Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 94 of 198
Found at i:30106270 original size:19 final size:20
Alignment explanation
Indices: 30106246--30106289 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
30106236 AGGCATGTAG
*
30106246 AGGGGA-CAAATGAGTGAAA
1 AGGGGATCAAAGGAGTGAAA
**
30106265 AGGGGATCATGGGAGTGAAA
1 AGGGGATCAAAGGAGTGAAA
30106285 AGGGG
1 AGGGG
30106290 GCTTAATGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.39, C:0.05, G:0.45, T:0.11
Consensus pattern (20 bp):
AGGGGATCAAAGGAGTGAAA
Found at i:30109548 original size:28 final size:28
Alignment explanation
Indices: 30109508--30109564 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
30109498 AACATGTAGC
*
30109508 AACAGTGTGGGCCTTAGCACAATACAGT
1 AACAATGTGGGCCTTAGCACAATACAGT
* *
30109536 AACAATGTGGGCCTTAGCCCAATATAGT
1 AACAATGTGGGCCTTAGCACAATACAGT
30109564 A
1 A
30109565 TCGGTACAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (28 bp):
AACAATGTGGGCCTTAGCACAATACAGT
Found at i:30109865 original size:32 final size:31
Alignment explanation
Indices: 30109795--30109883 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 31
30109785 ATAAATACAA
* **
30109795 TAATATGATTGGCACAAAGCCACCAGTAGTAG
1 TAATATGA-TGGCACAAAGCCATCAGTAACAG
* * *
30109827 TGATATGACTGGCACACAGCCATCAGTAACGG
1 TAATATGA-TGGCACAAAGCCATCAGTAACAG
*
30109859 TAATATGATCAGCACAAAGCCATCA
1 TAATATGAT-GGCACAAAGCCATCA
30109884 ACAGCATTGC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
31 1 0.02
32 45 0.98
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (31 bp):
TAATATGATGGCACAAAGCCATCAGTAACAG
Found at i:30110182 original size:27 final size:27
Alignment explanation
Indices: 30110138--30110205 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
30110128 GGGCAAAATA
30110138 GTCA-TTTACCCTAAAGGGGCATTACG
1 GTCATTTTACCCTAAAGGGGCATTACG
* * * **
30110164 GTCATTTTACCTTACAGGGGTATTTTG
1 GTCATTTTACCCTAAAGGGGCATTACG
*
30110191 GTCATCTTACCCTAA
1 GTCATTTTACCCTAA
30110206 GAGGTATCTC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 4 0.12
27 29 0.88
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTAAAGGGGCATTACG
Found at i:30110246 original size:27 final size:27
Alignment explanation
Indices: 30110162--30110359 Score: 197
Period size: 27 Copynumber: 7.3 Consensus size: 27
30110152 AGGGGCATTA
30110162 CGGTCATTTTA-CCTTAC-AGGGGTATTT
1 CGGTCATTTTACCCTT-CGA-GGGTATTT
* * ** *
30110189 TGGTCATCTTACCCTAAGA-GGTATCT
1 CGGTCATTTTACCCTTCGAGGGTATTT
*
30110215 CGATCATTTTACCCTTCGAGGGTATTT
1 CGGTCATTTTACCCTTCGAGGGTATTT
* *
30110242 CGATCATTTTA-CCTTATGAGGGTATTT
1 CGGTCATTTTACCCTT-CGAGGGTATTT
* *
30110269 CGGTCACTTTTACCTTTTGAGGGTATTT
1 CGGTCA-TTTTACCCTTCGAGGGTATTT
* * *
30110297 TGGTTATTTTAGCCTTCGAGGGTATTT
1 CGGTCATTTTACCCTTCGAGGGTATTT
*
30110324 CGGTCATTTTACCTTTCGAGGGTATTT
1 CGGTCATTTTACCCTTCGAGGGTATTT
*
30110351 CGATCATTT
1 CGGTCATTT
30110360 ATTGACCTCT
Statistics
Matches: 141, Mismatches: 24, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
26 24 0.17
27 90 0.64
28 24 0.17
29 3 0.02
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (27 bp):
CGGTCATTTTACCCTTCGAGGGTATTT
Found at i:30115343 original size:25 final size:25
Alignment explanation
Indices: 30115315--30115372 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
30115305 ACAGCTCATG
30115315 TGAGCATTTATAGTCACAACTTGTA
1 TGAGCATTTATAGTCACAACTTGTA
* * *
30115340 TGAGCATTTATCGTCACAGCTTGTG
1 TGAGCATTTATAGTCACAACTTGTA
*
30115365 TAAGCATT
1 TGAGCATT
30115373 ATTCTCGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (25 bp):
TGAGCATTTATAGTCACAACTTGTA
Found at i:30118597 original size:16 final size:17
Alignment explanation
Indices: 30118568--30118600 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30118558 ATCACAATAA
30118568 AATAAAATTCTAATATT
1 AATAAAATTCTAATATT
*
30118585 AATAAACTT-TAATATT
1 AATAAAATTCTAATATT
30118601 TTTATATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAAAATTCTAATATT
Found at i:30123061 original size:45 final size:46
Alignment explanation
Indices: 30123010--30123133 Score: 173
Period size: 45 Copynumber: 2.7 Consensus size: 46
30123000 GAAGCTGTGT
*
30123010 CATAGTATCTTTCAACTATGGTCTTAT-TCATTTCCA-GTATAGTGA
1 CATAGTATCTTTCAACTATGGTCTT-TCTCATTTCCAGGTATAATGA
* *
30123055 CATAGTATCTTTCAACTATGGTCTTTCTC-GTTCCAGGTATAATGT
1 CATAGTATCTTTCAACTATGGTCTTTCTCATTTCCAGGTATAATGA
* *
30123100 CATGGTATCTTTCAACCATGGTCTTTCTCATTTC
1 CATAGTATCTTTCAACTATGGTCTTTCTCATTTC
30123134 TCAAGTCAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
44 6 0.09
45 61 0.87
46 3 0.04
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.43
Consensus pattern (46 bp):
CATAGTATCTTTCAACTATGGTCTTTCTCATTTCCAGGTATAATGA
Found at i:30125675 original size:73 final size:74
Alignment explanation
Indices: 30125546--30125756 Score: 232
Period size: 73 Copynumber: 2.8 Consensus size: 74
30125536 TACATTTAAC
* **
30125546 ATTCGAATCTCACATATACCTATATAATTTCATACCCCAT-TTCAATACAAGAACTTATACATGT
1 ATTCGAATCTAACATATA--TATATAATTTCATA-CTTATATTCAATACAAGAACTTATACATGT
* *
30125610 ACATATATACAT
63 ACACACATACAT
* * *
30125622 ATTCGAATCTAACATATATATATAATTT-ATACTTATATTCGAA-ACAAGTACTTATACTTGTAT
1 ATTCGAATCTAACATATATATATAATTTCATACTTATATTC-AATACAAGAACTTATACATGTAC
30125685 ACACATACAT
65 ACACATACAT
* * *
30125695 ATTCGAATTTAACATATACATATATAATTTCATACTTATACTCAATATAAGCAA-TTATACAT
1 ATTCGAATCTAACATAT--ATATATAATTTCATACTTATATTCAATACAAG-AACTTATACAT
30125757 ATGTATACAT
Statistics
Matches: 115, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
72 3 0.03
73 47 0.41
74 12 0.10
75 13 0.11
76 39 0.34
77 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (74 bp):
ATTCGAATCTAACATATATATATAATTTCATACTTATATTCAATACAAGAACTTATACATGTACA
CACATACAT
Found at i:30125775 original size:76 final size:74
Alignment explanation
Indices: 30125546--30125796 Score: 230
Period size: 76 Copynumber: 3.4 Consensus size: 74
30125536 TACATTTAAC
* * **
30125546 ATTCGAATCTCACATATACCTATATAATTTCATACCCCAT-TTCAATACAAGAACTTATACA-TG
1 ATTCGAATCTAACATATACATATATAATTTCATA-CTTATATTCAATACAAGAA-TTATACATTG
*
30125609 TACATATATACAT
64 T--ATACATACAT
*
30125622 ATTCGAATCTAACATAT--ATATATAATTT-ATACTTATATTCGAA-ACAAGTACTTATAC-TTG
1 ATTCGAATCTAACATATACATATATAATTTCATACTTATATTC-AATACAAG-AATTATACATTG
30125682 TATACACATACAT
64 TAT--ACATACAT
* * *
30125695 ATTCGAATTTAACATATACATATATAATTTCATACTTATACTCAATATAAGCAATTATACATATG
1 ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATACAAG-AATTATACAT-TG
* *
30125760 TATACATGCTT
64 TATACATACAT
* *
30125771 ATTCG-ATCCAAACATATACAAATATA
1 ATTCGAAT-CTAACATATACATATATA
30125797 TTATACATAT
Statistics
Matches: 146, Mismatches: 16, Indels: 26
0.78 0.09 0.14
Matches are distributed among these distances:
71 2 0.01
72 3 0.02
73 43 0.29
74 13 0.09
75 15 0.10
76 64 0.44
77 1 0.01
78 5 0.03
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (74 bp):
ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATACAAGAATTATACATTGTA
TACATACAT
Found at i:30130351 original size:151 final size:151
Alignment explanation
Indices: 30130050--30130352 Score: 509
Period size: 150 Copynumber: 2.0 Consensus size: 151
30130040 TGCAACATTA
* * **
30130050 AGGACTAAATTGAATAAATTTAAAAGTGCCATGAGATTATGTTGTAGATGAAAAGTATATTGTCC
1 AGGACTAAATTAAATAAATTGAAAAGTGCCATGAGATTATGTTGTAGATGAAAAGTATAAGGTCC
* * *
30130115 CTAATGAAAGAATGTGAAATCAGATTTTAATTCGATGTTGAATATAAAAAGATATGTGTATCCCG
66 CTAATGAAAGAATGTGAAATCAAATTTTAATCCAATGTTGAATATAAAAAGATATGTGTATCCCG
30130180 AGTATAGGGACTAAACTGAAT
131 AGTATAGGGACTAAACTGAAT
*
30130201 AGGACTAAATTAAATAAATTGAAAA-TTCCATGAGATTATGTTGTAGATGAAAAGTATAAGGTCC
1 AGGACTAAATTAAATAAATTGAAAAGTGCCATGAGATTATGTTGTAGATGAAAAGTATAAGGTCC
*
30130265 CTAATGAAAGAATGTGAAATCAAATTTTTATCCAATGTTGAATATAAAAAAGATATGTGTATCCC
66 CTAATGAAAGAATGTGAAATCAAATTTTAATCCAATGTTGAATAT-AAAAAGATATGTGTATCCC
30130330 GAGTATAGGGACTAAACTGAAT
130 GAGTATAGGGACTAAACTGAAT
30130352 A
1 A
30130353 AAATGAAAAA
Statistics
Matches: 142, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
150 77 0.54
151 65 0.46
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (151 bp):
AGGACTAAATTAAATAAATTGAAAAGTGCCATGAGATTATGTTGTAGATGAAAAGTATAAGGTCC
CTAATGAAAGAATGTGAAATCAAATTTTAATCCAATGTTGAATATAAAAAGATATGTGTATCCCG
AGTATAGGGACTAAACTGAAT
Found at i:30130913 original size:19 final size:18
Alignment explanation
Indices: 30130891--30130955 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 18
30130881 GTTTGCCTGG
30130891 ATGCACTTCGTGTGTCAAT
1 ATGCACTTCGTGTG-CAAT
*
30130910 ATGCACTTCATGTGCCAAT
1 ATGCACTTCGTGTG-CAAT
*
30130929 ATGCACTTCGTGTGCCAT
1 ATGCACTTCGTGTGCAAT
30130947 GATGCACTT
1 -ATGCACTT
30130956 TCGCTTGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 3 0.07
19 38 0.93
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.34
Consensus pattern (18 bp):
ATGCACTTCGTGTGCAAT
Found at i:30131362 original size:14 final size:14
Alignment explanation
Indices: 30131343--30131390 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
30131333 TGATAAAGAT
30131343 TGAATAGAAAGAAA
1 TGAATAGAAAGAAA
* *
30131357 TGAATAGATAG-TA
1 TGAATAGAAAGAAA
*
30131370 TGAGATAGAATGAAA
1 TGA-ATAGAAAGAAA
30131385 TGAATA
1 TGAATA
30131391 AGTTACGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 4 0.15
14 19 0.70
15 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (14 bp):
TGAATAGAAAGAAA
Found at i:30133838 original size:16 final size:16
Alignment explanation
Indices: 30133818--30133870 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
30133808 TTGGTTCGCT
*
30133818 GTAATGGAATAGAGAT
1 GTAATGGAATAGAGAC
*
30133834 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGAC
30133850 GTAATGGAATAGAGAC
1 GTAATGGAATAGAGAC
30133866 GTAAT
1 GTAAT
30133871 AGATAAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.42, C:0.04, G:0.32, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGAC
Found at i:30134125 original size:18 final size:18
Alignment explanation
Indices: 30134102--30134148 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
30134092 TTATTATTAA
30134102 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
30134120 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
30134138 AT-TAATATTAA
1 ATATAAT-TTAA
30134149 ATATTCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:30134212 original size:121 final size:121
Alignment explanation
Indices: 30134080--30134312 Score: 423
Period size: 121 Copynumber: 1.9 Consensus size: 121
30134070 ATTTAATCAT
