Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold42
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: 3911082
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 18191 characters in sequence are not A, C, G, or T
File 6 of 24
Found at i:773034 original size:53 final size:53
Alignment explanation
Indices: 772954--773060 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
772944 AGAGCAACTG
* *
772954 ATGTTTGAAATAGTTGTTGCTCAAACAGTTTTCATTTAGAATAACTATTGTTT
1 ATGTTTGAAAAAGTTGCTGCTCAAACAGTTTTCATTTAGAATAACTATTGTTT
773007 ATGTTTGAAAAAGTTGCTGCTCAAACAGTTTTCATTTAGAATAACTATTGTTT
1 ATGTTTGAAAAAGTTGCTGCTCAAACAGTTTTCATTTAGAATAACTATTGTTT
773060 A
1 A
773061 AGACAGTTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (53 bp):
ATGTTTGAAAAAGTTGCTGCTCAAACAGTTTTCATTTAGAATAACTATTGTTT
Found at i:773194 original size:16 final size:16
Alignment explanation
Indices: 773173--773218 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
773163 TGATATTCAT
773173 AATAACTTTTAGTT-GA
1 AATAACTTTT-GTTCGA
773189 AATAACTTTTGTTCGA
1 AATAACTTTTGTTCGA
* *
773205 AACAACTTGTGTTC
1 AATAACTTTTGTTC
773219 AAAAAAGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (16 bp):
AATAACTTTTGTTCGA
Found at i:776509 original size:16 final size:15
Alignment explanation
Indices: 776484--776524 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
776474 ATTTTTTTAA
776484 AATTTTAATTCATTTT
1 AATTTTAATT-ATTTT
*
776500 AATTTAAATTATTTT
1 AATTTTAATTATTTT
*
776515 TATTTTAATT
1 AATTTTAATT
776525 TGATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTTAATTATTTT
Found at i:776960 original size:157 final size:154
Alignment explanation
Indices: 776645--776984 Score: 414
Period size: 157 Copynumber: 2.2 Consensus size: 154
776635 GTTTTAATGC
* * * * *
776645 AAAACTACCAAAATACCCTTAGGATTTACTTTAGACGTGAAAGTATCCCAATAACCCTAAAAGAC
1 AAAATTACAAAAATACCCTTAGG-TATACTTTAGACATGAAAATATCCCAATAACCCTAAAAGAC
* *
776710 TTAAAAATGATCATAAATGGGATGAACCTATCCTAAATACCCACATTTGGCATAAAAGAATCCCG
65 TTAAAAATGATCATAAATAGGATGAACCTATCCTAAATACCCACATTTGGCATAAAAGAATCCAG
* * *
776775 ATGACAACTTAGGATTCAATTTTTAA
130 ATGACAACCTAGGACTCAA-TTCTAA
** * * * * *
776801 AAAATTATGAAAATACCCCTATAGGTATACTTTTGACATGAAAATATCTCGATAACCTTAAAGGA
1 AAAATTACAAAAATA-CCCT-TAGGTATACTTTAGACATGAAAATATCCCAATAACCCTAAAAGA
* *
776866 CTTAAAAA-GAATCATAAATAGGATGAATCTATCCTAAATACCCACATTTGGCATAAAAGCATCC
64 CTTAAAAATG-ATCATAAATAGGATGAACCTATCCTAAATACCCACATTTGGCATAAAAGAATCC
**
776930 TAG-TGACAACCTAGGACTCGGTTCTAA
128 -AGATGACAACCTAGGACTCAATTCTAA
*
776957 AAAATTACAAAAATATCCTTAGGTATAC
1 AAAATTACAAAAATACCCTTAGGTATAC
776985 CTTCGACTTG
Statistics
Matches: 157, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
154 9 0.06
155 3 0.02
156 31 0.20
157 109 0.69
158 5 0.03
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (154 bp):
AAAATTACAAAAATACCCTTAGGTATACTTTAGACATGAAAATATCCCAATAACCCTAAAAGACT
TAAAAATGATCATAAATAGGATGAACCTATCCTAAATACCCACATTTGGCATAAAAGAATCCAGA
TGACAACCTAGGACTCAATTCTAA
Found at i:778734 original size:3 final size:3
Alignment explanation
Indices: 778726--778751 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
778716 TATTGTTACT
778726 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
778752 TATTTCATTA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:779402 original size:153 final size:149
Alignment explanation
Indices: 779080--779486 Score: 437
Period size: 153 Copynumber: 2.7 Consensus size: 149
779070 ATATAAATGA
* * *
779080 AAAACTCATAAAATAAATTAAATTTTTACAAACTAATTTAATATGAATTTAATAAA-AATATTGG
1 AAAACTCATAAAATAAATTGAATTTTTA-AAACTAATTTAATATG-AGTTAA-AAATAATATT-T
* ** ** * *
779144 ATGAATTTTAAAAATT-TAAACCGAGAAAAATCCAACCGGAGAAGTTTACGAAGAAGAAAACTCC
62 AAGAATTTTAAAAATTATAAACTTAGAAAAATCTTACAGAAGAAGTTTACGAAGAAGAAAAC-CC
* *
779208 ATATCTTGGTATCAGAAAAATTCT
126 ATATCTCGGTAACAGAAAAATTCT
779232 AAAACTCATAAAATAAATTGAATTTTTCAAAACTAATTTAATATGAGTTAAACAATAATATTTAA
1 AAAACTCATAAAATAAATTGAATTTTT-AAAACTAATTTAATATGAGTTAAA-AATAATATTTAA
* * ** * *
779297 AAATTTTCTAAAATTATAAACTTAGAAAAATCTTACAGAAGGAA-TTTACGGTGTAGAAAA-CCG
64 GAATTTT-AAAAATTATAAACTTAGAAAAATCTTACAGAA-GAAGTTTACGAAGAAGAAAACCCA
*
779360 TATCTCGGTAACAGGAAAAAATTTT
127 TATCTCGGTAACA-G-AAAAATTCT
* * *
779385 AAAACTCATAAAATAAATTGAATTTTTTAAAAATGAA-TTAATATTAGCTCAAAAATAATATTTG
1 AAAACTCATAAAATAAATTGAA-TTTTTAAAACT-AATTTAATATGAG-TTAAAAATAATATTT-
*
779449 AAGAATTTTAAAAATTATAAACTTAGAAAACTCTTACA
62 AAGAATTTTAAAAATTATAAACTTAGAAAAATCTTACA
779487 AGAAAAATTC
Statistics
Matches: 218, Mismatches: 25, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
150 1 0.00
151 27 0.12
152 55 0.25
153 113 0.52
154 22 0.10
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (149 bp):
AAAACTCATAAAATAAATTGAATTTTTAAAACTAATTTAATATGAGTTAAAAATAATATTTAAGA
ATTTTAAAAATTATAAACTTAGAAAAATCTTACAGAAGAAGTTTACGAAGAAGAAAACCCATATC
TCGGTAACAGAAAAATTCT
Found at i:780806 original size:40 final size:40
Alignment explanation
Indices: 780748--780871 Score: 110
Period size: 40 Copynumber: 3.1 Consensus size: 40
780738 AACGAGTTAG
780748 AAAGGTTGACCA-AGGCAAAACTGATAAAATCAACCAATTA
1 AAAGGTTGACCATA-GCAAAACTGATAAAATCAACCAATTA
* * *
780788 AAAGGTTGGCCATAGCAAAA-TCGATAAAACCAA-TAAGTTA
1 AAAGGTTGACCATAGCAAAACT-GATAAAATCAACCAA-TTA
* * * * * *
780828 GAAGGGTTGACCATGGCGAAACTGATAAAGTAAACCAATAA
1 -AAAGGTTGACCATAGCAAAACTGATAAAATCAACCAATTA
780869 AAA
1 AAA
780872 AGTTAGCCAG
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
39 3 0.05
40 32 0.49
41 27 0.42
42 3 0.05
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (40 bp):
AAAGGTTGACCATAGCAAAACTGATAAAATCAACCAATTA
Found at i:780850 original size:81 final size:79
Alignment explanation
Indices: 780742--781060 Score: 275
Period size: 81 Copynumber: 4.0 Consensus size: 79
780732 TGTATAAACG
* *
780742 AGTTAGAAAGGTTGACCAAGGCAAAACTGATAAAATCAACCAATTAAAAGGTTGGCCATAGCAAA
1 AGTTAGAAAGGTTGACCAAGGCAAAACTGATAAAGTCAACCAATTAAAAAGTTGGCCA-AGCAAA
*
780807 ATCGATAAAACCAATA
65 A-CGATAAAGCCAATA
* * * * * * * *
780823 AGTTAGAAGGGTTGACCATGGCGAAACTGATAAAGTAAACCAATAAAAAAGTTAGCCAGGGCGAA
1 AGTTAGAAAGGTTGACCAAGGCAAAACTGATAAAGTCAACCAATTAAAAAGTTGGCCA-AGCAAA
**
780888 ACGGATAAAGCCAACG
65 AC-GATAAAGCCAATA
* * * * * * * * *
780904 GGTTTGAAAGGTTAACTAAGGCGAAACTGATAAAGTTAACTAATT--AAGGTTGGTCAAGGCAAA
1 AGTTAGAAAGGTTGACCAAGGCAAAACTGATAAAGTCAACCAATTAAAAAGTTGGCCAA-GCAAA
*
780967 ACCAATAAAGCCAATA
65 A-CGATAAAGCCAATA
* * * * * *
780983 GGTTA-AAGGGTTGACTAGGGCAAAACCGATAAAGTCAACCAATTAAAAAGTTGGCCAGGGCAAA
1 AGTTAGAAAGGTTGACCAAGGCAAAACTGATAAAGTCAACCAATTAAAAAGTTGGCCA-AGC-AA
*
781047 AATGATAAAGCCAA
64 AACGATAAAGCCAA
781061 CGGGTTAGAG
Statistics
Matches: 187, Mismatches: 44, Indels: 15
0.76 0.18 0.06
Matches are distributed among these distances:
78 32 0.17
79 27 0.14
80 23 0.12
81 105 0.56
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (79 bp):
AGTTAGAAAGGTTGACCAAGGCAAAACTGATAAAGTCAACCAATTAAAAAGTTGGCCAAGCAAAA
CGATAAAGCCAATA
Found at i:780855 original size:41 final size:41
Alignment explanation
Indices: 780742--780856 Score: 119
Period size: 40 Copynumber: 2.8 Consensus size: 41
780732 TGTATAAACG
* *
780742 AGTTAGAAAGGTTGACCAAGGCAAAACTGATAAAATCAACCA
1 AGTTAGAAAGGTTGACCATGGC-AAACTGATAAAACCAACCA
* * * *
780784 A-TTA-AAAGGTTGGCCATAGCAAAATCGATAAAACCAA-TA
1 AGTTAGAAAGGTTGACCATGGCAAACT-GATAAAACCAACCA
*
780823 AGTTAGAAGGGTTGACCATGGCGAAACTGATAAA
