAATACATTATGCTTTGTATTGATACAT
*
594652 TGTATCCATACATTATGCTTTGTATTGATACAT
1 TGTATCAATACATTATGCTTTGTATTGATACAT
*
594685 TGTATCGATACAT
1 TGTATCAATACAT
594698 GAAACTGGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (33 bp):
TGTATCAATACATTATGCTTTGTATTGATACAT
Found at i:598173 original size:13 final size:13
Alignment explanation
Indices: 598155--598180 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
598145 TTCACTATGC
598155 ATCGATACAATGT
1 ATCGATACAATGT
598168 ATCGATACAATGT
1 ATCGATACAATGT
598181 CTCATGTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATCGATACAATGT
Found at i:598244 original size:13 final size:13
Alignment explanation
Indices: 598226--598252 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
598216 CTGCCAGTTC
598226 ATGTATCGATACA
1 ATGTATCGATACA
598239 ATGTATCGATACA
1 ATGTATCGATACA
598252 A
1 A
598253 AGCAATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Done.