30134080 ATTTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTAATA
1 ATTTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTAATA
* *
30134145 TTAAATATTCTTATATGA-ATTTATTAAAATCATAATATATAATACTATAAAATATA
66 TTAAACATTCTTATAT-ATATTTACTAAAATCATAATATATAATACTATAAAATATA
30134201 ATTTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTAATA
1 ATTTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTAATA
*
30134266 TTAAACATTTTTATATATATTTACTAAAATCATAATATATAATACTA
66 TTAAACATTCTTATATATATTTACTAAAATCATAATATATAATACTA
30134313 CAATACTTAC
Statistics
Matches: 108, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
120 1 0.01
121 107 0.99
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (121 bp):
ATTTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTAATA
TTAAACATTCTTATATATATTTACTAAAATCATAATATATAATACTATAAAATATA
Found at i:30134246 original size:18 final size:18
Alignment explanation
Indices: 30134223--30134269 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
30134213 TTATTATTAA
30134223 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
30134241 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
30134259 AT-TAATATTAA
1 ATATAAT-TTAA
30134270 ACATTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:30134430 original size:14 final size:15
Alignment explanation
Indices: 30134411--30134443 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
30134401 CTTTATTCTT
*
30134411 AAAATTCAAAAA-TA
1 AAAATTAAAAAACTA
30134425 AAAATTAAAAAACTA
1 AAAATTAAAAAACTA
30134440 AAAA
1 AAAA
30134444 ATTTAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATTAAAAAACTA
Found at i:30136204 original size:49 final size:49
Alignment explanation
Indices: 30136113--30136216 Score: 147
Period size: 49 Copynumber: 2.1 Consensus size: 49
30136103 AAAAGAAAAC
* ** * *
30136113 AAAA-TAAAATTAAGTTTAATATCATGAATCAAAAGGGGAACACTTTAT
1 AAAATTAAAATTAAGTTCAATATCATGAATCAAAAACGCAACACTGTAT
*
30136161 AAAATTAAAATTAAGTTCAATATCATGAATCAAAAACTCAACACTGTAT
1 AAAATTAAAATTAAGTTCAATATCATGAATCAAAAACGCAACACTGTAT
30136210 AAAATTA
1 AAAATTA
30136217 TAACACATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
48 4 0.08
49 45 0.92
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.29
Consensus pattern (49 bp):
AAAATTAAAATTAAGTTCAATATCATGAATCAAAAACGCAACACTGTAT
Found at i:30138920 original size:9 final size:10
Alignment explanation
Indices: 30138896--30138940 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
30138886 GAATGTAAGC
30138896 TTTATTATATA
1 TTTATTA-ATA
30138907 TTTATTAA-A
1 TTTATTAATA
30138916 TTTATTAATA
1 TTTATTAATA
*
30138926 --TATTTATA
1 TTTATTAATA
30138934 TTTATTA
1 TTTATTA
30138941 TGTATGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
8 7 0.24
9 9 0.31
10 6 0.21
11 7 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTATTAATA
Found at i:30139005 original size:16 final size:15
Alignment explanation
Indices: 30138984--30139013 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30138974 ATTATATCAA
30138984 TTTAATATACTATTTT
1 TTTAATATA-TATTTT
30139000 TTTAATATATATTT
1 TTTAATATATATTT
30139014 AATTATCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAATATATATTTT
Found at i:30139413 original size:10 final size:10
Alignment explanation
Indices: 30139398--30139422 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30139388 ACAGCAAAGG
30139398 AATCACAGTC
1 AATCACAGTC
30139408 AATCACAGTC
1 AATCACAGTC
30139418 AATCA
1 AATCA
30139423 GCCAATCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.20
Consensus pattern (10 bp):
AATCACAGTC
Found at i:30139705 original size:12 final size:13
Alignment explanation
Indices: 30139676--30139713 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
30139666 ATGTACATTT
30139676 TTCAATTATAACA
1 TTCAATTATAACA
30139689 TTCAATT-TAAC-
1 TTCAATTATAACA
30139700 TATCAATTATAACA
1 T-TCAATTATAACA
30139714 AGTCTTGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.05
12 10 0.45
13 11 0.50
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (13 bp):
TTCAATTATAACA
Found at i:30148723 original size:16 final size:16
Alignment explanation
Indices: 30148702--30148732 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30148692 TTTCCTTAAA
30148702 TAAAAAAATTCATATT
1 TAAAAAAATTCATATT
*
30148718 TAAAAAAATTTATAT
1 TAAAAAAATTCATAT
30148733 AGCTTTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAAAAATTCATATT
Found at i:30151914 original size:27 final size:26
Alignment explanation
Indices: 30151861--30151914 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
30151851 AATATAATAT
*
30151861 AATTATAAAATAATTAATTGTACTTA
1 AATTATAAAATAATTAATTGTAATTA
* *
30151887 AATTATTAAAATATTTAATTTTAATTA
1 AATTA-TAAAATAATTAATTGTAATTA
30151914 A
1 A
30151915 CTTTATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
AATTATAAAATAATTAATTGTAATTA
Found at i:30159709 original size:25 final size:25
Alignment explanation
Indices: 30159681--30159955 Score: 153
Period size: 25 Copynumber: 11.1 Consensus size: 25
30159671 CACACCGCAA
*
30159681 CTCTTATGAGCGTCCCGATATATGG
1 CTCTTATGAGCTTCCCGATATATGG
*
30159706 CTCTT-TGGAGCTTCCCGAT-TAAAGG
1 CTCTTAT-GAGCTTCCCGATAT-ATGG
* * **
30159731 CTCTTTGTGAGCTTCCTGAT-TAATTA
1 CTC-TTATGAGCTTCCCGATAT-ATGG
*
30159757 CTCTCCA-GAGCTTCCCGATATA--G
1 CTCT-TATGAGCTTCCCGATATATGG
* *
30159780 CTCGCT-TGAACTTCCCGATATATGG
1 CTC-TTATGAGCTTCCCGATATATGG
* **
30159805 CTATTCGGAGCTTCCCGAT-TAATGG
1 CTCTTATGAGCTTCCCGATAT-ATGG
*
30159830 CTCCTTA-GAG-TTACCCGTTAT-TGG
1 CT-CTTATGAGCTT-CCCGATATATGG
* *
30159854 CTCGTATGAGCTTCCTGAT-TATGG
1 CTCTTATGAGCTTCCCGATATATGG
* * *
30159878 CTCTTATGAGCTTCCTGTTATACGG
1 CTCTTATGAGCTTCCCGATATATGG
* * * *
30159903 C-CTGGATAAGCTTCCCGTTACATGG
1 CTCT-TATGAGCTTCCCGATATATGG
* *
30159928 CTCATATGAGCTTCCCGTTATATGG
1 CTCTTATGAGCTTCCCGATATATGG
30159953 CTC
1 CTC
30159956 GAGAGAGAGC
Statistics
Matches: 194, Mismatches: 35, Indels: 42
0.72 0.13 0.15
Matches are distributed among these distances:
23 21 0.11
24 40 0.21
25 108 0.56
26 24 0.12
27 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (25 bp):
CTCTTATGAGCTTCCCGATATATGG
Found at i:30159751 original size:26 final size:25
Alignment explanation
Indices: 30159704--30159753 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
30159694 CCCGATATAT
30159704 GGCTCTTTGGAGCTTCCCGATTAAA
1 GGCTCTTTGGAGCTTCCCGATTAAA
*
30159729 GGCTCTTTGTGAGCTTCCTGATTAA
1 GGCTCTTTG-GAGCTTCCCGATTAA
30159754 TTACTCTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (25 bp):
GGCTCTTTGGAGCTTCCCGATTAAA
Found at i:30167038 original size:14 final size:15
Alignment explanation
Indices: 30167019--30167056 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
30167009 ACTTCTACTC
30167019 CTTTTTCTATC-TTT
1 CTTTTTCTATCTTTT
*
30167033 CTTTTTCTTTCTTTT
1 CTTTTTCTATCTTTT
30167048 CTTTCTTCT
1 CTTT-TTCT
30167057 TTTTCCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 7 0.33
16 4 0.19
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTTCTATCTTTT
Found at i:30167065 original size:19 final size:19
Alignment explanation
Indices: 30167028--30167065 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
30167018 CCTTTTTCTA
*
30167028 TCTTTCTTTTTCTTTCTTT
1 TCTTTCTTTTTCTTCCTTT
30167047 TCTTTCTTCTTT-TTCCTTT
1 TCTTTCTT-TTTCTTCCTTT
30167066 AATTTGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TCTTTCTTTTTCTTCCTTT
Found at i:30172227 original size:13 final size:13
Alignment explanation
Indices: 30172209--30172251 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
30172199 TGACTTGGGT
*
30172209 CACACGACCAAGC
1 CACACGGCCAAGC
30172222 CACACGGCCAAGC
1 CACACGGCCAAGC
30172235 CACACGGCCAAGC
1 CACACGGCCAAGC
30172248 CACA
1 CACA
30172252 TGCCCATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.47, G:0.19, T:0.00
Consensus pattern (13 bp):
CACACGGCCAAGC
Found at i:30174577 original size:9 final size:9
Alignment explanation
Indices: 30174565--30174589 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30174555 TGTGCCCGTG
30174565 TGGCCCACT
1 TGGCCCACT
30174574 TGGCCCACT
1 TGGCCCACT
30174583 TGGCCCA
1 TGGCCCA
30174590 AATTGGACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.44, G:0.24, T:0.20
Consensus pattern (9 bp):
TGGCCCACT
Found at i:30179586 original size:16 final size:17
Alignment explanation
Indices: 30179558--30179592 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
30179548 AGAGAGTTGA
30179558 GAGAGGAGATGAGAGAT
1 GAGAGGAGATGAGAGAT
30179575 GAGAGG-GATGAGAGAT
1 GAGAGGAGATGAGAGAT
30179591 GA
1 GA
30179593 TGGATAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (17 bp):
GAGAGGAGATGAGAGAT
Found at i:30180996 original size:710 final size:716
Alignment explanation
Indices: 30179615--30181046 Score: 1816
Period size: 710 Copynumber: 2.0 Consensus size: 716
30179605 GAAATGAACT
* * *
30179615 CTTATTTATAGGTGAAGCAAGAGAGTTAGTTTGCTAAAATTAGGAGTGTCCATCCTTTGAAACCT
1 CTTATTTATAGGTGAAGCAAGAGAGATAGTTTGCTAAAAATAGGAGTGTCCATCCTTTGAAACAT
* *
30179680 CCTCCAAGAGTGGCCGACCATTAATTGATGAAATGTGGCTGATTTTTCCTTGATTTTTGGTCAAT
66 CCTCCAAGAGTGGACGACCATTAATTGATGAAATGTGGCTGATTTTCCCTTGATTTTTGGTCAAT
**
30179745 TTGAATGCCACAACAACTCAGGACTAAGACTCGGTCTCCAACAAATCTTCAGGTAAATCTCTAAT
131 TTGAATGCCACAACAACTCAGGACTAAGACTCGGTCAACAACAAATCTTCAGGTAAATCTCTAAT
* * **
30179810 TTCTTCAACTCTTCAAGGGCCTTGTATAATTAAACCAAAATTTGGTTTATAATCAGCCATGTGCA
196 TTCTTCAACTCTTCAAGGACCTTGTACAATTAAACCAAAAAGTGGTTTATAATCAGCCATGTGCA
* * * * * *
30179875 GCCAAAAATTGGGTTGGCTTAGTCCCCACTTTGGACGGTTTTGCAATTAGAAGAAAAATCTCAGA
261 GCCAAAAATTGGGTTGACTTAGTCCCCAATTTGGACGGTTTTGCAATTACAACAAAAATATCAAA
* * * *
30179940 CCTGTCAAAAATAGCAGATAGTTTAGAGGGCCAAATGAATTAATTTAACCACTTTAATTAATCAA
326 CCTGTCAAAAAAAGCAGAAAGTTTAGAGGACCAAATGAATTAATTTAACCAATTTAATT-ATCAA
* *
30180005 TTTACATAATTAATTAAACTCAATTTTATTAATGAAATATTTAAAATGAATTATTAAAATATAAG
390 -TT--ATAATTAA-TAAACTCAATATTATCAATGAAATATTTAAAATGAATTATTAAAATATAAG
* * * * *
30180070 ATTATATTTTTTTATTTAATTTAATCATGCATGGCCCACTTCATAGCTTAAAATATAATATGCTT
451 ATTATATTTTATCATTTAAATTAATCATGCATGACCCACTTCATAGCTTAAAATATAATATGATT
30180135 AAATTAATATAAAATAAGTCATTTTATGCATGAAAACTATATAATAAAACATAAAATCAAATTTT
516 AAATTAATATAAAATAAGTCATTTTATGCATGAAAACTATATAATAAAACATAAAATCAAATTTT
* *
30180200 AATAATTTCTATGTCCTGATTTCATATTTTCACATATTTCATTAATTTATTAAACAATTACTTGG
581 AATAATTTCTATGTCCTAATTTCATATTTTCACATATTTCATTAATTTATTAAACAATTACTTAG
* * * *
30180265 TTTTAACAATAATTTTAAGTAAAAAGGTGATGAATTATATAGAAAAAATCCTATATATTTTTTC-
646 TTTTAACAAGAATTTTAAGTAAAAAGGTGATAAATCACATAGAAAAAATCCTATATA-TTTTTCA