1 AGTTAGAAAGGTTGACCATGGC-AAACTGATAAA
780857 GTAAACCAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
39 6 0.10
40 26 0.44
41 22 0.37
42 5 0.08
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (41 bp):
AGTTAGAAAGGTTGACCATGGCAAACTGATAAAACCAACCA
Found at i:781040 original size:159 final size:161
Alignment explanation
Indices: 780738--781083 Score: 421
Period size: 159 Copynumber: 2.2 Consensus size: 161
780728 CATATGTATA
* * *
780738 AACGAGTTAGAAAGGTTGACCAAGGCAAAACTGATAAAATCAACCAATTAAAAGGTTGGCCATAG
1 AACGGGTTAGAAAGGTTAACTAAGGCAAAACTGATAAAATCAACCAATT-AAAGGTTGGCCATAG
* * * * *
780803 CAAAATCGATAAAACCAATAAGTTAGAAGGGTTGACCATGGCGAAACTGATAAAGTAAACCAATA
65 CAAAACCAATAAAACCAATAAGTTAGAAGGGTTGACCAGGGCAAAACCGATAAAGTAAACCAATA
* *
780868 AAAAAGTTAGCCAGGGCGAAACGGATAAAGCC
130 AAAAAGTTAGCCAGGGCAAAAAGGATAAAGCC
* * * * * *
780900 AACGGGTTTGAAAGGTTAACTAAGGCGAAACTGATAAAGTTAACTAATT-AAGGTTGGTCA-AGG
1 AACGGGTTAGAAAGGTTAACTAAGGCAAAACTGATAAAATCAACCAATTAAAGGTTGGCCATA-G
* * * * *
780963 CAAAACCAATAAAGCCAATAGGTTA-AAGGGTTGACTAGGGCAAAACCGATAAAGTCAACCAATT
65 CAAAACCAATAAAACCAATAAGTTAGAAGGGTTGACCAGGGCAAAACCGATAAAGTAAACCAATA
* *
781027 AAAAAGTTGGCCAGGGCAAAAATGATAAAGCC
130 AAAAAGTTAGCCAGGGCAAAAAGGATAAAGCC
*
781059 AACGGGTTAGAGAA-ATTAACTAAGG
1 AACGGGTTAGA-AAGGTTAACTAAGG
781084 TTAGAAGGGT
Statistics
Matches: 157, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
159 82 0.52
160 34 0.22
162 41 0.26
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (161 bp):
AACGGGTTAGAAAGGTTAACTAAGGCAAAACTGATAAAATCAACCAATTAAAGGTTGGCCATAGC
AAAACCAATAAAACCAATAAGTTAGAAGGGTTGACCAGGGCAAAACCGATAAAGTAAACCAATAA
AAAAGTTAGCCAGGGCAAAAAGGATAAAGCC
Found at i:783163 original size:138 final size:139
Alignment explanation
Indices: 782959--783281 Score: 427
Period size: 138 Copynumber: 2.3 Consensus size: 139
782949 TGGATGCCCG
* *
782959 TAGGAATATTAGAAATTCTGAAAAATTAGAATAACAATTTTTATTTAACTTTTAATTTTTGAAAA
1 TAGGAATATTAGAAATTCT-AAAAATTAGGATAATAATTTTTATTTAACTTTTAATTTTTGAAAA
* ** * *
783024 TTAATTTCGTACCTTGATAGAGAACCGAAAAGATAC-AAAAATTTGAAAA-TTTTCATAGCCCTA
65 TTAATTTCGTACCTTAATAGAGAACAAAAAAGATACGAAAAATTTGAAAAGTTTTCATACCCCCA
783087 CAGATACCCA
130 CAGATACCCA
* * *
783097 TAGGAATCTTATAAATTCTAAAAGTTAGGATAATAATTTTTATTTAACTTTTAAATTTTTGAAAA
1 TAGGAATATTAGAAATTCTAAAAATTAGGATAATAATTTTTATTTAACTTTT-AATTTTTGAAAA
* * * *
783162 TTTATTTCGTACCTTAATGGAGAACAAAAAAGATACGAAAAGTTTTAAAAGTTTTCATACCCCCA
65 TTAATTTCGTACCTTAATAGAGAACAAAAAAGATACGAAAAATTTGAAAAGTTTTCATACCCCCA
*
783227 CGGATACCCA
130 CAGATACCCA
* * *
783237 TGGGAATATTAGAAATTTCAAAAAACTTAGG-TGATAATTTTTATT
1 TAGGAATATTAGAAA-TTCTAAAAA-TTAGGATAATAATTTTTATT
783282 GGATGAAAAA
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
137 30 0.19
138 60 0.38
139 11 0.07
140 33 0.21
141 20 0.13
142 5 0.03
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (139 bp):
TAGGAATATTAGAAATTCTAAAAATTAGGATAATAATTTTTATTTAACTTTTAATTTTTGAAAAT
TAATTTCGTACCTTAATAGAGAACAAAAAAGATACGAAAAATTTGAAAAGTTTTCATACCCCCAC
AGATACCCA
Found at i:785259 original size:13 final size:13
Alignment explanation
Indices: 785241--785266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
785231 CAATTTTTTG
785241 TGTATCGATACAT
1 TGTATCGATACAT
785254 TGTATCGATACAT
1 TGTATCGATACAT
785267 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:785283 original size:32 final size:33
Alignment explanation
Indices: 785221--785284 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
785211 TACAAGCCAA
**
785221 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
*
785254 TGTATCGATAC-ATACTTTGTGTATTGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
785285 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:787389 original size:21 final size:20
Alignment explanation
Indices: 787360--787402 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
787350 GGCTAGTATG
*
787360 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
787381 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
787401 GG
1 GG
787403 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:787861 original size:13 final size:13
Alignment explanation
Indices: 787843--787867 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
787833 ATAATCTCCC
787843 TGTATCGATACAG
1 TGTATCGATACAG
787856 TGTATCGATACA
1 TGTATCGATACA
787868 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:789964 original size:15 final size:15
Alignment explanation
Indices: 789944--789974 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
789934 ATTTCGTTTG
*
789944 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
789959 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
789974 G
1 G
789975 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:794059 original size:13 final size:13
Alignment explanation
Indices: 794041--794066 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
794031 CAATTTTTTG
794041 TGTATCGATACAT
1 TGTATCGATACAT
794054 TGTATCGATACAT
1 TGTATCGATACAT
794067 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:794078 original size:32 final size:33
Alignment explanation
Indices: 794021--794084 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
794011 TACAAGCCAA
**
794021 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
794054 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
794085 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:794479 original size:18 final size:19
Alignment explanation
Indices: 794456--794491 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
794446 CCAAGATCCT
794456 AACATAT-AACAAAAATCA
1 AACATATCAACAAAAATCA
*
794474 AACATATCAATAAAAATC
1 AACATATCAACAAAAATC
794492 CTTAAACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (19 bp):
AACATATCAACAAAAATCA
Found at i:795390 original size:165 final size:164
Alignment explanation
Indices: 795144--795543 Score: 377
Period size: 165 Copynumber: 2.4 Consensus size: 164
795134 ATTATACGTA
* * * * * *
795144 AAAAAAT-CAAAAAATAAGAAATAAATTGAATTTTTCAAAATTGATTTAATAGGA-GTTTA-ATG
1 AAAAAATAAAAAAAATAA-AAATGAA-TGAATTTTTCAAAACTAATTTAAT--GATGATTAGATA
* * *
795206 ACAATATTAGA-AGAATTTTAAAAATTTAAAA-CTAAGAAAAATCCCCCCGAAAACATTTA-TAG
62 ATAATATTTGATA-AATTTTAAAAATTTAAAATC-AAGAAAAATCCCCCCGAAAAAATTTACT-G
* * * * **
795268 AGTAGAAAACTCCATTTTTCGAAGA-TAG-GGGATTTTGAAG
124 AGAAGAAAACTCCATATTTCGAAAACAAGAGAAATTTT-AAG
** *
795308 AAAAAATTCAAAACTCAA-GAAAATGAATGAATTTTTCAAAACTAATTTAATGATGATTAGATAA
1 AAAAAA-T-AAAA-AAAATAAAAATGAATGAATTTTTCAAAACTAATTTAATGATGATTAGATAA
* * *
795372 TAATATTTGATAAATTTTAAAAATTTAAAATCAATAAAAATCCTCTCGAAAAAATTTACTGAGAA
63 TAATATTTGATAAATTTTAAAAATTTAAAATCAAGAAAAATCCCCCCGAAAAAATTTACTGAGAA
***
795437 GAAAACTTTGTATTTCGAAAACAAGAGAAATTTTAAG
128 GAAAACTCCATATTTCGAAAACAAGAGAAATTTTAAG
* * * * *
795474 GAAAAATAAAAAAAATAAAAATGAATGAATTTTTCAAAATTGATTTACTGATGATTAGATGATAA
1 AAAAAATAAAAAAAATAAAAATGAATGAATTTTTCAAAACTAATTTAATGATGATTAGATAATAA
795539 TATTT
66 TATTT
795544 AAAGAATTTT
Statistics
Matches: 192, Mismatches: 32, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
163 4 0.02
164 63 0.33
165 95 0.49
166 19 0.10
167 9 0.05
168 2 0.01
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.31
Consensus pattern (164 bp):
AAAAAATAAAAAAAATAAAAATGAATGAATTTTTCAAAACTAATTTAATGATGATTAGATAATAA
TATTTGATAAATTTTAAAAATTTAAAATCAAGAAAAATCCCCCCGAAAAAATTTACTGAGAAGAA
AACTCCATATTTCGAAAACAAGAGAAATTTTAAG
Found at i:796302 original size:40 final size:40
Alignment explanation
Indices: 796258--796371 Score: 129
Period size: 41 Copynumber: 2.8 Consensus size: 40
796248 TTACAGGGCA
*
796258 AAATCGATAAAGCCAACCAATTAAAAGGTTGGCAAGGGTG
1 AAATCGATAAAGCCAACCAATTAAAAGGTTGGCAAGGATG
*** * * *
796298 AAATCGATAAAGCCAACGGGTTATAAGGGTTGACCAGGATG
1 AAATCGATAAAGCCAACCAATTA-AAAGGTTGGCAAGGATG
* * *
796339 AAACCGATAAAGTCAACCAATCAAAAGGTTGGC
1 AAATCGATAAAGCCAACCAATTAAAAGGTTGGC
796372 TAGTGTAAGC
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
40 28 0.48
41 30 0.52
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.18
Consensus pattern (40 bp):
AAATCGATAAAGCCAACCAATTAAAAGGTTGGCAAGGATG
Found at i:797245 original size:19 final size:20
Alignment explanation
Indices: 797200--797255 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
797190 CTGCCAATTT
*
797200 CATGTATCGATACAATTAAG
1 CATGTATCGATACAATGAAG
*
797220 TATGTATCGATACAATGAA-
1 CATGTATCGATACAATGAAG
*
797239 CATGTATCCATACAATG
1 CATGTATCGATACAATG
797256 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATGAAG
Found at i:797690 original size:81 final size:81
Alignment explanation
Indices: 797569--798359 Score: 734
Period size: 81 Copynumber: 9.8 Consensus size: 81
797559 GGGTAAAATT
* * * * *
797569 GATAAAGCCAATGGGTTAGAAGGGTTGACCAGGGTGAAATTGATATAGTCAACCAATTAAAAGTT
1 GATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCGAAACTGATAAAGTCAACCAATTAAAAGGT
*
797634 TGGCTAGGGCGAAACC
66 TGGCCAGGGCGAAACC
* * * * * * * *
797650 TATAAAGCCAACAGATTATAAGGGTTGACCAGGGCAAAATTGATAAAGTTAACCAATTAAAAAGT
1 GATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCGAAACTGATAAAGTCAACCAATTAAAAGGT
* *
797715 TGGACAGGGC-AAAGCT
66 TGGCCAGGGCGAAA-CC
* * * * *
797731 GATAAAGCCAACGGGTTAGAAGGGTTGACTAAGGCGAAACTAATAAAATCAATCAATTAAAAGGT
1 GATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCGAAACTGATAAAGTCAACCAATTAAAAGGT
**
797796 TGGCCAGGGAAAAACC
66 TGGCCAGGGCGAAACC
* * * * *
797812 GATAAAGCCAATGGGTTA-AAAGGTTGACCATGGCAAAACTGATAAAGTCAACTAATTAAAAGGT
1 GATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCGAAACTGATAAAGTCAACCAATTAAAAGGT
* *
797876 TGGCCAAGGCGAAATC
66 TGGCCAGGGCGAAACC
* ** * * *** * * * *
797892 AATAAAGCTGATGGGTTAGAAGGATTGACCATAACGAAATTGATAAAGTTAACCAAATAAAGGGT
1 GATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCGAAACTGATAAAGTCAACCAATTAAAAGGT
* *
797957 TTGCCAGGGCAAAACC
66 TGGCCAGGGCGAAACC
* * *
797973 GATAAAGCCAACGGGTTAGAAGGGTTGA-CAGGGCAAAACCGATAAAGTCAACCAATTAGAAGGT
1 GATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCGAAACTGATAAAGTCAACCAATTAAAAGGT
* * * *
798037 TGGCTAGGGTGATATC
66 TGGCCAGGGCGAAACC
* * * * * *
798053 GATAAAGCTAAC-GATTAGAAGGGTTGACTAGGGCAAAACTGATAAAATCAACTAATTAAAAGGT
1 GATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCGAAACTGATAAAGTCAACCAATTAAAAGGT
* *
798117 TGGCCAGGG-TAAAAC
66 TGGCCAGGGCGAAACC
* * * * *
798132 GATAAAGCCAACAGGTTAGAAAGGTTGACCAGGGTGAAA-TCGATAAAGTCAACTAGTTAGAAA-
1 GATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCGAAACT-GATAAAGTCAACCAATTA-AAAG
* * **
798195 GTTGGTCAGAGCGAAATT
64 GTTGGCCAGGGCGAAACC
*** * ** ** *
798213 GATAAAGCCAACAATTTAAAAGGGTTGACCAGGGTTAAACCAATAAAGTCAACTAATTAGAAA-G
1 GATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCGAAACTGATAAAGTCAACCAATTA-AAAGG
* **
798277 TTAGCCAGGGTAAAACC
65 TTGGCCAGGGCGAAACC
* ** *
798294 GATAAAGCCAATGGGTTAGAAGGGTTGACCAAAGTGAAACTGATAAAGTCAACCAATTAAAAGGT
1 GATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCGAAACTGATAAAGTCAACCAATTAAAAGGT
798359 T
66 T
798360 CATATAGTAT
Statistics
Matches: 569, Mismatches: 131, Indels: 20
0.79 0.18 0.03
Matches are distributed among these distances:
79 29 0.05
80 203 0.36
81 334 0.59
82 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (81 bp):
GATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCGAAACTGATAAAGTCAACCAATTAAAAGGT
TGGCCAGGGCGAAACC
Found at i:797817 original size:40 final size:40
Alignment explanation
Indices: 797773--798359 Score: 153
Period size: 40 Copynumber: 14.6 Consensus size: 40
797763 GGCGAAACTA
*
797773 ATAAAATCAATCAATTAAAAGGTTGGCCAGGGAAAAACCG
1 ATAAAGTCAATCAATTAAAAGGTTGGCCAGGGAAAAACCG
* *** * * * *
797813 ATAAAGCCAATGGGTTAAAAGGTTGACCATGGCAAAACTG
1 ATAAAGTCAATCAATTAAAAGGTTGGCCAGGGAAAAACCG
* ** * *
797853 ATAAAGTCAA-CTAATTAAAAGGTTGGCCAAGGCGAAATCA
1 ATAAAGTCAATC-AATTAAAAGGTTGGCCAGGGAAAAACCG
* *** * * * **
797893 ATAAAG-CTGATGGGTTAGAAGGATTGACCA--TAACGAAATTG
1 ATAAAGTC-AATCAATTAAAAGG-TTGGCCAGGGAA--AAACCG
* * * * * *
797934 ATAAAGTTAACCAAATAAAGGGTTTGCCAGGGCAAAACCG
1 ATAAAGTCAATCAATTAAAAGGTTGGCCAGGGAAAAACCG
* ** * * *
797974 ATAAAGCCAA-CGGGTTAGAAGGGTT-GACAGGGCAAAACCG
1 ATAAAGTCAATC-AATTA-AAAGGTTGGCCAGGGAAAAACCG
* * * ** * *
798014 ATAAAGTCAACCAATTAGAAGGTTGGCTAGGGTGATATCG
1 ATAAAGTCAATCAATTAAAAGGTTGGCCAGGGAAAAACCG
* * * * * *
798054 ATAAAG-CTAA-CGATTAGAAGGGTTGACTAGGGCAAAACTG
1 ATAAAGTC-AATCAATTA-AAAGGTTGGCCAGGGAAAAACCG
* *
798094 ATAAAATCAA-CTAATTAAAAGGTTGGCCAGGGTAAAA-CG
1 ATAAAGTCAATC-AATTAAAAGGTTGGCCAGGGAAAAACCG
* * * ** *
798133 ATAAAGCCAA-CAGGTTAGAAAGGTTGACCAGGGTGAAATCG
1 ATAAAGTCAATCA-ATTA-AAAGGTTGGCCAGGGAAAAACCG
* * * ** **
798174 ATAAAGTCAA-CTAGTTAGAAA-GTTGGTCAGAGCGAAATTG
1 ATAAAGTCAATC-AATTA-AAAGGTTGGCCAGGGAAAAACCG
* * ** *
798214 ATAAAGCCAA-CAATTTAAAAGGGTTGACCAGGGTTAAACCA
1 ATAAAGTCAATCAA-TTAAAA-GGTTGGCCAGGGAAAAACCG
* *
798255 ATAAAGTCAA-CTAATTAGAAA-GTTAGCCAGGGTAAAACCG
1 ATAAAGTCAATC-AATTA-AAAGGTTGGCCAGGGAAAAACCG
* *** * * ** ** *
798295 ATAAAGCCAATGGGTTAGAAGGGTTGACCAAAGTGAAACTG
1 ATAAAGTCAATCAATTA-AAAGGTTGGCCAGGGAAAAACCG
*
798336 ATAAAGTCAACCAATTAAAAGGTT
1 ATAAAGTCAATCAATTAAAAGGTT
798360 CATATAGTAT
Statistics
Matches: 398, Mismatches: 121, Indels: 56
0.69 0.21 0.10
Matches are distributed among these distances:
38 1 0.00
39 30 0.08
40 256 0.64
41 104 0.26
42 7 0.02
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (40 bp):
ATAAAGTCAATCAATTAAAAGGTTGGCCAGGGAAAAACCG
Found at i:797910 original size:161 final size:161
Alignment explanation
Indices: 797564--798359 Score: 755
Period size: 161 Copynumber: 4.9 Consensus size: 161
797554 AGCTAGGGTA
* * * * * *
797564 AAATTGATAAAGCCAATGGGTTAGAAGGGTTGACCAGGGTGAAATTGATATAGTCAACCAATTAA
1 AAATCGATAAAGCCAACGGGTTAGAAGGGTTGACTAGGGCGAAACTGATAAAGTCAA-CAATTAA
* * * * * * * *
797629 AAGTTTGGCTAGGGCGAAACCTATAAAGCCAACAGATTATAAGGGTTGACCAGGGCAAAATTGAT
65 AAGGTTGGCCAGGGCAAAACCGATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCAAAACTGAT
* * * *
797694 AAAGTTAACCAATTAAAAAGTTGGACAGGGC-
130 AAAGTCAACCAATTAAAAGGTTGGCCAAGGCG
* * * *
797725 AAAGCTGATAAAGCCAACGGGTTAGAAGGGTTGACTAAGGCGAAACTAATAAAATCAATCAATTA
1 AAATC-GATAAAGCCAACGGGTTAGAAGGGTTGACTAGGGCGAAACTGATAAAGTCAA-CAATTA
* * * *
797790 AAAGGTTGGCCAGGGAAAAACCGATAAAGCCAATGGGTTA-AAAGGTTGACCATGGCAAAACTGA
64 AAAGGTTGGCCAGGGCAAAACCGATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCAAAACTGA
*
797854 TAAAGTCAACTAATTAAAAGGTTGGCCAAGGCG
129 TAAAGTCAACCAATTAAAAGGTTGGCCAAGGCG
* ** * * * *** * * *
797887 AAATCAATAAAGCTGATGGGTTAGAAGGATTGACCATAACGAAATTGATAAAGTTAACCAAATAA
1 AAATCGATAAAGCCAACGGGTTAGAAGGGTTGACTAGGGCGAAACTGATAAAGTCAA-CAATTAA
* * *
797952 AGGGTTTGCCAGGGCAAAACCGATAAAGCCAACGGGTTAGAAGGGTTGA-CAGGGCAAAACCGAT
65 AAGGTTGGCCAGGGCAAAACCGATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCAAAACTGAT
* * * *
798016 AAAGTCAACCAATTAGAAGGTTGGCTAGGGTG
130 AAAGTCAACCAATTAAAAGGTTGGCCAAGGCG