30180329 GTTTACA
710 GTTTACA
* * * * *
30180336 CTTATTTATAGGTG-AGGAGAGAGCGATAGTTTGCTAAAAATAGGAGTTTCCATCTTTTGAAGCA
1 CTTATTTATAGGTGAAGCA-AGAGAGATAGTTTGCTAAAAATAGGAGTGTCCATCCTTTGAAACA
* * * * *
30180400 TCTTCCATGGGTGGACGGCCA-TAATT-TTAGAAA-GTTGAGCTGATTTTCCCTTGATTTTTTGG
65 TCCTCCAAGAGTGGACGACCATTAATTGAT-GAAATG-TG-GCTGATTTTCCCTTGA-TTTTTGG
* ***
30180462 TCAATTTGAGTGCCACAACAACTCAGGACTAAGACTCGGTCAAGTGCAAATCTTCAGGTAAATCT
126 TCAATTTGAATGCCACAACAACTCAGGACTAAGACTCGGTCAACAACAAATCTTCAGGTAAATCT
*
30180527 CTAATTTCTTCAACTCTTCAAGGACCTTGTGCAATTAAACCAAAAAGTGGTTTATGAAT-AGCCA
191 CTAATTTCTTCAACTCTTCAAGGACCTTGTACAATTAAACCAAAAAGTGGTTTAT-AATCAGCCA
** ** * * * * * **
30180591 TGTGCAGCTGAATTTTGGGTTGACTTGGTCTCTAATTTGGACGGTTTTGTAA-TCCAACAAAGCT
255 TGTGCAGCCAAAAATTGGGTTGACTTAGTCCCCAATTTGGACGGTTTTGCAATTACAACAAAAAT
* *
30180655 ATCAAACCTGTCCAAAATAAATCA-ACAAG-TTAGAGGACCAAA-GAATTAAATTTATCCAATTT
320 ATCAAACCTGT-CAAAA-AAAGCAGA-AAGTTTAGAGGACCAAATGAATT-AATTTAACCAATTT
*
30180717 AA-T-T-AA-T-TAATTAA-AATC-CAA-ATTATCAATGAAATATTGTAAAATGAATTATT-AAA
381 AATTATCAATTATAATTAATAAACTCAATATTATCAATGAAATATT-TAAAATGAATTATTAAAA
** *
30180773 TAT-ATTTTATATTTTATCATTTAAATTAATCATGCATGACCCACTTTAT-GTCTTAAAAAATAT
445 TATAAGATTATATTTTATCATTTAAATTAATCATGCATGACCCACTTCATAG-CTT--AAAATAT
* *
30180836 AATAT-ATTCAAATTAATATAAAATAAG-C-TATTTATTGCATGAAAACTATATAATAAAGCATG
507 AATATGATT-AAATTAATATAAAATAAGTCAT-TTTA-TGCATGAAAACTATATAATAAAACATA
*
30180898 AAATCACATTTTAATAATTTCTATGTCCTAATTTCATATTTTCACATATTTCATTAATTTATTAA
569 AAATCAAATTTTAATAATTTCTATGTCCTAATTTCATATTTTCACATATTTCATTAATTTATTAA
* * * *
30180963 ACAATTACTTAGTTTTAACAACGGA-TTTAAGTAAAAATGTGATAAATCACATAGGATAAATCCT
634 ACAATTACTTAGTTTTAACAA-GAATTTTAAGTAAAAAGGTGATAAATCACATAGAAAAAATCCT
30181027 ATATATTTTTCAGTTTACA
698 ATATATTTTTCAGTTTACA
30181046 C
1 C
30181047 AGCCCCAAAC
Statistics
Matches: 619, Mismatches: 73, Indels: 49
0.84 0.10 0.07
Matches are distributed among these distances:
707 1 0.00
708 43 0.07
709 34 0.05
710 201 0.32
711 4 0.01
713 7 0.01
716 1 0.00
718 2 0.00
719 3 0.00
720 14 0.02
721 105 0.17
722 195 0.32
723 9 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (716 bp):
CTTATTTATAGGTGAAGCAAGAGAGATAGTTTGCTAAAAATAGGAGTGTCCATCCTTTGAAACAT
CCTCCAAGAGTGGACGACCATTAATTGATGAAATGTGGCTGATTTTCCCTTGATTTTTGGTCAAT
TTGAATGCCACAACAACTCAGGACTAAGACTCGGTCAACAACAAATCTTCAGGTAAATCTCTAAT
TTCTTCAACTCTTCAAGGACCTTGTACAATTAAACCAAAAAGTGGTTTATAATCAGCCATGTGCA
GCCAAAAATTGGGTTGACTTAGTCCCCAATTTGGACGGTTTTGCAATTACAACAAAAATATCAAA
CCTGTCAAAAAAAGCAGAAAGTTTAGAGGACCAAATGAATTAATTTAACCAATTTAATTATCAAT
TATAATTAATAAACTCAATATTATCAATGAAATATTTAAAATGAATTATTAAAATATAAGATTAT
ATTTTATCATTTAAATTAATCATGCATGACCCACTTCATAGCTTAAAATATAATATGATTAAATT
AATATAAAATAAGTCATTTTATGCATGAAAACTATATAATAAAACATAAAATCAAATTTTAATAA
TTTCTATGTCCTAATTTCATATTTTCACATATTTCATTAATTTATTAAACAATTACTTAGTTTTA
ACAAGAATTTTAAGTAAAAAGGTGATAAATCACATAGAAAAAATCCTATATATTTTTCAGTTTAC
A
Found at i:30194321 original size:26 final size:26
Alignment explanation
Indices: 30194292--30194354 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
30194282 CTACCTACAG
30194292 TAGTTTCAGAATATCATAACATATAT
1 TAGTTTCAGAATATCATAACATATAT
* * *
30194318 TAGTTTTAGAATATCATAGCATGTAT
1 TAGTTTCAGAATATCATAACATATAT
*
30194344 CAGTTTCAGAA
1 TAGTTTCAGAA
30194355 CAGTTACATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (26 bp):
TAGTTTCAGAATATCATAACATATAT
Found at i:30208433 original size:40 final size:40
Alignment explanation
Indices: 30208373--30208623 Score: 220
Period size: 40 Copynumber: 6.3 Consensus size: 40
30208363 GCTTTCATAA
*
30208373 GTACTGAAGTACAAACAAGGGCACATATGTGCATTCAAGG
1 GTACCGAAGTACAAACAAGGGCACATATGTGCATTCAAGG
* * *
30208413 GTACCGAAGTACAAACAAGGGCACGTATATGCATTCAGGG
1 GTACCGAAGTACAAACAAGGGCACATATGTGCATTCAAGG
* * * *
30208453 GTATCGAAGTACAAACAGGGGTACGTATGTGCATTCAAGG
1 GTACCGAAGTACAAACAAGGGCACATATGTGCATTCAAGG
* * * * * *
30208493 GTACCAAAGTAAAAATATGGGCACATATGTGAATAT-AGGG
1 GTACCGAAGTACAAACAAGGGCACATATGTGCAT-TCAAGG
* * * * * * *
30208533 GTAGCAAAGTACAAATAGGGGAACATATGTGAATTCAGGG
1 GTACCGAAGTACAAACAAGGGCACATATGTGCATTCAAGG
* * * *
30208573 GTACCGAAGTAGAAACACGAGCAC-TAATATGCAATTC-AGG
1 GTACCGAAGTACAAACAAGGGCACAT-ATGTGC-ATTCAAGG
*
30208613 ATACCGAAGTA
1 GTACCGAAGTA
30208624 AATTCATTTA
Statistics
Matches: 174, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
39 2 0.01
40 167 0.96
41 5 0.03
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (40 bp):
GTACCGAAGTACAAACAAGGGCACATATGTGCATTCAAGG
Found at i:30208494 original size:20 final size:20
Alignment explanation
Indices: 30208388--30208496 Score: 60
Period size: 20 Copynumber: 5.5 Consensus size: 20
30208378 GAAGTACAAA
* *
30208388 CAAGGGCACATATGTGCATT
1 CAAGGGTACGTATGTGCATT
* * **
30208408 CAAGGGTACCG-AAGTACAAA
1 CAAGGGTA-CGTATGTGCATT
* *
30208428 CAAGGGCACGTATATGCATT
1 CAAGGGTACGTATGTGCATT
* * * **
30208448 CAGGGGTATCG-AAGTACAAA
1 CAAGGGTA-CGTATGTGCATT
*
30208468 CAGGGGTACGTATGTGCATT
1 CAAGGGTACGTATGTGCATT
30208488 CAAGGGTAC
1 CAAGGGTAC
30208497 CAAAGTAAAA
Statistics
Matches: 61, Mismatches: 24, Indels: 8
0.66 0.26 0.09
Matches are distributed among these distances:
19 4 0.07
20 54 0.89
21 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.20
Consensus pattern (20 bp):
CAAGGGTACGTATGTGCATT
Found at i:30208623 original size:80 final size:80
Alignment explanation
Indices: 30208373--30208623 Score: 258
Period size: 80 Copynumber: 3.1 Consensus size: 80
30208363 GCTTTCATAA
* * * *
30208373 GTACTGAAGTACAAACAAGGGCACATATGTGCATTCAAGGGTACCGAAGTACAAACAAGGGCACG
1 GTACCGAAGTACAAACAGGGGAACATATGTGCATTCAAGGGTACCGAAGTAAAAACAAGGGCAC-
30208438 TATATGC-ATTCAGGG
65 TATATGCAATTCAGGG
* * * * * *
30208453 GTATCGAAGTACAAACAGGGGTACGTATGTGCATTCAAGGGTACCAAAGTAAAAATATGGGCAC-
1 GTACCGAAGTACAAACAGGGGAACATATGTGCATTCAAGGGTACCGAAGTAAAAACAAGGGCACT
*
30208517 ATATGTGAATAT-AGGG
66 ATATG-CAAT-TCAGGG
* * * * * * * *
30208533 GTAGCAAAGTACAAATAGGGGAACATATGTGAATTCAGGGGTACCGAAGTAGAAACACGAGCACT
1 GTACCGAAGTACAAACAGGGGAACATATGTGCATTCAAGGGTACCGAAGTAAAAACAAGGGCACT
30208598 AATATGCAATTCA-GG
66 -ATATGCAATTCAGGG
*
30208613 ATACCGAAGTA
1 GTACCGAAGTA
30208624 AATTCATTTA
Statistics
Matches: 139, Mismatches: 26, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
78 5 0.04
80 124 0.89
81 5 0.04
82 5 0.04
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (80 bp):
GTACCGAAGTACAAACAGGGGAACATATGTGCATTCAAGGGTACCGAAGTAAAAACAAGGGCACT
ATATGCAATTCAGGG
Found at i:30208623 original size:120 final size:120
Alignment explanation
Indices: 30208391--30208625 Score: 260
Period size: 120 Copynumber: 2.0 Consensus size: 120
30208381 GTACAAACAA
* * * * *
30208391 GGGCACATATGTGCATTCAAGGGTACCGAAGTACAAACAAGGGCACGTATATGCATTCAGGGGTA
1 GGGCACATATGTGAATTCAAGGGTACCAAAGTACAAACAAGGGAACATATATGAATTCAGGGGTA
* * * * * *
30208456 TCGAAGTACAAACAGGGGTACGTATGTGCATTCAAGGGTACCAAAGTAAAAATAT
66 CCGAAGTACAAACACGAGCACGTATATGCATTCAAGGATACCAAAGTAAAAATAT
* * * * *
30208511 GGGCACATATGTGAATAT-AGGGGTAGCAAAGTACAAATAGGGGAACATATGTGAATTCAGGGGT
1 GGGCACATATGTGAAT-TCAAGGGTACCAAAGTACAAACAAGGGAACATATATGAATTCAGGGGT
* *
30208575 ACCGAAGTAGAAACACGAGCAC-TAATATGCAATTC-AGGATACCGAAGTAAA
65 ACCGAAGTACAAACACGAGCACGT-ATATGC-ATTCAAGGATACCAAAGTAAA
30208626 TTCATTTATA
Statistics
Matches: 94, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
119 1 0.01
120 88 0.94
121 5 0.05
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.20
Consensus pattern (120 bp):
GGGCACATATGTGAATTCAAGGGTACCAAAGTACAAACAAGGGAACATATATGAATTCAGGGGTA
CCGAAGTACAAACACGAGCACGTATATGCATTCAAGGATACCAAAGTAAAAATAT
Found at i:30213059 original size:50 final size:50
Alignment explanation
Indices: 30212984--30213226 Score: 342
Period size: 50 Copynumber: 4.9 Consensus size: 50
30212974 CATTTGGGTA
*
30212984 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
30213034 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
*
30213084 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * *
30213134 GAGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * * * *
30213184 GAGAACTCCCATGTAAGACTATATTTGGGATATGGAATTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
30213227 GTACAGAAAA
Statistics
Matches: 175, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 175 1.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.21
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:30219733 original size:21 final size:22
Alignment explanation
Indices: 30219667--30219825 Score: 89
Period size: 21 Copynumber: 7.1 Consensus size: 22
30219657 TTAACATTGC
**
30219667 TTTAAATTTATCATTAGCATTAT
1 TTTAAATTTATCA-TAATATTAT
*
30219690 TTTAATATTTAAT-ATACTATTAT
1 TTTAA-ATTT-ATCATAATATTAT
30219713 TTTAAA-TTATCATAATATTA-
1 TTTAAATTTATCATAATATTAT
*
30219733 TTTAAATTTATCATACT-TCGTAAT
1 TTTAAATTTATCATAATAT--T-AT
* * *
30219757 TTGAAATTTATCATGTACTATAAT
1 TTTAAATTTATCA--TAATATTAT
*
30219781 TTTAAACTTATCAT-ATCATTA-
1 TTTAAATTTATCATAAT-ATTAT
* * *
30219802 TTTATATCTATCAT-ATACTAT
1 TTTAAATTTATCATAATATTAT
30219823 TTT
1 TTT
30219826 TATGTATATA
Statistics
Matches: 109, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
20 12 0.11
21 36 0.33
22 6 0.06
23 18 0.17
24 30 0.28
25 2 0.02
26 4 0.04
27 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (22 bp):
TTTAAATTTATCATAATATTAT
Found at i:30219919 original size:30 final size:29
Alignment explanation
Indices: 30219863--30219921 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
30219853 TATAATTGGT
* *
30219863 ATGTATTTTTTTAATAGTCTTATTTTATA
1 ATGTATTTTTTTAAAAATCTTATTTTATA
* *
30219892 ATGTATTTATTTTAAAAATTTTCTTTTATA
1 ATGTATTT-TTTTAAAAATCTTATTTTATA
30219922 TTTTTACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (29 bp):
ATGTATTTTTTTAAAAATCTTATTTTATA
Found at i:30226389 original size:14 final size:14
Alignment explanation
Indices: 30226367--30226405 Score: 69
Period size: 15 Copynumber: 2.7 Consensus size: 14
30226357 GATATCAAGT
30226367 TGAAAAAAAAATTCG
1 TGAAAAAAAAATT-G
30226382 TGAAAAAAAAATTG
1 TGAAAAAAAAATTG
30226396 TGAAAAAAAA
1 TGAAAAAAAA
30226406 CTAGTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.67, C:0.03, G:0.13, T:0.18
Consensus pattern (14 bp):
TGAAAAAAAAATTG
Found at i:30235214 original size:9 final size:9
Alignment explanation
Indices: 30235200--30235231 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
30235190 TCGTAAAAAT
30235200 AAAAATAGA
1 AAAAATAGA
30235209 AAAAATAGA
1 AAAAATAGA
30235218 AAAAATAGA