* * * * *
798048 ATATCGATAAAGCTAAC-GATTAGAAGGGTTGACTAGGGCAAAACTGATAAAATCAACTAATTAA
1 AAATCGATAAAGCCAACGGGTTAGAAGGGTTGACTAGGGCGAAACTGATAAAGTCAAC-AATTAA
* * * **
798112 AAGGTTGGCCAGGGTAAAA-CGATAAAGCCAACAGGTTAGAAAGGTTGACCAGGGTGAAA-TCGA
65 AAGGTTGGCCAGGGCAAAACCGATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCAAAACT-GA
* * *
798175 TAAAGTCAACTAGTTAGAAA-GTTGGTC-AGAGCG
129 TAAAGTCAACCAATTA-AAAGGTTGGCCAAG-GCG
* *** * * ** **
798208 AAATTGATAAAGCCAACAATTTAAAAGGGTTGACCAGGGTTAAACCAATAAAGTCAACTAATTAG
1 AAATCGATAAAGCCAACGGGTTAGAAGGGTTGACTAGGGCGAAACTGATAAAGTCAAC-AATTA-
* * * ** **
798273 AAA-GTTAGCCAGGGTAAAACCGATAAAGCCAATGGGTTAGAAGGGTTGACCAAAGTGAAACTGA
64 AAAGGTTGGCCAGGGCAAAACCGATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCAAAACTGA
798337 TAAAGTCAACCAATTAAAAGGTT
129 TAAAGTCAACCAATTAAAAGGTT
798360 CATATAGTAT
Statistics
Matches: 517, Mismatches: 105, Indels: 25
0.80 0.16 0.04
Matches are distributed among these distances:
159 29 0.06
160 95 0.18
161 241 0.47
162 151 0.29
163 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (161 bp):
AAATCGATAAAGCCAACGGGTTAGAAGGGTTGACTAGGGCGAAACTGATAAAGTCAACAATTAAA
AGGTTGGCCAGGGCAAAACCGATAAAGCCAACGGGTTAGAAGGGTTGACCAGGGCAAAACTGATA
AAGTCAACCAATTAAAAGGTTGGCCAAGGCG
Found at i:800554 original size:21 final size:22
Alignment explanation
Indices: 800530--800571 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
800520 AGAAAAAGAG
800530 AAACAAGAAA-AAAAAAGAAAA
1 AAACAAGAAATAAAAAAGAAAA
* *
800551 AAACATGAAATGAAAAAGAAA
1 AAACAAGAAATAAAAAAGAAA
800572 GTGTACATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.79, C:0.05, G:0.12, T:0.05
Consensus pattern (22 bp):
AAACAAGAAATAAAAAAGAAAA
Found at i:801355 original size:112 final size:112
Alignment explanation
Indices: 801152--801364 Score: 279
Period size: 112 Copynumber: 1.9 Consensus size: 112
801142 TTAGAAGAAC
* *
801152 ATCAAATTTGTCTGATTTTCAAAGAAATTCATATTTTTACATTCTTATCCATTTGTGCCTAAGGA
1 ATCAAATTTGTCTGATTTTCAAAGAAATTCATATTTTTACATTCTGATCCATTCGTGCCTAAGGA
* * *
801217 AATGGGGTACGTATCTTATGAATTTTGAAATATTTAAACCCAACAAT
66 AATGGGGCACGTATCCTATCAATTTTGAAATATTTAAACCCAACAAT
* * *
801264 ATCAAATTTGTCTGATTTTCAAA-AAATTCATA-TTTTATATGATCTGATCTATTCGTG-CTTAG
1 ATCAAATTTGTCTGATTTTCAAAGAAATTCATATTTTTACAT--TCTGATCCATTCGTGCCTAAG
* * *
801326 GAAAATGGGGCATGTATCCTATCAGTTTTGAAATTTTTA
64 G-AAATGGGGCACGTATCCTATCAATTTTGAAATATTTA
801365 GGCTAACCAA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
110 7 0.08
111 14 0.16
112 66 0.76
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (112 bp):
ATCAAATTTGTCTGATTTTCAAAGAAATTCATATTTTTACATTCTGATCCATTCGTGCCTAAGGA
AATGGGGCACGTATCCTATCAATTTTGAAATATTTAAACCCAACAAT
Found at i:823365 original size:52 final size:52
Alignment explanation
Indices: 823280--823404 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
823270 ATATGAAAAG
* * *
823280 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
823332 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
823384 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
823405 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:823417 original size:52 final size:51
Alignment explanation
Indices: 823280--823424 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
823270 ATATGAAAAG
* *
823280 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
823332 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
823384 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
823425 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:823431 original size:13 final size:13
Alignment explanation
Indices: 823413--823437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
823403 CAAAGATCAG
823413 TGTATCGATACAA
1 TGTATCGATACAA
823426 TGTATCGATACA
1 TGTATCGATACA
823438 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:823520 original size:13 final size:13
Alignment explanation
Indices: 823502--823526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
823492 CAAAAAAATA
823502 TGTATCGATACAT
1 TGTATCGATACAT
823515 TGTATCGATACA
1 TGTATCGATACA
823527 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:823520 original size:33 final size:33
Alignment explanation
Indices: 823480--823546 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
823470 AGTAGCTTAA
823480 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
823513 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
823546 A
1 A
823547 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:827522 original size:20 final size:20
Alignment explanation
Indices: 827499--827571 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
827489 ACAATTCAAA
827499 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
827519 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
827540 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
827560 GTATCGATACAT
1 GTATCGATACAT
827572 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:827543 original size:21 final size:21
Alignment explanation
Indices: 827517--827592 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
827507 ACATGTTGCA
827517 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
827538 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
827558 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
827579 ATGTATCGATACAT
1 ATGTATCGATACAT
827593 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:827550 original size:41 final size:41
Alignment explanation
Indices: 827499--827592 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
827489 ACAATTCAAA
*
827499 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
827540 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
827581 GTATCGATACAT
1 GTATCGATACAT
827593 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:827649 original size:13 final size:13
Alignment explanation
Indices: 827631--827656 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
827621 TACAGCAAGT
827631 ATGTATCGATACA
1 ATGTATCGATACA
827644 ATGTATCGATACA
1 ATGTATCGATACA
827657 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:831736 original size:15 final size:15
Alignment explanation
Indices: 831716--831746 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
831706 TAAAAATGTC
*
831716 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
831731 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
831746 C
1 C
831747 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:833839 original size:20 final size:21
Alignment explanation
Indices: 833760--833838 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
833750 AATGTCCAAA
*
833760 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
833780 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
833805 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
833825 TTGTATCGATACAT
1 ATGTATCGATACAT
833839 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:833843 original size:13 final size:13
Alignment explanation
Indices: 833825--833863 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
833815 ACATTTTTCT
833825 TTGTATCGATACA
1 TTGTATCGATACA
833838 TTGTATCGATACA
1 TTGTATCGATACA
*
833851 CTGTATCGATACA
1 TTGTATCGATACA
833864 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:836326 original size:20 final size:20
Alignment explanation
Indices: 836303--836375 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
836293 ACAATTCAAA
836303 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
836323 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
836344 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
836364 GTATCGATACAT
1 GTATCGATACAT
836376 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:836347 original size:21 final size:21
Alignment explanation
Indices: 836321--836396 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
836311 ACATGTTGCA
836321 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
836342 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
836362 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
836383 ATGTATCGATACAT
1 ATGTATCGATACAT
836397 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:836354 original size:41 final size:41
Alignment explanation
Indices: 836303--836396 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
836293 ACAATTCAAA
*
836303 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
836344 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
836385 GTATCGATACAT
1 GTATCGATACAT
836397 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:836453 original size:13 final size:13
Alignment explanation
Indices: 836435--836460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
836425 TACAGCAAGT
836435 ATGTATCGATACA
1 ATGTATCGATACA
836448 ATGTATCGATACA
1 ATGTATCGATACA
836461 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:839467 original size:6 final size:6
Alignment explanation
Indices: 839456--839511 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
839446 AATTTTTTTC
*
839456 TAATTT TAATTT T-ATTT TAA-TT TAA-TT TAATTT TTATTT T-A-TT
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT
839499 T-ATTT TAATTT TA
1 TAATTT TAATTT TA
839512 TTTAAAATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
4 4 0.09
5 19 0.42
6 22 0.49
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TAATTT
Found at i:839472 original size:11 final size:11
Alignment explanation
Indices: 839458--839514 Score: 75
Period size: 11 Copynumber: 5.4 Consensus size: 11
839448 TTTTTTTCTA
839458 ATTTTAATTTT
1 ATTTTAATTTT
839469 ATTTTAA-TTT
1 ATTTTAATTTT
*
839479 AATTTAATTTTT
1 ATTTTAA-TTTT
839491 ATTTT-A-TTT
1 ATTTTAATTTT
839500 ATTTTAATTTT
1 ATTTTAATTTT
839511 ATTT
1 ATTT
839515 AAAATATAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 8 0.20
10 10 0.25
11 15 0.38
12 7 0.17
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTAATTTT
Found at i:839473 original size:21 final size:21
Alignment explanation
Indices: 839447--839514 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 21
839437 ATTACCTTAA
*
839447 ATTTTTTTCTAATTTTAATTTT
1 ATTTTATT-TAATTTTAATTTT
839469 ATTTTAATTTAA-TTTAATTTTT
1 ATTTT-ATTTAATTTTAA-TTTT
839491 ATTTTATTT-ATTTTAATTTT
1 ATTTTATTTAATTTTAATTTT
839511 ATTT
1 ATTT
839515 AAAATATAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 9 0.21
21 14 0.33
22 17 0.40
23 2 0.05
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTTATTTAATTTTAATTTT
Found at i:839474 original size:5 final size:5
Alignment explanation
Indices: 839458--839514 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
839448 TTTTTTTCTA
* *
839458 ATTTT AATTTT ATTTT AATTTA ATTTA ATTTTT ATTTT A-TTT ATTTT
1 ATTTT -ATTTT ATTTT -ATTTT ATTTT A-TTTT ATTTT ATTTT ATTTT
839505 AATTTT ATTT
1 -ATTTT ATTT
839515 AAAATATAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
4 4 0.09
5 23 0.51
6 18 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:841518 original size:23 final size:23
Alignment explanation
Indices: 841488--841541 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
841478 GTATCTGTTA
841488 GAGATGAAAAGTGGATCAAAAGT
1 GAGATGAAAAGTGGATCAAAAGT
*
841511 GAGATGAAAAGTGGATCAAAATT
1 GAGATGAAAAGTGGATCAAAAGT
*
841534 GAGCTGAA
1 GAGATGAA
841542 TGTTGAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.46, C:0.06, G:0.30, T:0.19
Consensus pattern (23 bp):
GAGATGAAAAGTGGATCAAAAGT
Found at i:841522 original size:12 final size:12
Alignment explanation
Indices: 841488--841541 Score: 58
Period size: 11 Copynumber: 4.7 Consensus size: 12
841478 GTATCTGTTA
841488 GAGATGAAAAGT
1 GAGATGAAAAGT
*
841500 G-GATCAAAAGT
1 GAGATGAAAAGT
841511 GAGATGAAAAGT
1 GAGATGAAAAGT
* *
841523 G-GATCAAAATT
1 GAGATGAAAAGT
*
841534 GAGCTGAA
1 GAGATGAA
841542 TGTTGAATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 19 0.56
12 15 0.44
ACGTcount: A:0.46, C:0.06, G:0.30, T:0.19
Consensus pattern (12 bp):
GAGATGAAAAGT
Found at i:843114 original size:2 final size:2
Alignment explanation
Indices: 843107--843138 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
843097 GCCACTAATG
*
843107 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
843139 TCTTCATTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:844395 original size:49 final size:49
Alignment explanation
Indices: 844322--844430 Score: 193
Period size: 49 Copynumber: 2.2 Consensus size: 49
844312 CTGGGCTAGT
*
844322 TCACAA-AGATGGATTTTTTATATGGCAACCATTATAAATCAAATACTC
1 TCACAATAAATGGATTTTTTATATGGCAACCATTATAAATCAAATACTC
*
844370 TCACAATAAATGGATTTTTTTTATGGCAACCATTATAAATCAAATACTC
1 TCACAATAAATGGATTTTTTATATGGCAACCATTATAAATCAAATACTC
844419 TCACAATAAATG
1 TCACAATAAATG
844431 ACATTAGTCA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
48 6 0.10
49 52 0.90
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (49 bp):
TCACAATAAATGGATTTTTTATATGGCAACCATTATAAATCAAATACTC
Found at i:847816 original size:2 final size:2
Alignment explanation
Indices: 847804--847846 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
847794 AGGTCGGTCC
847804 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
847845 AT
1 AT
847847 TCTTAGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:850594 original size:28 final size:30
Alignment explanation
Indices: 850566--850623 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
850556 TTACCGATGA
850566 TTATAAAAG-TTAATTAAAATTTATTTGATT
1 TTATAAAAGATTAATTAAAATTTATTTGA-T
* *
850596 TTTTAAAAGAATTATTTAAAATTTATTT
1 TTATAAAAG-ATTAATTAAAATTTATTT
850624 TTAATACACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.33
32 16 0.67
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (30 bp):
TTATAAAAGATTAATTAAAATTTATTTGAT
Found at i:850906 original size:14 final size:15
Alignment explanation
Indices: 850882--850919 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
850872 ATAGATACTA
850882 ATTATATTTTTCTTT
1 ATTATATTTTTCTTT
850897 ATTA-ATTTTTCTTT
1 ATTATATTTTTCTTT
850911 -TTATATTTT
1 ATTATATTTT
850920 ATGTAGCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 15 0.68
15 4 0.18
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTATATTTTTCTTT
Found at i:855960 original size:23 final size:23
Alignment explanation
Indices: 855934--855978 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
855924 AAAAAAAAAG
855934 TTTTCTTTTCTCAAAATTCATAA
1 TTTTCTTTTCTCAAAATTCATAA
* *
855957 TTTTCTTTTTTTAAAATTCATA
1 TTTTCTTTTCTCAAAATTCATA
855979 CATACTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTCTTTTCTCAAAATTCATAA
Found at i:856731 original size:32 final size:33
Alignment explanation
Indices: 856694--856758 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
856684 TTATCTTAAT
* *
856694 TTTAATGATATGAAA-ATGAAA-ATTATTTATAA
1 TTTAATAATATCAAAGAT-AAATATTATTTATAA
*