1 AAAAATAGA
30235227 AAAAA
1 AAAAA
30235232 GAAAAAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (9 bp):
AAAAATAGA
Found at i:30236219 original size:24 final size:24
Alignment explanation
Indices: 30236192--30236252 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
30236182 TTTATGTCCC
30236192 AAAATTACAGTGGATTGAACCTTG
1 AAAATTACAGTGGATTGAACCTTG
* **
30236216 AAAATTACTGTGGATTGAGGCTTG
1 AAAATTACAGTGGATTGAACCTTG
*
30236240 AAGATTACAGTGG
1 AAAATTACAGTGG
30236253 GGGCACTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (24 bp):
AAAATTACAGTGGATTGAACCTTG
Found at i:30236643 original size:46 final size:46
Alignment explanation
Indices: 30236590--30237037 Score: 475
Period size: 46 Copynumber: 9.3 Consensus size: 46
30236580 GCAGTGGAAC
*
30236590 AGATTAAAGCTGAAGGCAGCGATTCTTATTTCCCTGGCGTCGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTCGCAGT
* * * *
30236636 AGATTAAAGCTGAAGGCAGCGAAACTCATTTCCTTGGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTCGCAGT
*
30236682 GGAACAGATTAAAGCTGAAGGCAGCGATTCTTATTTCCCTGGCGTCGCAGT
1 -----AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTCGCAGT
* *
30236733 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCTCTGGCATCGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTCGCAGT
* * * *
30236779 AGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTGGCGTTGCAATGGAAC
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTCGC-A--G--T
* * *
30236830 AGATTAAAGCTGAAGGCA-CGAATCTCATTTCCTTGGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTCGCAGT
* *
30236875 GGAACAGATTAAAGCTGAAGGCAGTGAATCTTATTTCTCTGGCGTCGCAGT
1 -----AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTCGCAGT
* * *
30236926 AGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTGGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTCGCAGT
* * ** * *
30236972 GGAACAGACTAAAGCTAAAGGCAGCGAATCTTATTTCAATGACGTCACAGT
1 -----AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTCGCAGT
30237023 AGATTAAAGCTGAAG
1 AGATTAAAGCTGAAG
30237038 TGGAGCGGAT
Statistics
Matches: 341, Mismatches: 40, Indels: 42
0.81 0.09 0.10
Matches are distributed among these distances:
46 176 0.52
47 2 0.01
49 2 0.01
50 42 0.12
51 119 0.35
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (46 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTCGCAGT
Found at i:30236683 original size:97 final size:97
Alignment explanation
Indices: 30236560--30237037 Score: 691
Period size: 97 Copynumber: 4.9 Consensus size: 97
30236550 TGAAGACAAC
*
30236560 AATCTCATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGATTCTTATTTCCCT
1 AATCTCATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCT
30236625 GGCGTCGCAGTAGATTAAAGCTGAAGGCAGCG
66 GGCGTCGCAGTAGATTAAAGCTGAAGGCAGCG
* *
30236657 AAACTCATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGATTCTTATTTCCCT
1 AATCTCATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCT
30236722 GGCGTCGCAGTAGATTAAAGCTGAAGGCAGCG
66 GGCGTCGCAGTAGATTAAAGCTGAAGGCAGCG
* * * * *
30236754 AATCTTATTT-CTCTGGCATCGCAGT-----AGATTAAAGCTGAAGGCAGCGAATCTCATTTCCT
1 AATCTCATTTCCT-TGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCC
* *
30236813 TGGCGTTGCAATGGAACAGATTAAAGCTGAAGGCA-CG
65 TGGCGTCGC-A--G--TAGATTAAAGCTGAAGGCAGCG
* *
30236850 AATCTCATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATTTCTCT
1 AATCTCATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCT
30236915 GGCGTCGCAGTAGATTAAAGCTGAAGGCAGCG
66 GGCGTCGCAGTAGATTAAAGCTGAAGGCAGCG
* * **
30236947 AATCTCATTTCCTTGGCGTTGCAGTGGAACAGACTAAAGCTAAAGGCAGCGAATCTTATTTCAAT
1 AATCTCATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCT
* *
30237012 GACGTCACAGTAGATTAAAGCTGAAG
66 GGCGTCGCAGTAGATTAAAGCTGAAG
30237038 TGGAGCGGAT
Statistics
Matches: 342, Mismatches: 26, Indels: 26
0.87 0.07 0.07
Matches are distributed among these distances:
92 39 0.11
93 1 0.00
95 1 0.00
96 41 0.12
97 220 0.64
98 1 0.00
100 1 0.00
101 38 0.11
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (97 bp):
AATCTCATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCT
GGCGTCGCAGTAGATTAAAGCTGAAGGCAGCG
Found at i:30238904 original size:45 final size:44
Alignment explanation
Indices: 30238809--30238935 Score: 123
Period size: 45 Copynumber: 2.8 Consensus size: 44
30238799 ACATTGTTTT
* * *
30238809 AAATTTATCATTAGTATTAATTTAATATTTAAT-ATACTATTATTTT
1 AAATTTATCATTAATATT-ATTTAA-ATTT-ATCATACTATAATTTG
30238855 AAA-TTATCATTAATATTATTTAAATTTATCATACATCATAATTTG
1 AAATTTATCATTAATATTATTTAAATTTATCATAC-T-ATAATTTG
* * *
30238900 AAATTTATCATGTACTATAATTTTAAACTTATCATA
1 AAATTTATCAT-TAATATTA-TTTAAATTTATCATA
30238936 TCATTATTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 2 0.03
43 8 0.12
44 7 0.10
45 22 0.32
46 10 0.14
47 6 0.09
48 14 0.20
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (44 bp):
AAATTTATCATTAATATTATTTAAATTTATCATACTATAATTTG
Found at i:30238906 original size:24 final size:21
Alignment explanation
Indices: 30238806--30238935 Score: 93
Period size: 24 Copynumber: 5.7 Consensus size: 21
30238796 TTAACATTGT
*
30238806 TTTAAATTTATCATTAGTATTAA
1 TTTAAATTTATCA-TACTA-TAA
*
30238829 TTTAATATTTAAT-ATACTATTAT
1 TTTAA-ATTT-ATCATACTA-TAA
* *
30238852 TTTAAA-TTATCATTAATATTA
1 TTTAAATTTATCA-TACTATAA
30238873 TTTAAATTTATCATACATCATAA
1 TTTAAATTTATCATAC-T-ATAA
30238896 TTTGAAATTTATCATGTACTATAA
1 TTT-AAATTTATCA--TACTATAA
*
30238920 TTTTAAACTTATCATA
1 -TTTAAATTTATCATA
30238936 TCATTATTTA
Statistics
Matches: 88, Mismatches: 8, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
20 2 0.02
21 12 0.14
22 14 0.16
23 23 0.26
24 28 0.32
25 6 0.07
26 3 0.03
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTAAATTTATCATACTATAA
Found at i:30238956 original size:21 final size:22
Alignment explanation
Indices: 30238929--30238974 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
30238919 ATTTTAAACT
30238929 TATCATAT-C-ATTATTTATATA
1 TATCATATACTATT-TTTATATA
*
30238950 TATCATATACTATTTTTATGTA
1 TATCATATACTATTTTTATATA
30238972 TAT
1 TAT
30238975 ATTTTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 11 0.50
23 3 0.14
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (22 bp):
TATCATATACTATTTTTATATA
Found at i:30239042 original size:16 final size:15
Alignment explanation
Indices: 30239003--30239048 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
30238993 TATAATTGGT
30239003 ATGTATTT-TTTTTA
1 ATGTATTTATTTTTA
*
30239017 ATAGT-CTTATTTTATA
1 AT-GTATTTATTTT-TA
30239033 ATGTATTTATTTTTA
1 ATGTATTTATTTTTA
30239048 A
1 A
30239049 AATTTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
14 4 0.15
15 11 0.42
16 11 0.42
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (15 bp):
ATGTATTTATTTTTA
Found at i:30239060 original size:30 final size:30
Alignment explanation
Indices: 30239003--30239062 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
30238993 TATAATTGGT
*
30239003 ATGTATTTTTTTTAATAGTCTTATTTTATA
1 ATGTATTTTTTTTAATAATCTTATTTTATA
* *
30239033 ATGTATTTATTTTTAA-AATTTTCTTTTATA
1 ATGTATTT-TTTTTAATAATCTTATTTTATA
30239063 TTTTTACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.63
Consensus pattern (30 bp):
ATGTATTTTTTTTAATAATCTTATTTTATA
Found at i:30239497 original size:24 final size:25
Alignment explanation
Indices: 30239469--30239525 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
30239459 CAATTTTTGG
* *
30239469 TTATTTCAATTTCTTGTATAT-TA-T
1 TTATTTAAATTT-TTGTACATATACT
30239493 TTATTTTAAATTTTTGTACATATACT
1 TTA-TTTAAATTTTTGTACATATACT
30239519 TTATTTA
1 TTATTTA
30239526 TTTACAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 10 0.36
25 14 0.50
26 4 0.14
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (25 bp):
TTATTTAAATTTTTGTACATATACT
Found at i:30239522 original size:26 final size:25
Alignment explanation
Indices: 30239476--30239524 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
30239466 TGGTTATTTC
*
30239476 AATTTCTTGTATATTATTTATTTTA
1 AATTTCTTGTACATTATTTATTTTA
30239501 AATTT-TTGTACATATACTTTATTT
1 AATTTCTTGTACAT-TA-TTTATTT
30239525 ATTTACAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 7 0.33
26 7 0.33
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (25 bp):
AATTTCTTGTACATTATTTATTTTA
Found at i:30240481 original size:22 final size:22
Alignment explanation
Indices: 30240439--30240517 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
30240429 ATAAAAAATG
**
30240439 GAGCTTAGTACGTTAGCCATGA
1 GAGCTTAGTACGTTAAACATGA
* * *
30240461 GGGTTTAGTTCGTTAAACATGA
1 GAGCTTAGTACGTTAAACATGA
30240483 GAGCTTAGTACGTTAAACATGA
1 GAGCTTAGTACGTTAAACATGA
30240505 GAGCTTAGTACGT
1 GAGCTTAGTACGT
30240518 GAAATTTATC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (22 bp):
GAGCTTAGTACGTTAAACATGA
Found at i:30243264 original size:102 final size:100
Alignment explanation
Indices: 30243081--30243284 Score: 338
Period size: 102 Copynumber: 2.0 Consensus size: 100
30243071 CTTGGAGCAA
*
30243081 CTTATTTGCTTAAAATATTAAGGGCTCTAACCGAAGGAACCGGATAAGTAAAAACATCAACTCAT
1 CTTATTTGCTTAAAATATAAAGGGCTCTAACCGAAGGAACCGGATAAGT-AAAACATCAACTCAT
30243146 GGAATAAAAGAATGACATTTGAGACACTTGTATGAT
65 GGAATAAAAGAATGACATTTGAGACACTTGTATGAT
* *
30243182 CTTATTTGCTTAAAATCTAAAAGGGCTCTAACCGAAGGAACTGGATAAGT-AAACATCAACTCAT
1 CTTATTTGCTTAAAATAT-AAAGGGCTCTAACCGAAGGAACCGGATAAGTAAAACATCAACTCAT
30243246 GGAATAAAAGAATTTGACATTTGAGACACTTGTATGAT
65 GGAATAAAAGAA--TGACATTTGAGACACTTGTATGAT
30243284 C
1 C
30243285 AACACACATA
Statistics
Matches: 97, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
100 26 0.27
101 17 0.18
102 54 0.56
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (100 bp):
CTTATTTGCTTAAAATATAAAGGGCTCTAACCGAAGGAACCGGATAAGTAAAACATCAACTCATG
GAATAAAAGAATGACATTTGAGACACTTGTATGAT
Found at i:30251949 original size:43 final size:43
Alignment explanation
Indices: 30251887--30251993 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
30251877 AAAAAACGCC
* * ***
30251887 GCTAAAAATCATGATCTTTAGCAACACTTTTGTCACAAACACT
1 GCTAAAGATCATGACCTTTAGCAACACTTTACCCACAAACACT
** * *
30251930 GCTAAAGATCATGACCTTTAGCGGCGCTTTACCCACAAACGCT
1 GCTAAAGATCATGACCTTTAGCAACACTTTACCCACAAACACT
*
30251973 ACTAAAGATCATGACCTTTAG
1 GCTAAAGATCATGACCTTTAG
30251994 TTGCGCCTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (43 bp):
GCTAAAGATCATGACCTTTAGCAACACTTTACCCACAAACACT
Found at i:30252754 original size:235 final size:233
Alignment explanation
Indices: 30252340--30252807 Score: 873
Period size: 235 Copynumber: 2.0 Consensus size: 233
30252330 TTTATTGCTT
*
30252340 CTATAAACTCCAATTAGACATTGTTGAGGGAATATAACACATTCTAATAAAGTAACAGGCTAATG
1 CTATAAACTCCAATTAGACATTGTTGAGGAAATATAACACATTCTAATAAAGTAACAGGCTAATG
*
30252405 GATATTTTACTTCTGAGTTGTGACTTAATTGATTTAATTCACTCACTGGCACTGAAGGTGGTCTC
66 GATATTTTACTTCTGAGTTGTGACTTAATTGATTTAATTCACTCACTGACACTGAAGGTGGTCTC
*
30252470 TCCTCTTCAACAGGTCTTTCATGCAAGAACCTATCTCTGAGTTGTGACTGCAAAATTAAGATAAG
131 TCCTCTTCAACAGGTCTTTCATGCAAGAACCTATCTCTGAGTAGTGACTGCAAAATTAAGATAAG
*
30252535 AGGGCTGCGCTAGTTTAGCATGGGAACATGTGAAAACAAA
196 AGGGCT--GCTAGTTTAGCATGGCAACATGTGAAAACAAA
30252575 CTATAAACTCCAATTAGACATTGTTGAGGAAATATAACACATTCTAATAAAGTAACAGGCTAATG
1 CTATAAACTCCAATTAGACATTGTTGAGGAAATATAACACATTCTAATAAAGTAACAGGCTAATG
30252640 GATATTTTACTTCTGAGTTGTGACTTAATTGATTTAATTCACTCACTGACACTGAAGGTGGTCTC
66 GATATTTTACTTCTGAGTTGTGACTTAATTGATTTAATTCACTCACTGACACTGAAGGTGGTCTC
*
30252705 TCCTCTTCAACAGGTCTTTCATGCAAGAGCCTATCTCTGAGTAGTGACTGCAAAATTAAGATAAG
131 TCCTCTTCAACAGGTCTTTCATGCAAGAACCTATCTCTGAGTAGTGACTGCAAAATTAAGATAAG
30252770 AGGGCTGCTAGTTTAGCATGGCAACATGTGAAAACAAA
196 AGGGCTGCTAGTTTAGCATGGCAACATGTGAAAACAAA
30252808 AGGATTTTCA
Statistics
Matches: 228, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
233 31 0.14
235 197 0.86
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (233 bp):
CTATAAACTCCAATTAGACATTGTTGAGGAAATATAACACATTCTAATAAAGTAACAGGCTAATG
GATATTTTACTTCTGAGTTGTGACTTAATTGATTTAATTCACTCACTGACACTGAAGGTGGTCTC
TCCTCTTCAACAGGTCTTTCATGCAAGAACCTATCTCTGAGTAGTGACTGCAAAATTAAGATAAG
AGGGCTGCTAGTTTAGCATGGCAACATGTGAAAACAAA
Found at i:30257329 original size:15 final size:15
Alignment explanation
Indices: 30257309--30257338 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30257299 AACCATGAAT
*
30257309 CATAATCTCTAAACC
1 CATAATCTATAAACC
30257324 CATAATCTATAAACC
1 CATAATCTATAAACC
30257339 TTAAAATGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (15 bp):
CATAATCTATAAACC
Found at i:30257742 original size:40 final size:40
Alignment explanation
Indices: 30257697--30257772 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
30257687 CTAAAGACCC
* *
30257697 GAGCATTAGCGGCGCTTATTGGAAAACGCCGCTAAAAATA
1 GAGCATTAGCGACGCTTATTGAAAAACGCCGCTAAAAATA
* *
30257737 GAGCATTAGCGACGCTTTTTTAAAAACGCCGCTAAA
1 GAGCATTAGCGACGCTTATTGAAAAACGCCGCTAAA
30257773 GCCCCAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (40 bp):
GAGCATTAGCGACGCTTATTGAAAAACGCCGCTAAAAATA
Found at i:30257890 original size:39 final size:41
Alignment explanation
Indices: 30257818--30257922 Score: 137
Period size: 39 Copynumber: 2.6 Consensus size: 41
30257808 AAAACACCGA
*
30257818 TAATGCTCTATTTTTAGCGGCG-TTTCTCAAAAAGCGCCGC
1 TAATGCTCTATTTTTAGCTGCGTTTTCTCAAAAAGCGCCGC
* * *
30257858 TAATGCTCTA-TTTTAGCTGTGTTTTC-CTAAAAGTGCCGC
1 TAATGCTCTATTTTTAGCTGCGTTTTCTCAAAAAGCGCCGC
30257897 TAATGCT-TGATTTTTAGCTGCGTTTT
1 TAATGCTCT-ATTTTTAGCTGCGTTTT
30257923 TTGTCCAAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 1 0.02
39 28 0.49
40 28 0.49
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (41 bp):
TAATGCTCTATTTTTAGCTGCGTTTTCTCAAAAAGCGCCGC
Found at i:30260731 original size:12 final size:12
Alignment explanation
Indices: 30260714--30260739 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30260704 TTTGGTGTAA
30260714 GTAAAAGCCTGG
1 GTAAAAGCCTGG
30260726 GTAAAAGCCTGG
1 GTAAAAGCCTGG
30260738 GT
1 GT
30260740 TCGAATAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.19
Consensus pattern (12 bp):
GTAAAAGCCTGG
Found at i:30262452 original size:27 final size:27
Alignment explanation
Indices: 30262421--30262724 Score: 373
Period size: 27 Copynumber: 11.3 Consensus size: 27
30262411 CCCCAAAGTA
30262421 GGTAAAATGATCGAAATACCCCTATAG
1 GGTAAAATGATCGAAATACCCCTATAG
* * * *
30262448 GGTAAAATAAACAAAATACTCCTATAG
1 GGTAAAATGATCGAAATACCCCTATAG
30262475 GGTAAAATGA-CGAAATACCCCTATAG
1 GGTAAAATGATCGAAATACCCCTATAG
* * *
30262501 GATAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGATCGAAATACCCCTATAG
* * *
30262528 GATAAAAAGATCGAAATACCCCTATAA
1 GGTAAAATGATCGAAATACCCCTATAG
* *
30262555 GGTAAAATAATTGAAATACCCC-ATAG
1 GGTAAAATGATCGAAATACCCCTATAG
*
30262581 GGTAAAATAATCGAAAATATCCCC-ATAG
1 GGTAAAATGATCG-AAATA-CCCCTATAG
30262609 GGTAAAATGATCGAAATAGCCCC-ATAG
1 GGTAAAATGATCGAAATA-CCCCTATAG
*
30262636 GGTAAAATGATCGAAATACCCTTATAG
1 GGTAAAATGATCGAAATACCCCTATAG
* * * *
30262663 GATAGAATGACCGAAATACCCCCATAG
1 GGTAAAATGATCGAAATACCCCTATAG
* *
30262690 GGTAAAATGATTGAAATACCCCCATAG
1 GGTAAAATGATCGAAATACCCCTATAG
30262717 GGTAAAAT
1 GGTAAAAT
30262725 AAATATTATA
Statistics
Matches: 242, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
26 41 0.17
27 181 0.75
28 20 0.08
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.20
Consensus pattern (27 bp):
GGTAAAATGATCGAAATACCCCTATAG
Found at i:30268017 original size:3 final size:3
Alignment explanation
Indices: 30268009--30268034 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
30267999 TTGGCACCTT
30268009 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
30268035 TATCTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:30279125 original size:40 final size:39
Alignment explanation
Indices: 30279071--30279187 Score: 164
Period size: 40 Copynumber: 2.9 Consensus size: 39
30279061 ATCCTCAGAT
*
30279071 CAACCGAACACACCAAACAGAAGCTCATAAGAGCTGATC
1 CAACCGAACACACCAAACAGAAGCTTATAAGAGCTGATC
*
30279110 CAACCGGAACACACCAAACAGAAGCTTATAAGAGATGATC
1 CAACC-GAACACACCAAACAGAAGCTTATAAGAGCTGATC
* *
30279150 CAATC-AAAACAGGCCAAACAGAAGCTTATAAGAGCTGA
1 CAACCGAACACA--CCAAACAGAAGCTTATAAGAGCTGA
30279188 ACAGAAGCTT
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
38 5 0.07
39 5 0.07
40 60 0.86
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.12
Consensus pattern (39 bp):
CAACCGAACACACCAAACAGAAGCTTATAAGAGCTGATC
Found at i:30279192 original size:21 final size:21
Alignment explanation
Indices: 30279166--30279207 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
30279156 AAACAGGCCA
30279166 AACAGAAGCTTATAAGAGCTG
1 AACAGAAGCTTATAAGAGCTG
30279187 AACAGAAGCTTATAAGAGCTG
1 AACAGAAGCTTATAAGAGCTG
30279208 GTCCACCCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (21 bp):
AACAGAAGCTTATAAGAGCTG
Found at i:30279221 original size:61 final size:60
Alignment explanation
Indices: 30279126--30279247 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 60
30279116 GAACACACCA
* * *
30279126 AACAGAAGCTTATAAGAGATGATCCAATCAAAACAGGCCAAACAGAAGCTTATAAGAGCTG
1 AACAGAAGCTTATAAGAGATGATCCAACCAAAACACGCC-AACAGAAGCTCATAAGAGCTG
* * * *
30279187 AACAGAAGCTTATAAGAGCTGGTCCACCCGAAACACGCCAACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTTATAAGAGATGATCCAACCAAAACACGCCAACAGAAGCTCATAAGAGCTG
30279247 A
1 A
30279248 TCCACTCGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 21 0.39
61 33 0.61
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (60 bp):
AACAGAAGCTTATAAGAGATGATCCAACCAAAACACGCCAACAGAAGCTCATAAGAGCTG
Found at i:30279241 original size:39 final size:40
Alignment explanation
Indices: 30279186--30279272 Score: 131
Period size: 39 Copynumber: 2.2 Consensus size: 40
30279176 TATAAGAGCT
* *
30279186 GAACAGAAGCTTATAAGAGCTGGTCCACCCGAAACACGCC
1 GAACAGAAGCTCATAAGAGCTGATCCACCCGAAACACGCC
* *
30279226 -AACAGAAGCTCATAAGAGCTGATCCACTCGAATCACGCC
1 GAACAGAAGCTCATAAGAGCTGATCCACCCGAAACACGCC
30279265 GAACAGAA
1 GAACAGAA
30279273 AGTATAACGC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 35 0.83
40 7 0.17
ACGTcount: A:0.38, C:0.29, G:0.21, T:0.13
Consensus pattern (40 bp):
GAACAGAAGCTCATAAGAGCTGATCCACCCGAAACACGCC
Found at i:30279270 original size:100 final size:101
Alignment explanation
Indices: 30279086--30279272 Score: 259
Period size: 100 Copynumber: 1.9 Consensus size: 101
30279076 GAACACACCA
* *
30279086 AACAGAAGCTCATAAGAGCTGATCCAACCGGAACACACCAAACAGAAGCTTATAAGAGATGATCC
1 AACAGAAGCTCATAAGAGCTGATCCAACCGAAACACACCAAACAGAAGCTCATAAGAGATGATCC
*
30279151 AATCAAAACAGGCCAAACAGAAGCTTATAAGAGCTG
66 AATCAAAACACGCCAAACAGAAGCTTATAAGAGCTG
* * * * *
30279187 AACAGAAGCTTATAAGAGCTGGTCCACCCGAAACACGCC-AACAGAAGCTCATAAGAGCTGATCC
1 AACAGAAGCTCATAAGAGCTGATCCAACCGAAACACACCAAACAGAAGCTCATAAGAGATGATCC
* * * *
30279251 ACTCGAATCACGCCGAACAGAA
66 AATCAAAACACGCCAAACAGAA
30279273 AGTATAACGC
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
100 40 0.54
101 34 0.46
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.13
Consensus pattern (101 bp):
AACAGAAGCTCATAAGAGCTGATCCAACCGAAACACACCAAACAGAAGCTCATAAGAGATGATCC
AATCAAAACACGCCAAACAGAAGCTTATAAGAGCTG
Found at i:30280707 original size:40 final size:41
Alignment explanation
Indices: 30280624--30280873 Score: 294
Period size: 40 Copynumber: 6.2 Consensus size: 41
30280614 CATAAATGCT
** * *
30280624 ATTCAGGGGTATTGAAGTACAAACAGGGGCACGCATGTGCA
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGCA
* *
30280665 ATTCAGGGGTACCGAAGTAC-AACAGGGGCATGTATATACA
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGCA
* * *
30280705 ATTCAGGGGTACCAAAGAAC-AACAGGGGTATGTATGTGCA
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGCA
* * *
30280745 ATT-AGGAGTACTGAAGTACAAACAGGGCCATGTATGTGCA
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGCA
* *
30280785 ATTTAGGGGGTACCAAAGTAC-AACAGGGGCA-GTTATGTGCA
1 ATTCA-GGGGTACCGAAGTACAAACAGGGGCATG-TATGTGCA
* * *
30280826 ATTCAAGTGTACCGAAGTACAAACAGGGGCACGTATGTGCA
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGCA
30280867 ATTCAGG
1 ATTCAGG
30280874 TATAATTATC
Statistics
Matches: 177, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 12 0.07
40 88 0.50
41 64 0.36
42 13 0.07
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (41 bp):
ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGCA
Found at i:30280828 original size:121 final size:121
Alignment explanation
Indices: 30280604--30280869 Score: 320
Period size: 121 Copynumber: 2.2 Consensus size: 121
30280594 TTAGATCATG
* ** * * * *
30280604 AACAGGGGCACATAAATGCTATTCAGGGGTATTGAAGTACAAACAGGGGCACGCATGTGCAATTC
1 AACAGGGGCACGTATGTGCAATT-AGGAGTACTGAAGTACAAACAGGGCCACGCATGTGCAATTC
* *
30280669 AGGGGTACCGAAGTACAACAGGGGCATGTATATACAATTCAGGGGTACCAAAGAAC-
65 AGGGGTACCAAAGTACAACAGGGGCATGTATATACAATTCAAGGGTACCAAAGAACA
* * * * *
30280725 AACAGGGGTATGTATGTGCAATTAGGAGTACTGAAGTACAAACAGGGCCATGTATGTGCAATTTA
1 AACAGGGGCACGTATGTGCAATTAGGAGTACTGAAGTACAAACAGGGCCACGCATGTGCAATTCA
* * * * *
30280790 GGGGGTACCAAAGTACAACAGGGGCA-GTTATGTGCAATTCAAGTGTACCGAAGTACA
66 -GGGGTACCAAAGTACAACAGGGGCATG-TATATACAATTCAAGGGTACCAAAGAACA