856726 TTTAATAATATCAAAGATAAATATTTTTTATAA
1 TTTAATAATATCAAAGATAAATATTATTTATAA
856759 ATATGATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (33 bp):
TTTAATAATATCAAAGATAAATATTATTTATAA
Found at i:859011 original size:18 final size:18
Alignment explanation
Indices: 858990--859028 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
858980 TTAAAACTTG
858990 AAAAAATTAAAAAATTTA
1 AAAAAATTAAAAAATTTA
* *
859008 AAAAGATTAAAAATTTTA
1 AAAAAATTAAAAAATTTA
859026 AAA
1 AAA
859029 TACAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAAATTAAAAAATTTA
Found at i:860282 original size:28 final size:30
Alignment explanation
Indices: 860246--860303 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
860236 TTATTTTATC
860246 CATATTTTAAAATATTTATGTATT-TATTT
1 CATATTTTAAAATATTTATGTATTGTATTT
* * *
860275 CATA-TTTATATTATTTTTGTATTGTATTT
1 CATATTTTAAAATATTTATGTATTGTATTT
860304 TCTTAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.62
Consensus pattern (30 bp):
CATATTTTAAAATATTTATGTATTGTATTT
Found at i:860469 original size:18 final size:17
Alignment explanation
Indices: 860432--860479 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
860422 TTTTAAAAAG
860432 TTATTTTATTAAATAATT
1 TTATTTTA-TAAATAATT
**
860450 TTAATTTTATAAATTTTT
1 TT-ATTTTATAAATAATT
860468 TTATTTT-TAAAT
1 TTATTTTATAAAT
860480 GATATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
18 11 0.41
19 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATAAATAATT
Found at i:862118 original size:3 final size:3
Alignment explanation
Indices: 862110--862135 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
862100 TATCAATGCA
862110 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
862136 CATCATCTAT
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:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:862842 original size:2 final size:2
Alignment explanation
Indices: 862835--862866 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
862825 TTAAATTTAA
862835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
862867 CTAACTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:864256 original size:13 final size:13
Alignment explanation
Indices: 864235--864280 Score: 60
Period size: 12 Copynumber: 3.7 Consensus size: 13
864225 AATTTCGTGC
864235 AGAATTTTTAATT
1 AGAATTTTTAATT
*
864248 AGGATTTTTAA-T
1 AGAATTTTTAATT
*
864260 AGAATGTTTAATT
1 AGAATTTTTAATT
864273 A-AATTTTT
1 AGAATTTTT
864281 TGTTAGTACC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 16 0.57
13 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (13 bp):
AGAATTTTTAATT
Found at i:864458 original size:27 final size:26
Alignment explanation
Indices: 864426--864487 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 26
864416 ATTTAATATC
*
864426 ATTTCAATATACGTTTTACATATAAA
1 ATTTCAATAAACGTTTTACATATAAA
* *
864452 ATTTTCAATTAAACTTTTTACATATAGA
1 A-TTTCAA-TAAACGTTTTACATATAAA
864480 ATTTCAAT
1 ATTTCAAT
864488 TAAATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 2 0.06
27 12 0.39
28 17 0.55
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.45
Consensus pattern (26 bp):
ATTTCAATAAACGTTTTACATATAAA
Found at i:864477 original size:28 final size:28
Alignment explanation
Indices: 864439--864629 Score: 123
Period size: 27 Copynumber: 6.9 Consensus size: 28
864429 TCAATATACG
864439 TTTTACATATAAAATTTTCAATTAAACT
1 TTTTACATATAAAATTTTCAATTAAACT
* *
864467 TTTTACATATAGAA-TTTCAATTAAATT
1 TTTTACATATAAAATTTTCAATTAAACT
* * * *
864494 TTTTATAT-TTAAATATTCAATTAAACC
1 TTTTACATATAAAATTTTCAATTAAACT
* *
864521 ATTTAAATATAACAATTTT-AACTT----T
1 TTTTACATATAA-AATTTTCAA-TTAAACT
* *
864546 TTATTACATGTAGAATTTTCAATTAGAA-T
1 TT-TTACATATAAAATTTTCAATTA-AACT
* *
864575 TTTTACA-AGTAAAATTTTTAATTAGACTT
1 TTTTACATA-TAAAATTTTCAATTAAAC-T
* *
864604 TTTTAC-TACTATAATTTTTAATTAAA
1 TTTTACATA-TAAAATTTTCAATTAAA
864630 TTAAAACCAA
Statistics
Matches: 125, Mismatches: 24, Indels: 27
0.71 0.14 0.15
Matches are distributed among these distances:
25 9 0.07
26 12 0.10
27 36 0.29
28 35 0.28
29 33 0.26
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.48
Consensus pattern (28 bp):
TTTTACATATAAAATTTTCAATTAAACT
Found at i:864525 original size:27 final size:26
Alignment explanation
Indices: 864426--864519 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 26
864416 ATTTAATATC
* *
864426 ATTTCAA-TATACGTTTTACATATAAA
1 ATTTCAATTAAACTTTTTACATAT-AA
864452 ATTTTCAATTAAACTTTTTACATATAGA
1 A-TTTCAATTAAACTTTTTACATATA-A
* * *
864480 ATTTCAATTAAATTTTTTATATTTAA
1 ATTTCAATTAAACTTTTTACATATAA
864506 ATATTCAATTAAAC
1 AT-TTCAATTAAAC
864520 CATTTAAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
26 4 0.07
27 38 0.66
28 16 0.28
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTTCAATTAAACTTTTTACATATAA
Found at i:864606 original size:29 final size:28
Alignment explanation
Indices: 864544--864627 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
864534 AATTTTAACT
* * *
864544 TTTTATTACATGTAGAATTTTCAATTAGA
1 TTTT-TTACAAGTAAAATTTTTAATTAGA
*
864573 ATTTTTACAAGTAAAATTTTTAATTAGA
1 TTTTTTACAAGTAAAATTTTTAATTAGA
* * *
864601 CTTTTTTACTACTATAATTTTTAATTA
1 -TTTTTTACAAGTAAAATTTTTAATTA
864628 AATTAAAACC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 21 0.46
29 25 0.54
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (28 bp):
TTTTTTACAAGTAAAATTTTTAATTAGA
Found at i:868260 original size:20 final size:20
Alignment explanation
Indices: 868233--868284 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
868223 ATTTAGCATG
*
868233 TCTAGGTCAAAATCGAGTCT
1 TCTAGGTCAAAATCAAGTCT
*
868253 TTTAGGTCAAAATCAAGTCT
1 TCTAGGTCAAAATCAAGTCT
*
868273 TCTAAGTCAAAA
1 TCTAGGTCAAAA
868285 CTAAATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (20 bp):
TCTAGGTCAAAATCAAGTCT
Found at i:870949 original size:51 final size:51
Alignment explanation
Indices: 870850--870960 Score: 156
Period size: 51 Copynumber: 2.2 Consensus size: 51
870840 ACGGGATTGT
870850 AGTATCCCCGATAGTGAAAAATCGATATTTTAGAAATAAAAATAGGGTT-A
1 AGTATCCCCGATAGTGAAAAATCGATATTTTAGAAATAAAAATAGGGTTGA
* *
870900 GAGTATCCCCGATGGTGAAAAATCGATATTTT-GAAA-ATAAAATCGGGGTTGA
1 -AGTATCCCCGATAGTGAAAAATCGATATTTTAGAAATA-AAAAT-AGGGTTGA
870952 AGTATCCCC
1 AGTATCCCC
870961 TCGAAAATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
49 1 0.02
50 9 0.16
51 44 0.80
52 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (51 bp):
AGTATCCCCGATAGTGAAAAATCGATATTTTAGAAATAAAAATAGGGTTGA
Found at i:870984 original size:79 final size:78
Alignment explanation
Indices: 870890--871337 Score: 427
Period size: 79 Copynumber: 5.7 Consensus size: 78
870880 TAGAAATAAA
* *
870890 AATAGGGTTAGAGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAATCGGGGTTGAAGT
1 AATAGGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAA-CGGGGTTGGAGT
870955 ATCCCCTCGAAAAT
65 ATCCCCTCGAAAAT
* * * * * * *
870969 AATAAGATTGGAGTATCCTCGATGGTGGATAATTGATATTTT-AGAAATAAAACCGGGTTGGAGT
1 AATAGGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTGA-AAATAAAACGGGGTTGGAGT
* **
871033 TTCCTTTCGAAAAT
65 ATCCCCTCGAAAAT
** * * * * * **
871047 AACGGGGTTAGAGTATCTCCGATGGTGAAAAAATTGATGATTTAG-AAATAAAACTAGGGTTACA
1 AATAGGGTTGGAGTATCCCCGATGGTG-AAAAATCGAT-ATTTTGAAAATAAAAC-GGGGTTGGA
* * *
871111 ATATCCCTTCGGAAAT
63 GTATCCCCTCGAAAAT
** * * * * * * *
871127 AACGGGGTTGGAGTATCCCCAATGGTGGAAAGTGGATCTTTT-AGAAATAAAATGGGGGATGGAG