30280847 AACAGGGGCACGTATGTGCAATT
1 AACAGGGGCACGTATGTGCAATT
30280870 CAGGTATAAT
Statistics
Matches: 121, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
120 37 0.31
121 63 0.52
122 21 0.17
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.21
Consensus pattern (121 bp):
AACAGGGGCACGTATGTGCAATTAGGAGTACTGAAGTACAAACAGGGCCACGCATGTGCAATTCA
GGGGTACCAAAGTACAACAGGGGCATGTATATACAATTCAAGGGTACCAAAGAACA
Found at i:30285222 original size:2 final size:2
Alignment explanation
Indices: 30285215--30285239 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30285205 ATCAAATTCT
30285215 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30285240 TAATAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30288214 original size:88 final size:88
Alignment explanation
Indices: 30288065--30288451 Score: 528
Period size: 88 Copynumber: 4.4 Consensus size: 88
30288055 AAAAAATCAC
* * *
30288065 ATTTTCAACCTACTCCACTGTTGCTCAGGGAGATAAGGCTGAGGTCTTCGATCTACTTCGCTGCC
1 ATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGATGAGATCTTCGATCTACTTCGCTGCC
* *
30288130 AGTACAAGAAGACAAGATCTACT
66 AATACAAGAAGACAAGATCTGCT
* * *
30288153 ATTTTTAACCTACTCCACTGCTGCTCAGGGAGAAAAGGATG-GTATCTTCAATCTACTTCGCTGC
1 ATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGATGAG-ATCTTCGATCTACTTCGCTGC
* *
30288217 CAATATAGGAAGACAAGATCTGCT
65 CAATACAAGAAGACAAGATCTGCT
* * * * * * *
30288241 ATTTTTAACCTACTCCACTGCTGCTCA-GG-GATAAGGCTGAGGTATTCGACCCACTTTGCTGCC
1 ATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGATGAGATCTTCGATCTACTTCGCTGCC
*
30288304 AATACAAGAAGATAAGATCTGCT
66 AATACAAGAAGACAAGATCTGCT
* * *
30288327 ATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGATGAGGTCTTTGATCTACTTCGCAGCC
1 ATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGATGAGATCTTCGATCTACTTCGCTGCC
*
30288392 AATACAGGAAGACAAGATCTGCT
66 AATACAAGAAGACAAGATCTGCT
* *
30288415 ATTTTCAACCTACTCCATTACTGCTCAGGGAGATAAG
1 ATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAG
30288452 ATTTATGGTT
Statistics
Matches: 262, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
86 70 0.27
87 6 0.02
88 186 0.71
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (88 bp):
ATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGATGAGATCTTCGATCTACTTCGCTGCC
AATACAAGAAGACAAGATCTGCT
Found at i:30288367 original size:174 final size:174
Alignment explanation
Indices: 30288065--30288445 Score: 566
Period size: 174 Copynumber: 2.2 Consensus size: 174
30288055 AAAAAATCAC
* * * *
30288065 ATTTTCAACCTACTCCACTGTTGCTCAGGGAGATAAGGCTGAGGTCTTCGATCTACTTCGCTGCC
1 ATTTTCAACCTACTCCACTGCTGCTCA-GG-GATAAGGCTGAGGTATTCGACCCACTTCGCTGCC
* *
30288130 AGTACAAGAAGACAAGATCTACTATTTTTAACCTACTCCACTGCTGCTCAGGGAGAAAAGGATG-
64 AATACAAGAAGACAAGATCTACTATTTTCAACCTACTCCACTGCTGCTCAGGGAGAAAAGGATGA
* *
30288194 GTATCTTCAATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCT
129 G-ATCTTCAATCTACTTCGCAGCCAATACAGGAAGACAAGATCTGCT
* *
30288241 ATTTTTAACCTACTCCACTGCTGCTCAGGGATAAGGCTGAGGTATTCGACCCACTTTGCTGCCAA
1 ATTTTCAACCTACTCCACTGCTGCTCAGGGATAAGGCTGAGGTATTCGACCCACTTCGCTGCCAA
* * * *
30288306 TACAAGAAGATAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGATGAGG
66 TACAAGAAGACAAGATCTACTATTTTCAACCTACTCCACTGCTGCTCAGGGAGAAAAGGATGAGA
**
30288371 TCTTTGATCTACTTCGCAGCCAATACAGGAAGACAAGATCTGCT
131 TCTTCAATCTACTTCGCAGCCAATACAGGAAGACAAGATCTGCT
* *
30288415 ATTTTCAACCTACTCCATTACTGCTCAGGGA
1 ATTTTCAACCTACTCCACTGCTGCTCAGGGA
30288446 GATAAGATTT
Statistics
Matches: 185, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
174 157 0.85
175 3 0.02
176 25 0.14
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (174 bp):
ATTTTCAACCTACTCCACTGCTGCTCAGGGATAAGGCTGAGGTATTCGACCCACTTCGCTGCCAA
TACAAGAAGACAAGATCTACTATTTTCAACCTACTCCACTGCTGCTCAGGGAGAAAAGGATGAGA
TCTTCAATCTACTTCGCAGCCAATACAGGAAGACAAGATCTGCT
Found at i:30303071 original size:21 final size:22
Alignment explanation
Indices: 30303030--30303071 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
30303020 TTTGCACTAC
*
30303030 GCCATAACACCATTAAGCATAT
1 GCCATAACACCATTAAACATAT
30303052 GCCA-AACA-CATCTAAACATA
1 GCCATAACACCAT-TAAACATA
30303072 CCAATTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 3 0.17
21 11 0.61
22 4 0.22
ACGTcount: A:0.45, C:0.29, G:0.07, T:0.19
Consensus pattern (22 bp):
GCCATAACACCATTAAACATAT
Found at i:30307868 original size:40 final size:40
Alignment explanation
Indices: 30307813--30307898 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
30307803 AAACTTTAAT
*
30307813 TTTATTTAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
*
30307853 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGGC
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
30307893 TTTATT
1 TTTATT
30307899 TTTATTAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.47
Consensus pattern (40 bp):
TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
Found at i:30308135 original size:24 final size:24
Alignment explanation
Indices: 30308116--30308189 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
30308106 GTTACATTAA
30308116 TTAAAGGAGAGAATTATACATCAT
1 TTAAAGGAGAGAATTATACATCAT
**
30308140 TTAAAGGAG-CTA-T-TACATCAT
1 TTAAAGGAGAGAATTATACATCAT
* *
30308161 TTAAAGGAGAGCATTATACATCCT
1 TTAAAGGAGAGAATTATACATCAT
30308185 TTAAA
1 TTAAA
30308190 AATCAGCATC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
21 17 0.40
22 2 0.05
23 2 0.05
24 21 0.50
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (24 bp):
TTAAAGGAGAGAATTATACATCAT
Found at i:30308165 original size:45 final size:45
Alignment explanation
Indices: 30308098--30308189 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
30308088 AGTTACATAC
* * *
30308098 AAGGGGCTGTTACATTAATTAAAGGAGAGAATTATACATCATTTA
1 AAGGAGCTATTACATCAATTAAAGGAGAGAATTATACATCATTTA
* * *
30308143 AAGGAGCTATTACATCATTTAAAGGAGAGCATTATACATCCTTTA
1 AAGGAGCTATTACATCAATTAAAGGAGAGAATTATACATCATTTA
30308188 AA
1 AA
30308190 AATCAGCATC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (45 bp):
AAGGAGCTATTACATCAATTAAAGGAGAGAATTATACATCATTTA
Found at i:30308972 original size:21 final size:21
Alignment explanation
Indices: 30308946--30308985 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30308936 TGAATATACG
30308946 TCTGTTTGTCAGAACATTTTT
1 TCTGTTTGTCAGAACATTTTT
**
30308967 TCTGTTTGTGTGAACATTT
1 TCTGTTTGTCAGAACATTT
30308986 GGTTATTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.53
Consensus pattern (21 bp):
TCTGTTTGTCAGAACATTTTT
Found at i:30320276 original size:6 final size:7
Alignment explanation
Indices: 30320258--30320283 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
30320248 ATAAGGCAAC
30320258 ATTTTTT
1 ATTTTTT
30320265 ATTTTTT
1 ATTTTTT
30320272 ATTTTTT
1 ATTTTTT
30320279 ATTTT
1 ATTTT
30320284 CCTTTCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:30321175 original size:24 final size:23
Alignment explanation
Indices: 30321130--30321188 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 23
30321120 GTACGAAATG
* * *
30321130 TATTTTATGTTTTAAATGCATTA
1 TATTTAATATTTTAAATCCATTA
* *
30321153 TATATTAATATTTTAAGTCCATTG
1 TAT-TTAATATTTTAAATCCATTA
*
30321177 TATTTTATATTT
1 TATTTAATATTT
30321189 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.58
Consensus pattern (23 bp):
TATTTAATATTTTAAATCCATTA
Found at i:30321340 original size:13 final size:13
Alignment explanation
Indices: 30321322--30321349 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30321312 GTAATTTTTA
30321322 TTTTTTCATTATT
1 TTTTTTCATTATT
30321335 TTTTTTCATTATT
1 TTTTTTCATTATT
30321348 TT
1 TT
30321350 AATATACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTCATTATT
Found at i:30333687 original size:25 final size:24
Alignment explanation
Indices: 30333646--30333697 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 24
30333636 GTCATTAGGG
*
30333646 TTACCAATTTCAGCTCGTATGAGC
1 TTACCAATCTCAGCTCGTATGAGC
30333670 TTACCAATACTCAGCTCGTATGAGC
1 TTACCAAT-CTCAGCTCGTATGAGC
30333695 TTA
1 TTA
30333698 GTGTTGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (24 bp):
TTACCAATCTCAGCTCGTATGAGC
Found at i:30341630 original size:22 final size:21
Alignment explanation
Indices: 30341597--30341638 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
30341587 GTTCCTTGCT
30341597 TACATATGAAATGAAGATCAAC
1 TACATATGAAATGAA-ATCAAC
30341619 TACA-ATGCAAATGAAATCAA
1 TACATATG-AAATGAAATCAA
30341639 AGAAGTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.21
Consensus pattern (21 bp):
TACATATGAAATGAAATCAAC
Found at i:30345958 original size:20 final size:20
Alignment explanation
Indices: 30345915--30345958 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
30345905 ATACCAACTT
** *
30345915 AAAAATATCAATACTTTTAT
1 AAAAATATCAATACTAGTAG
*
30345935 AAAAATATCAATACTAGTGG
1 AAAAATATCAATACTAGTAG
30345955 AAAA
1 AAAA
30345959 TATTGATACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.30
Consensus pattern (20 bp):
AAAAATATCAATACTAGTAG
Found at i:30347465 original size:50 final size:50
Alignment explanation
Indices: 30347390--30347574 Score: 228
Period size: 51 Copynumber: 3.7 Consensus size: 50
30347380 GTGAAGTTGT
* *
30347390 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATG-A
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GGATGAA
* * **
30347440 TAGGTCACATGTGTAGTACTATGTGCAAGCTACTATGTGTACCGGATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GAA
* * * * *
30347491 TCGATCACGTGTGTAGTACAATGTGCAGGCTACTACGTGTATCGGATGAA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAA
*
30347541 AATGGTCACATGTGTAGTACTATGTGCAGGCTAC
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTAC
30347575 AATGTGAACC
Statistics
Matches: 113, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
49 3 0.03
50 42 0.37
51 68 0.60
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAA
Found at i:30347617 original size:102 final size:101
Alignment explanation
Indices: 30347400--30347584 Score: 264
Period size: 102 Copynumber: 1.8 Consensus size: 101
30347390 TAGGTCACGT
*
30347400 GTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTACTATGTG
1 GTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGAAAGGTCACATGTGTAGTACTATGTG
* * **
30347465 CAAGCTACTATGTGTACCGGATAGCTTCGATCACGT
66 CAAGCTACAATGTGAACCGGATAGCTTCGATCACAA
* * *
30347501 GTGTAGTACAATGTGCAGGCTACTACGTGTATC-GGATGAAAATGGTCACATGTGTAGTACTATG
1 GTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATG-AAA-GGTCACATGTGTAGTACTATG
*
30347565 TGCAGGCTACAATGTGAACC
64 TGCAAGCTACAATGTGAACC
30347585 AGGTATCATT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
100 4 0.05
101 33 0.44
102 38 0.51
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (101 bp):
GTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGAAAGGTCACATGTGTAGTACTATGTG
CAAGCTACAATGTGAACCGGATAGCTTCGATCACAA
Found at i:30352502 original size:22 final size:23
Alignment explanation
Indices: 30352471--30352513 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
30352461 CTGAAGGGAA
*
30352471 TGACAACTTAT-TGCATTTTTGC
1 TGACAACTTATCTACATTTTTGC
*
30352493 TGACAGCTTATCTACATTTTT
1 TGACAACTTATCTACATTTTT
30352514 ACTAGTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.47
Consensus pattern (23 bp):
TGACAACTTATCTACATTTTTGC
Found at i:30367292 original size:18 final size:19
Alignment explanation
Indices: 30367253--30367297 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
30367243 GAATGTTGGT
*
30367253 TGATGGTTTTGGTATGCATA
1 TGAT-GTTTTGGTATCCATA
*
30367273 TGTTGTTTTGGTA-CCATA
1 TGATGTTTTGGTATCCATA
30367291 TGATGTT
1 TGATGTT
30367298 GGATGGTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 10 0.45
19 9 0.41
20 3 0.14
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.49
Consensus pattern (19 bp):
TGATGTTTTGGTATCCATA
Found at i:30370564 original size:32 final size:33
Alignment explanation
Indices: 30370502--30370565 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
30370492 ATTCTCTTTT
*
30370502 ACTTTCTTATTTTTTATCCTCTTTTGTTATTTC
1 ACTTTCTTATTTTTTATCCTCTTTTATTATTTC
30370535 ACTTT-TTATTCTTTTA-CC-CTATTTATTATTT
1 ACTTTCTTATT-TTTTATCCTCT-TTTATTATTT
30370566 ATTTCATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 2 0.07
32 16 0.57
33 10 0.36
ACGTcount: A:0.16, C:0.17, G:0.02, T:0.66
Consensus pattern (33 bp):
ACTTTCTTATTTTTTATCCTCTTTTATTATTTC
Found at i:30372135 original size:37 final size:37
Alignment explanation
Indices: 30372085--30372159 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
30372075 AAATCATGTT
30372085 AGGTAATTATATTTGTAATCAAAATTTGTTTGAAGTA
1 AGGTAATTATATTTGTAATCAAAATTTGTTTGAAGTA
30372122 AGGTAATTATATTTGTAATCAAAATTTGTTTGAAGTA
1 AGGTAATTATATTTGTAATCAAAATTTGTTTGAAGTA
30372159 A
1 A
30372160 TATTGAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.43
Consensus pattern (37 bp):
AGGTAATTATATTTGTAATCAAAATTTGTTTGAAGTA
Found at i:30376068 original size:17 final size:17
Alignment explanation
Indices: 30376042--30376075 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30376032 TGTTTTACTG
*
30376042 CTCGATAGTTCTGACCT
1 CTCGACAGTTCTGACCT
30376059 CTCGACAGTTCTGACCT
1 CTCGACAGTTCTGACCT
30376076 TTCTTCACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (17 bp):
CTCGACAGTTCTGACCT
Found at i:30376797 original size:45 final size:45
Alignment explanation
Indices: 30376642--30376798 Score: 221
Period size: 45 Copynumber: 3.5 Consensus size: 45
30376632 AATAATAACA
* * * *
30376642 GATACACGGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAAT
1 GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
* * *
30376685 GATACTCGGTGGAATCAGCACATAGCAACCACCTTAATAATCAAT
1 GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
30376730 -AGTACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
1 GA-TACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
30376775 GATACCCGGTGGAATCAGCACACA
1 GATACCCGGTGGAATCAGCACACA
30376799 CCCGGTACAC
Statistics
Matches: 103, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
43 11 0.11
44 14 0.14
45 77 0.75
46 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (45 bp):
GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
Found at i:30384308 original size:31 final size:29
Alignment explanation
Indices: 30384236--30384309 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
30384226 ACTTTAGGTT
*
30384236 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTGAAATGTA
* ***
30384265 ACATTTTTGTCACTTATGTTATCGTGTTGTA
1 ACATTTTAGTCACTTATGTT-T-GAAATGTA
30384296 ACATTTTAGTCACT
1 ACATTTTAGTCACT
30384310 GAGCTATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 1 0.03
31 17 0.46
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTGAAATGTA
Found at i:30385079 original size:20 final size:20
Alignment explanation
Indices: 30385042--30385081 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
30385032 TAAAAAAACT
30385042 TATTTAAAATTTTAAATTAA
1 TATTTAAAATTTTAAATTAA
30385062 TATTTCAAAATTTT-AATTAA
1 TATTT-AAAATTTTAAATTAA
30385082 CTTGAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTTAAAATTTTAAATTAA
Found at i:30386745 original size:13 final size:13
Alignment explanation
Indices: 30386729--30386817 Score: 67
Period size: 13 Copynumber: 6.7 Consensus size: 13
30386719 TATAAAATGA
30386729 TTATATGAATTAG
1 TTATATGAATTAG
*
30386742 TTATATGGAAATAG
1 TTATAT-GAATTAG
* *
30386756 ATATACAT-AATGA-
1 -T-TATATGAATTAG
*
30386769 TTATATGAATTGG
1 TTATATGAATTAG
*
30386782 TTATATGGAAATAG
1 TTATAT-GAATTAG
30386796 TTATATGAATT-G
1 TTATATGAATTAG
30386808 TGTATATGAA
1 T-TATATGAA
30386818 ATGTTTATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
11 4 0.07
12 6 0.10
13 24 0.41
14 20 0.34
15 1 0.02
16 4 0.07
ACGTcount: A:0.40, C:0.01, G:0.18, T:0.40
Consensus pattern (13 bp):
TTATATGAATTAG
Found at i:30386799 original size:27 final size:26
Alignment explanation
Indices: 30386764--30386828 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
30386754 AGATATACAT
*
30386764 AATGATTATATGAATTG-GTTATATGGA
1 AATGTTTATATGAATTGTG-TATAT-GA
30386791 AATAG-TTATATGAATTGTGTATATGA
1 AAT-GTTTATATGAATTGTGTATATGA
30386817 AATGTTTATATG
1 AATGTTTATATG
30386829 GATAGAGAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
25 1 0.03
26 12 0.34
27 20 0.57
28 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (26 bp):
AATGTTTATATGAATTGTGTATATGA
Found at i:30386817 original size:40 final size:40
Alignment explanation
Indices: 30386724--30386800 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
30386714 GAATATATAA
*
30386724 AATGATTATATGAATTAGTTATATGGAAATAGATATACAT
1 AATGATTATATGAATTGGTTATATGGAAATAGATATACAT
*
30386764 AATGATTATATGAATTGGTTATATGGAAATAGTTATA
1 AATGATTATATGAATTGGTTATATGGAAATAGATATA
30386801 TGAATTGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.43, C:0.01, G:0.17, T:0.39
Consensus pattern (40 bp):
AATGATTATATGAATTGGTTATATGGAAATAGATATACAT
Found at i:30386826 original size:13 final size:13
Alignment explanation
Indices: 30386764--30386828 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
30386754 AGATATACAT
*
30386764 AATGATTATATGA
1 AATGTTTATATGA
* *
30386777 ATTGGTTATATGGA
1 AATGTTTATAT-GA
30386791 AATAG-TTATATGA
1 AAT-GTTTATATGA
* *
30386804 ATTGTGTATATGA
1 AATGTTTATATGA
30386817 AATGTTTATATG
1 AATGTTTATATG
30386829 GATAGAGAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
12 1 0.02
13 30 0.71
14 10 0.24
15 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (13 bp):
AATGTTTATATGA
Found at i:30390245 original size:3 final size:3
Alignment explanation
Indices: 30390237--30390270 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
30390227 AGTCAATGAT
30390237 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
30390271 AGCTTGGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:30393571 original size:13 final size:13
Alignment explanation
Indices: 30393553--30393578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30393543 GTTTGAAACC
30393553 TTCAAACTTGCCA
1 TTCAAACTTGCCA
30393566 TTCAAACTTGCCA
1 TTCAAACTTGCCA
30393579 CATGTGTGGC
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:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
TTCAAACTTGCCA
Found at i:30399882 original size:22 final size:22
Alignment explanation
Indices: 30399856--30399900 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
30399846 ATTATGAATA
*
30399856 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATACAATTTAATT
*
30399878 TTAATTTTAATACAATTTAATT
1 TTAATTATAATACAATTTAATT
30399900 T
1 T
30399901 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTATAATACAATTTAATT
Found at i:30409229 original size:27 final size:27
Alignment explanation
Indices: 30409104--30409282 Score: 103
Period size: 27 Copynumber: 6.6 Consensus size: 27
30409094 TAGTTTCGGT
* * *
30409104 GGACTACCCCGTGTTTAATGTCATAGC
1 GGACTACCCCGTGTTTAGTGTCCTAAC
** *
30409131 GGACTACCCTATATTTAGTGTACC-AAC
1 GGACTACCCCGTGTTTAGTGT-CCTAAC
** ** *
30409158 GGACTACGTCGCATTTAGTGGT-CTGAC
1 GGACTACCCCGTGTTTAGT-GTCCTAAC
* * * * *
30409185 AGAGTACTCTGTGCTTAGTGTCCTAAC
1 GGACTACCCCGTGTTTAGTGTCCTAAC
* *
30409212 GGACTACCCCGTGTTTAGTGTCCCAGTC
1 GGACTACCCCGTGTTTAGTGTCCTA-AC
* ****
30409240 -GACTACCCCGTGTTTAGAGTCCCGGT
1 GGACTACCCCGTGTTTAGTGTCCTAAC
30409266 GGACTACCCCGTGTTTA
1 GGACTACCCCGTGTTTA
30409283 TTATCCCAGC
Statistics
Matches: 114, Mismatches: 32, Indels: 12
0.72 0.20 0.08
Matches are distributed among these distances:
26 3 0.03
27 107 0.94
28 4 0.04
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (27 bp):
GGACTACCCCGTGTTTAGTGTCCTAAC
Found at i:30409289 original size:27 final size:26
Alignment explanation
Indices: 30409212--30409309 Score: 97
Period size: 27 Copynumber: 3.7 Consensus size: 26
30409202 GTGTCCTAAC
*
30409212 GGACTACCCCGTGTTTAGTGTCCCAGT
1 GGACTACCCCGTGTTTA-TATCCCAGT
* * *
30409239 CGACTACCCCGTGTTTAGAGTCCCGGT
1 GGACTACCCCGTGTTTATA-TCCCAGT
*
30409266 GGACTACCCCGTGTTTATTATCCCAGC
1 GGACTACCCCGTGTTTA-TATCCCAGT
** *
30409293 AAACTACTCCGTGTTTA
1 GGACTACCCCGTGTTTA
30409310 GTATTCTGAT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
27 57 0.98
28 1 0.02
ACGTcount: A:0.18, C:0.31, G:0.21, T:0.30
Consensus pattern (26 bp):
GGACTACCCCGTGTTTATATCCCAGT
Found at i:30411681 original size:7 final size:7
Alignment explanation
Indices: 30411665--30411709 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
30411655 AACAGCAAAA
30411665 AAAAAG-
1 AAAAAGC
30411671 AAAAAGC
1 AAAAAGC
30411678 AAAAAGC
1 AAAAAGC
*
30411685 ACAAA--
1 AAAAAGC
30411690 AAAAAG-
1 AAAAAGC
30411696 AAAAAGC
1 AAAAAGC
30411703 AAAAAGC
1 AAAAAGC
30411710 GCAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 4 0.12
6 12 0.35
7 18 0.53
ACGTcount: A:0.76, C:0.11, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAGC
Found at i:30411689 original size:26 final size:26
Alignment explanation
Indices: 30411651--30411721 Score: 108
Period size: 25 Copynumber: 2.7 Consensus size: 26
30411641 TTATTCTTTA
*
30411651 AAAAAACAGCAAAAAAAAAGAAAAAGC
1 AAAAAGCA-CAAAAAAAAAGAAAAAGC
30411678 AAAAAGCAC-AAAAAAAAGAAAAAGC
1 AAAAAGCACAAAAAAAAAGAAAAAGC
*
30411703 AAAAAGCGCAAAAAAAAAG
1 AAAAAGCACAAAAAAAAAG
30411722 TTGCCTACCT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
25 24 0.59
26 10 0.24
27 7 0.17
ACGTcount: A:0.76, C:0.11, G:0.13, T:0.00
Consensus pattern (26 bp):
AAAAAGCACAAAAAAAAAGAAAAAGC
Found at i:30425211 original size:4 final size:4
Alignment explanation
Indices: 30425202--30425235 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
30425192 TTAAGGGACT
*
30425202 ATAA ATAA ATAA ATAA GAAAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA A
30425236 GAAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 24 0.89
5 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:30425226 original size:17 final size:18
Alignment explanation
Indices: 30425204--30425245 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
30425194 AAGGGACTAT
30425204 AAATAAATAAAT-AAGAA
1 AAATAAATAAATAAAGAA
30425221 AAATAAATAAATAAAGAA
1 AAATAAATAAATAAAGAA
30425239 AAATAAA
1 AAATAAA
30425246 CAGACGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (18 bp):
AAATAAATAAATAAAGAA
Found at i:30428039 original size:20 final size:20
Alignment explanation
Indices: 30428019--30428325 Score: 120
Period size: 20 Copynumber: 15.1 Consensus size: 20
30428009 AGAGTATAAC
* *
30428019 CAGGGGCACGGAAGTGCAAC
1 CAGGGGCACCGAAGTGCAAA
* *
30428039 CAGGGGTACCGAAGTACAAA
1 CAGGGGCACCGAAGTGCAAA
* *
30428059 AAGGGGCA-CGTAAGTGCAAT
1 CAGGGGCACCG-AAGTGCAAA
* * * * *
30428079 TAGGAGTACCAAAGTACAAA
1 CAGGGGCACCGAAGTGCAAA
** *
30428099 CAGGGGCACATAAGTGCAAT
1 CAGGGGCACCGAAGTGCAAA
*
30428119 CAGGGGCACCGAAGTACAAA
1 CAGGGGCACCGAAGTGCAAA
*
30428139 TAGGGGCA-CGTAAGTGCAATCAGGA
1 CAGGGGCACCG-AAGTGC-A--A--A
* *
30428164 TAGGGGCA-CGTAAGTGCAAT
1 CAGGGGCACCG-AAGTGCAAA
* * *
30428184 CAGGGGTACCAAAGTACAAA
1 CAGGGGCACCGAAGTGCAAA
* * ** *
30428204 AAGAGGCACATAAGTGCAAT
1 CAGGGGCACCGAAGTGCAAA
* * ** *
30428224 CAAGGGTACTAAAGTACAAA
1 CAGGGGCACCGAAGTGCAAA
* * *
30428244 CAGGGCCA-CGTAAGTACAAT
1 CAGGGGCACCG-AAGTGCAAA
* * *
30428264 CAGGGGTACCAAAGTACAAA
1 CAGGGGCACCGAAGTGCAAA
*
30428284 CAGGGGCA-CGTAAGTGCAAT
1 CAGGGGCACCG-AAGTGCAAA
* * *
30428304 CAGGGGTATCGAAGTACAAA
1 CAGGGGCACCGAAGTGCAAA
30428324 CA
1 CA
30428326 TGGACATGTA
Statistics
Matches: 209, Mismatches: 65, Indels: 26
0.70 0.22 0.09
Matches are distributed among these distances:
19 5 0.02
20 177 0.85
21 6 0.03
22 1 0.00
23 1 0.00
24 1 0.00
25 18 0.09
ACGTcount: A:0.39, C:0.19, G:0.29, T:0.13
Consensus pattern (20 bp):
CAGGGGCACCGAAGTGCAAA
Found at i:30428075 original size:40 final size:40
Alignment explanation
Indices: 30428020--30428162 Score: 205
Period size: 40 Copynumber: 3.6 Consensus size: 40
30428010 GAGTATAACC
* *
30428020 AGGGGCACGGAAGTGCAACCAGGGGTACCGAAGTACAAAA
1 AGGGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAAA
* * * *
30428060 AGGGGCACGTAAGTGCAATTAGGAGTACCAAAGTACAAAC
1 AGGGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAAA
* * *
30428100 AGGGGCACATAAGTGCAATCAGGGGCACCGAAGTACAAAT
1 AGGGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAAA
30428140 AGGGGCACGTAAGTGCAATCAGG
1 AGGGGCACGTAAGTGCAATCAGG
30428163 ATAGGGGCAC
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 90 1.00
ACGTcount: A:0.37, C:0.19, G:0.32, T:0.12
Consensus pattern (40 bp):
AGGGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAAA
Found at i:30428172 original size:25 final size:25
Alignment explanation
Indices: 30428138--30428187 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
30428128 CGAAGTACAA
30428138 ATAGGGGCACGTAAGTGCAATCAGG
1 ATAGGGGCACGTAAGTGCAATCAGG
30428163 ATAGGGGCACGTAAGTGCAATCAGG
1 ATAGGGGCACGTAAGTGCAATCAGG
30428188 GGTACCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (25 bp):
ATAGGGGCACGTAAGTGCAATCAGG
Found at i:30428179 original size:65 final size:65
Alignment explanation
Indices: 30428100--30428225 Score: 198
Period size: 65 Copynumber: 1.9 Consensus size: 65
30428090 AAGTACAAAC
* * * *
30428100 AGGGGCACATAAGTGCAATCAGGGGCACCGAAGTACAAATAGGGGCACGTAAGTGCAATCAGGAT
1 AGGGGCACATAAGTGCAATCAGGGGCACCAAAGTACAAAAAGAGGCACATAAGTGCAATCAGGAT
* *
30428165 AGGGGCACGTAAGTGCAATCAGGGGTACCAAAGTACAAAAAGAGGCACATAAGTGCAATCA
1 AGGGGCACATAAGTGCAATCAGGGGCACCAAAGTACAAAAAGAGGCACATAAGTGCAATCA
30428226 AGGGTACTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.38, C:0.18, G:0.30, T:0.13
Consensus pattern (65 bp):
AGGGGCACATAAGTGCAATCAGGGGCACCAAAGTACAAAAAGAGGCACATAAGTGCAATCAGGAT
Found at i:30428196 original size:105 final size:105
Alignment explanation
Indices: 30428060--30428267 Score: 317
Period size: 105 Copynumber: 2.0 Consensus size: 105
30428050 AAGTACAAAA
* * * *
30428060 AGGGGCACGTAAGTGCAATTAGGAGTACCAAAGTACAAACAGGGGCACATAAGTGCAATCAGGGG
1 AGGGGCACGTAAGTGCAATCAGGAGTACCAAAGTACAAAAAGAGGCACATAAGTGCAATCAAGGG
* * * *
30428125 CACCGAAGTACAAATAGGGGCACGTAAGTGCAATCAGGAT
66 CACCAAAGTACAAACAGGGCCACGTAAGTACAATCAGGAT
*
30428165 AGGGGCACGTAAGTGCAATCAGGGGTACCAAAGTACAAAAAGAGGCACATAAGTGCAATCAAGGG
1 AGGGGCACGTAAGTGCAATCAGGAGTACCAAAGTACAAAAAGAGGCACATAAGTGCAATCAAGGG
* *
30428230 TACTAAAGTACAAACAGGGCCACGTAAGTACAATCAGG
66 CACCAAAGTACAAACAGGGCCACGTAAGTACAATCAGG
30428268 GGTACCAAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 92 1.00
ACGTcount: A:0.39, C:0.18, G:0.29, T:0.14
Consensus pattern (105 bp):
AGGGGCACGTAAGTGCAATCAGGAGTACCAAAGTACAAAAAGAGGCACATAAGTGCAATCAAGGG
CACCAAAGTACAAACAGGGCCACGTAAGTACAATCAGGAT
Found at i:30428223 original size:40 final size:39
Alignment explanation
Indices: 30428167--30428345 Score: 241
Period size: 40 Copynumber: 4.5 Consensus size: 39
30428157 ATCAGGATAG
*
30428167 GGGCACGTAAGTGCAATCAGGGGTACCAAAGTACAAAAA
1 GGGCACGTAAGTGCAATCAGGGGTACCAAAGTACAAACA
* * *
30428206 GAGGCACATAAGTGCAATCAAGGGTACTAAAGTACAAACA
1 G-GGCACGTAAGTGCAATCAGGGGTACCAAAGTACAAACA
*
30428246 GGGCCACGTAAGTACAATCAGGGGTACCAAAGTACAAACA
1 GGG-CACGTAAGTGCAATCAGGGGTACCAAAGTACAAACA
* *
30428286 GGGGCACGTAAGTGCAATCAGGGGTATCGAAGTACAAACA
1 -GGGCACGTAAGTGCAATCAGGGGTACCAAAGTACAAACA
* *
30428326 TGGACATGTAAGTGCAATCA
1 -GGGCACGTAAGTGCAATCA
30428346 TTTAATAATT
Statistics
Matches: 123, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
39 3 0.02
40 117 0.95
41 3 0.02
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.15
Consensus pattern (39 bp):
GGGCACGTAAGTGCAATCAGGGGTACCAAAGTACAAACA
Found at i:30428283 original size:145 final size:145
Alignment explanation
Indices: 30428020--30428307 Score: 443
Period size: 145 Copynumber: 2.0 Consensus size: 145
30428010 GAGTATAACC
* * * *
30428020 AGGGGCACGGAAGTGCAACCAGGGGTACCGAAGTACAAAAAGGGGCACGTAAGTGCAATTAGGAG
1 AGGGGCACGGAAGTGCAACCAGGGGTACCAAAGTACAAAAAGAGGCACATAAGTGCAATAAGGAG
* * * *
30428085 TACCAAAGTACAAACAGGGGCACATAAGTGCAATCAGGGGCACCGAAGTACAAATAGGGGCACGT
66 TACCAAAGTACAAACAGGGCCACATAAGTACAATCAGGGGCACCAAAGTACAAACAGGGGCACGT
30428150 AAGTGCAATCAGGAT
131 AAGTGCAATCAGGAT
* *
30428165 AGGGGCACGTAAGTGCAATCAGGGGTACCAAAGTACAAAAAGAGGCACATAAGTGCAATCAAGG-
1 AGGGGCACGGAAGTGCAACCAGGGGTACCAAAGTACAAAAAGAGGCACATAAGTGCAAT-AAGGA
* * *
30428229 GTACTAAAGTACAAACAGGGCCACGTAAGTACAATCAGGGGTACCAAAGTACAAACAGGGGCACG
65 GTACCAAAGTACAAACAGGGCCACATAAGTACAATCAGGGGCACCAAAGTACAAACAGGGGCACG
30428294 TAAGTGCAATCAGG
130 TAAGTGCAATCAGG
30428308 GGTATCGAAG
Statistics
Matches: 129, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
145 126 0.98
146 3 0.02
ACGTcount: A:0.39, C:0.19, G:0.30, T:0.13
Consensus pattern (145 bp):
AGGGGCACGGAAGTGCAACCAGGGGTACCAAAGTACAAAAAGAGGCACATAAGTGCAATAAGGAG
TACCAAAGTACAAACAGGGCCACATAAGTACAATCAGGGGCACCAAAGTACAAACAGGGGCACGT
AAGTGCAATCAGGAT
Found at i:30432465 original size:12 final size:12
Alignment explanation
Indices: 30432448--30432476 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
30432438 CTTTTATTAA
30432448 ATCATTTTAAAT
1 ATCATTTTAAAT
30432460 ATCATTTTAAAT
1 ATCATTTTAAAT
30432472 -TCATT
1 ATCATT
30432477 CTTTGCTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (12 bp):
ATCATTTTAAAT
Found at i:30435609 original size:3 final size:3
Alignment explanation
Indices: 30435601--30435630 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30435591 TGGGTTTGTT
30435601 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
30435631 TTCTTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:30440462 original size:27 final size:27
Alignment explanation
Indices: 30440431--30440519 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
30440421 AAATGAAATA
* *
30440431 AAATGGAAGCCTTTGTGATGAATAATG
1 AAATGAAAGCCTTTGTGACGAATAATG
* * *
30440458 AAATGAAAGCCTTTGGGGCGAATCATG
1 AAATGAAAGCCTTTGTGACGAATAATG
* * * *
30440485 GAATGAAAGCCTTTGTGGCAAATCATG
1 AAATGAAAGCCTTTGTGACGAATAATG
30440512 AAATGAAA
1 AAATGAAA
30440520 TGGAATGCCC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (27 bp):
AAATGAAAGCCTTTGTGACGAATAATG
Found at i:30457955 original size:25 final size:26
Alignment explanation
Indices: 30457902--30457955 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
30457892 TTCTCCTAAA
* *
30457902 TTTCAATTTTATTTAATTATTTGATT
1 TTTCAATTTTATTAAATTATTTAATT
30457928 TTTCAA-TTTATTAAATTA-TTAATAT
1 TTTCAATTTTATTAAATTATTTAAT-T
30457953 TTT
1 TTT
30457956 ATACTAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.16
25 15 0.60
26 6 0.24
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTAAATTATTTAATT
Found at i:30466894 original size:27 final size:27
Alignment explanation
Indices: 30466856--30466932 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 27
30466846 GTTTGTCAAC
30466856 CTGTTTGGCAAGCTGGGGTTCACAAGT
1 CTGTTTGGCAAGCTGGGGTTCACAAGT
* * ** *
30466883 CTGTTTGGCAAGGTGTGGTTTTCTAGT
1 CTGTTTGGCAAGCTGGGGTTCACAAGT
* * *
30466910 CTGTTTGGCGAGCTAGGATTCAC
1 CTGTTTGGCAAGCTGGGGTTCAC
30466933 CAATTTGTTT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.16, C:0.17, G:0.32, T:0.35
Consensus pattern (27 bp):
CTGTTTGGCAAGCTGGGGTTCACAAGT
Found at i:30469456 original size:26 final size:26
Alignment explanation
Indices: 30469396--30469458 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
30469386 TTACCCCCAA
* * *
30469396 TAAAATTTGGATGATTTTACCATTAG
1 TAAAATTTTGAAGATTTTACCACTAG
*
30469422 TAAAATTTTGAAGATTTTTCCACTAG
1 TAAAATTTTGAAGATTTTACCACTAG
*
30469448 TAAGATTTTGA
1 TAAAATTTTGA
30469459 GAAAATATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (26 bp):
TAAAATTTTGAAGATTTTACCACTAG
Done.