1 AATAGGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTGA-AAATAAAA-CGGGGTTGGAG
*
871191 TATCCCCTCAAAAAT
64 TATCCCCTCGAAAAT
* * *
871206 AATAGGGTTGGAATATCCCCGATGGTGAAAAATCGATATTTTAAAAATAAAGCTGGGGTTGGAGT
1 AATAGGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAAC-GGGGTTGGAGT
871271 ATCCCCTCGAAAAT
65 ATCCCCTCGAAAAT
* *
871285 AATAGGGTTGGAGTATCCTCGATGGTGAAGAAAAT-GATATTTTGGAAATAAAA
1 AATAGGGTTGGAGTATCCCCGATGGTG-A-AAAATCGATATTTTGAAAATAAAA
871338 ACATCAATGA
Statistics
Matches: 294, Mismatches: 63, Indels: 23
0.77 0.17 0.06
Matches are distributed among these distances:
78 45 0.15
79 181 0.62
80 63 0.21
81 5 0.02
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.28
Consensus pattern (78 bp):
AATAGGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAACGGGGTTGGAGTA
TCCCCTCGAAAAT
Found at i:871116 original size:158 final size:155
Alignment explanation
Indices: 870893--871337 Score: 489
Period size: 158 Copynumber: 2.8 Consensus size: 155
870883 AAATAAAAAT
*
870893 AGGGTTAGAGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAA-TCGGGGTTGAAGTAT
1 AGGGTTAGAGTATCCCCGATGGTGAAAAATCGATATTTAG-AAATAAAACT-GGGGTT-AAGTAT
* *
870957 CCCCTCGAAAATAATAAGATTGGAGTATCCTCGATGGTGGATAATTGATATTTTAGAAATAAAA-
63 CCCCTCGAAAATAATAGGGTTGGAGTATCCTCGATGGTGGA-AATTGATATTTTAGAAATAAAAT
* * ** *
871021 CCGGGTTGGAGTTTCCTTTCGAAAATAAC
127 CCGGGATGGAGTATCCCCTCAAAAATAAC
* * * * *
871050 GGGGTTAGAGTATCTCCGATGGTGAAAAAATTGATGATTTAGAAATAAAACTAGGGTTACAATAT
1 AGGGTTAGAGTATCCCCGATGGTG-AAAAATCGAT-ATTTAGAAATAAAACTGGGGTTA-AGTAT
* * ** * * * *
871115 CCCTTCGGAAATAACGGGGTTGGAGTATCCCCAATGGTGGAAAGTGGATCTTTTAGAAATAAAAT
63 CCCCTCGAAAATAATAGGGTTGGAGTATCCTCGATGGTGGAAA-TTGATATTTTAGAAATAAAAT
** *
871180 GGGGGATGGAGTATCCCCTCAAAAATAAT
127 CCGGGATGGAGTATCCCCTCAAAAATAAC
* * * * *
871209 AGGGTTGGAATATCCCCGATGGTGAAAAATCGATATTTTAAAAATAAAGCTGGGGTTGGAGTATC
1 AGGGTTAGAGTATCCCCGATGGTGAAAAATCGATA-TTTAGAAATAAAACTGGGGTT-AAGTATC
* *
871274 CCCTCGAAAATAATAGGGTTGGAGTATCCTCGATGGTGAAGAAAATGATATTTTGGAAATAAAA
64 CCCTCGAAAATAATAGGGTTGGAGTATCCTCGATGGTG--GAAATTGATATTTTAGAAATAAAA
871338 ACATCAATGA
Statistics
Matches: 234, Mismatches: 44, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
157 26 0.11
158 141 0.60
159 63 0.27
160 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.28
Consensus pattern (155 bp):
AGGGTTAGAGTATCCCCGATGGTGAAAAATCGATATTTAGAAATAAAACTGGGGTTAAGTATCCC
CTCGAAAATAATAGGGTTGGAGTATCCTCGATGGTGGAAATTGATATTTTAGAAATAAAATCCGG
GATGGAGTATCCCCTCAAAAATAAC
Found at i:873230 original size:13 final size:13
Alignment explanation
Indices: 873212--873236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
873202 GTATCAAGGT
873212 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
873225 TTTTTTTTTTTT
1 TTTTTTTTTTTT
873237 GCTACTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.04, G:0.00, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:873690 original size:19 final size:18
Alignment explanation
Indices: 873662--873700 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
873652 AGTTAAAAAT
873662 ATTTGAATGTATCAATAC
1 ATTTGAATGTATCAATAC
* *
873680 ATTTAGAATGTGTCGATAC
1 ATTT-GAATGTATCAATAC
873699 AT
1 AT
873701 CTGGGTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (18 bp):
ATTTGAATGTATCAATAC
Found at i:873844 original size:20 final size:20
Alignment explanation
Indices: 873819--873873 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
873809 TATTTTAGGC
873819 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
*
873839 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTCACTT
*
873859 ATATATCGATACATT
1 ATGTATCGATACATT
873874 TCCTTGACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:873896 original size:100 final size:100
Alignment explanation
Indices: 873739--873957 Score: 402
Period size: 100 Copynumber: 2.2 Consensus size: 100
873729 ACAATAAAAA
*
873739 ATGTATCGATACATTTACTTATGTATCGATACATTTCCTTGACAGTATGCAGGGTGGTTTTGTAT
1 ATGTATCGATACATTTACTTATATATCGATACATTTCCTTGACAGTATGCAGGGTGGTTTTGTAT
873804 CGATATATTTTAGGCATGTATCGATACATTCACTT
66 CGATATATTTTAGGCATGTATCGATACATTCACTT
**
873839 ATGTATCGATACATTTACTTATATATCGATACATTTCCTTGACAGTATGCATTGTGGTTTTGTAT
1 ATGTATCGATACATTTACTTATATATCGATACATTTCCTTGACAGTATGCAGGGTGGTTTTGTAT
873904 CGATATATTTTAGGCATGTATCGATACATTCACTT
66 CGATATATTTTAGGCATGTATCGATACATTCACTT
*
873939 ATGTATCAATACATTTACT
1 ATGTATCGATACATTTACT
873958 ATTTGTATCG
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 115 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (100 bp):
ATGTATCGATACATTTACTTATATATCGATACATTTCCTTGACAGTATGCAGGGTGGTTTTGTAT
CGATATATTTTAGGCATGTATCGATACATTCACTT
Found at i:873944 original size:20 final size:21
Alignment explanation
Indices: 873919--873972 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
873909 TATTTTAGGC
873919 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
* *
873939 ATGTATCAATACATTTACTAT
1 ATGTATCGATACATTCACTAT
* *
873960 TTGTATCGGTACA
1 ATGTATCGATACA
873973 AATTATAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:874863 original size:18 final size:17
Alignment explanation
Indices: 874816--874863 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
874806 AAATAAAAAT
*
874816 ATAAAAAAAATATGAAC
1 ATAATAAAAATATGAAC
*
874833 ATAATATAAATATGCGAAC
1 ATAATAAAAATAT--GAAC
874852 AT-ATAAAAATAT
1 ATAATAAAAATAT
874864 AAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 11 0.42
18 9 0.35
19 6 0.23
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.25
Consensus pattern (17 bp):
ATAATAAAAATATGAAC
Found at i:875778 original size:8 final size:8
Alignment explanation
Indices: 875767--875934 Score: 82
Period size: 8 Copynumber: 20.2 Consensus size: 8
875757 TAAATATGAT
875767 TATATAAA
1 TATATAAA
875775 TATAATATATA
1 TAT-ATA-A-A
875786 TATATATAA
1 TATATA-AA
875795 TA-ATTAAA
1 TATA-TAAA
875803 -ATATAATA
1 TATATAA-A
875811 TAATATAAA
1 T-ATATAAA
875820 TATATAAA
1 TATATAAA
875828 TATATTTTAAA
1 TATA---TAAA
*
875839 T-TTTAAA
1 TATATAAA
875846 TAATATAAA
1 T-ATATAAA
*
875855 T-TATTAA
1 TATATAAA
875862 TATATTAAAA
1 TATA-T-AAA
*
875872 TTTATAAA
1 TATATAAA
*
875880 AATATAAA
1 TATATAAA
* *
875888 TATTTTAA
1 TATATAAA
*
875896 -ACATAAA
1 TATATAAA
*
875903 TATA-ATA
1 TATATAAA
875910 TA-ATAAAA
1 TATAT-AAA
875918 TATATAAA
1 TATATAAA
875926 TATA-AAA
1 TATATAAA
875933 TA
1 TA
875935 AATATATTTA
Statistics
Matches: 124, Mismatches: 16, Indels: 41
0.69 0.09 0.23
Matches are distributed among these distances:
6 1 0.01
7 28 0.23
8 48 0.39
9 20 0.16
10 18 0.15
11 9 0.07
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (8 bp):
TATATAAA
Found at i:875812 original size:34 final size:35
Alignment explanation
Indices: 875768--875929 Score: 143
Period size: 34 Copynumber: 4.9 Consensus size: 35
875758 AAATATGATT
*
875768 ATATAAATATAATATATATATATATAATA-ATTAAA
1 ATAT-AATATAATATAAATATATATAATATATTAAA
875803 ATATAATATAATATAAATATATA-AATATATTTTAAA
1 ATATAATATAATATAAATATATATAATATA--TTAAA
* *
875839 TTTTAA-ATAATATAAAT-TAT-TAATATATTAAA
1 ATATAATATAATATAAATATATATAATATATTAAA
* *
875871 ATTTATAA-A-AATATAAATAT-TTTAA-ACA-T-AA
1 A--TATAATATAATATAAATATATATAATATATTAAA
875902 ATATAATATAATA-AAATATATA-AATATA
1 ATATAATATAATATAAATATATATAATATA
875930 AAATAAATAT
Statistics
Matches: 107, Mismatches: 8, Indels: 28
0.75 0.06 0.20
Matches are distributed among these distances:
29 5 0.05
30 9 0.08
31 10 0.09
32 6 0.06
33 16 0.15
34 37 0.35
35 15 0.14
36 9 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (35 bp):
ATATAATATAATATAAATATATATAATATATTAAA
Found at i:875813 original size:40 final size:41
Alignment explanation
Indices: 875743--875832 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 41
875733 TAGTTAAAGA
* *
875743 ATATTTAT-TAATATTAAATATGATTATATAA-ATATAATAT
1 ATATATATATAATATTAAATATGATAATATAATATA-AATAT
875783 ATATATATATAATAATTAAA-AT-ATAATATAATATAAATAT
1 ATATATATATAAT-ATTAAATATGATAATATAATATAAATAT
*
875823 ATAAATATAT
1 ATATATATAT
875833 TTTAAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
40 29 0.66
41 9 0.20
42 6 0.14
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (41 bp):
ATATATATATAATATTAAATATGATAATATAATATAAATAT
Found at i:882779 original size:24 final size:24
Alignment explanation
Indices: 882752--882802 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
882742 TTGTTTCCAC
882752 CATTATTTCTGCTCACCACCAAGG
1 CATTATTTCTGCTCACCACCAAGG
*
882776 C---ATTTCTGCTCACCACCTAGG
1 CATTATTTCTGCTCACCACCAAGG
*
882797 TATTAT
1 CATTAT
882803 CATTATCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
21 19 0.86
24 3 0.14
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (24 bp):
CATTATTTCTGCTCACCACCAAGG
Found at i:882901 original size:52 final size:51
Alignment explanation
Indices: 882788--883007 Score: 196
Period size: 52 Copynumber: 4.3 Consensus size: 51
882778 TTTCTGCTCA
* * * * * *
882788 CCACCTAGGTATTATCATTATCAA-TGACACTAAGTCAC-CTAATTTGATCG
1 CCACCAAGGCATTATCATTCT-AAGTGACACTAAGTCACTCCAATCTAATCG
* * * * * *
882838 CCACCATGGCATCATCACTCTAAGTGACATTAAGTCGCTCCAAGTCTAATTG
1 CCACCAAGGCATTATCATTCTAAGTGACACTAAGTCACTCCAA-TCTAATCG
* * * *
882890 CCACCAAGGCATTTTCATTCTTAA-TGACCCCT-AGTCACTCCCAATATGATCG
1 CCACCAAGGCATTATCATTC-TAAGTGA-CACTAAGTCACT-CCAATCTAATCG
*
882942 CCACCAAGGCATTATCATTCTTAGTGACACTAAGTCACTCCAAATCTAATCG
1 CCACCAAGGCATTATCATTCTAAGTGACACTAAGTCACTCC-AATCTAATCG
*
882994 CCATCAAGGCATTA
1 CCACCAAGGCATTA
883008 CTGCTACCAA
Statistics
Matches: 133, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
49 2 0.02
50 27 0.20
51 10 0.08
52 85 0.64
53 9 0.07
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (51 bp):
CCACCAAGGCATTATCATTCTAAGTGACACTAAGTCACTCCAATCTAATCG
Found at i:883044 original size:104 final size:104
Alignment explanation
Indices: 882832--883049 Score: 233
Period size: 104 Copynumber: 2.1 Consensus size: 104
882822 TCACCTAATT
* * * * *
882832 TGATCGCCACCATGGCATCATCACTCTAAGTGACATTAAGTCGCTCCAAGTCTAATTGCCACCAA
1 TGATCGCCACCAAGGCATCATCACTCTAAGTGACACTAAGTCACTCCAAATCTAATCGCCACCAA
* * * * * * *
882897 GGCATTTTCATTCTTAATGACCCCTAGTCACTCCCAATA
66 GGCATTTGCATACTCAATGACACCAAGTCACTCCAAACA
* * * *
882936 TGATCGCCACCAAGGCATTATCATTCTTAGTGACACTAAGTCACTCCAAATCTAATCGCCATCAA
1 TGATCGCCACCAAGGCATCATCACTCTAAGTGACACTAAGTCACTCCAAATCTAATCGCCACCAA
** *
883001 GGCATTACTGC-TAC-CAATGACACCAAGTTGCTCCAAACC
66 GGCATT--TGCATACTCAATGACACCAAGTCACTCCAAACA
883040 TGATCGCCAC
1 TGATCGCCAC
883050 TAAGAATTAT
Statistics
Matches: 93, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
104 89 0.96
105 2 0.02
106 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (104 bp):
TGATCGCCACCAAGGCATCATCACTCTAAGTGACACTAAGTCACTCCAAATCTAATCGCCACCAA
GGCATTTGCATACTCAATGACACCAAGTCACTCCAAACA
Found at i:888052 original size:16 final size:16
Alignment explanation
Indices: 888031--888085 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
888021 CCCGAGATAG
*
888031 CCCAAACTCGGAAA-AA
1 CCCAAACT-TGAAAGAA
888047 CCCAAACTTGAAAGAA
1 CCCAAACTTGAAAGAA
*
888063 CCCGAACTTGAAAGAA
1 CCCAAACTTGAAAGAA
888079 CCCAAAC
1 CCCAAAC
888086 CCGAGAGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
15 4 0.11
16 31 0.89
ACGTcount: A:0.47, C:0.31, G:0.13, T:0.09
Consensus pattern (16 bp):
CCCAAACTTGAAAGAA
Found at i:888095 original size:32 final size:31
Alignment explanation
Indices: 888041--888101 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
888031 CCCAAACTCG
**
888041 GAAAAACCCAAACTTGAAAGAACCCGAACTT
1 GAAAAACCCAAACCCGAAAGAACCCGAACTT
* *
888072 GAAAGAACCCAAACCCGAGAGAACTCGAAC
1 GAAA-AACCCAAACCCGAAAGAACCCGAAC
888102 CCGAGACTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.48, C:0.28, G:0.16, T:0.08
Consensus pattern (31 bp):
GAAAAACCCAAACCCGAAAGAACCCGAACTT
Found at i:888596 original size:16 final size:15
Alignment explanation
Indices: 888575--888605 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
888565 ATGTTACACT
888575 TAGAATAGCAATATAA
1 TAGAATAG-AATATAA
888591 TAGAATAGAATATAA
1 TAGAATAGAATATAA
888606 AAGCTATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (15 bp):
TAGAATAGAATATAA
Found at i:888619 original size:84 final size:84
Alignment explanation
Indices: 888516--888690 Score: 314
Period size: 84 Copynumber: 2.1 Consensus size: 84
888506 ATTAAAAAAT
* *
888516 ATATAAAAGCTGTAACAGATAATACTATATTAATAATGAAAAAAATTATATGTTACACTTAGAAT
1 ATATAAAAGCTATAACAGATAATACTATATTAAAAATGAAAAAAATTATATGTTACACTTAGAAT
888581 AGCAATATAATAGAATAGA
66 AGCAATATAATAGAATAGA
888600 ATATAAAAGCTATAACAGATAATACTATATTAAAAATGAAAAAAATTATATGTTACACTTAGAAT
1 ATATAAAAGCTATAACAGATAATACTATATTAAAAATGAAAAAAATTATATGTTACACTTAGAAT
* *
888665 AGCAATATAGTATAATAGA
66 AGCAATATAATAGAATAGA
888684 ATATAAA
1 ATATAAA
888691 GTTAACATAA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.30
Consensus pattern (84 bp):
ATATAAAAGCTATAACAGATAATACTATATTAAAAATGAAAAAAATTATATGTTACACTTAGAAT
AGCAATATAATAGAATAGA
Found at i:889215 original size:56 final size:56
Alignment explanation
Indices: 889146--889252 Score: 151
Period size: 56 Copynumber: 1.9 Consensus size: 56
889136 TTGTCGTTAA
* *
889146 TATTAATTTGGTCTAAGCTTCAATCTGCGTTTGGGTTTATTGTTGTTGCCTGTTGC
1 TATTAATTCGGTCTAAGCTTCAATCTGCGTTTAGGTTTATTGTTGTTGCCTGTTGC
* * * * *
889202 TATTAATTCGGTCTAATCTTCAATTTGGGTTTAGTTTTGTTGTTGTTGCCT
1 TATTAATTCGGTCTAAGCTTCAATCTGCGTTTAGGTTTATTGTTGTTGCCT
889253 ACTATTGCCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 44 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.50
Consensus pattern (56 bp):
TATTAATTCGGTCTAAGCTTCAATCTGCGTTTAGGTTTATTGTTGTTGCCTGTTGC
Found at i:889445 original size:12 final size:11
Alignment explanation
Indices: 889425--889468 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 11
889415 GATTAAATGG
889425 TTTTTAAATAT
1 TTTTTAAATAT
889436 TTTATTAAATAT
1 TTT-TTAAATAT
*
889448 ATTTTAAA-A-
1 TTTTTAAATAT
889457 TTTTTAAATAT
1 TTTTTAAATAT
889468 T
1 T
889469 AATTCAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 7 0.25
10 2 0.07
11 9 0.32
12 10 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:889452 original size:23 final size:20
Alignment explanation
Indices: 889426--889467 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 20
889416 ATTAAATGGT
889426 TTTTAAATATTTTATTAAATATA
1 TTTTAAA-A-TTT-TTAAATATA
889449 TTTTAAAATTTTTAAATAT
1 TTTTAAAATTTTTAAATAT
889468 TAATTCAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 1 0.05
23 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAAAATTTTTAAATATA
Found at i:889461 original size:9 final size:10
Alignment explanation
Indices: 889425--889468 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 10
889415 GATTAAATGG
889425 TTTTTAAATA
1 TTTTTAAATA
889435 TTTTATTAAATA
1 -TTT-TTAAATA
889447 TATTTTAAA-A
1 T-TTTTAAATA
889457 TTTTTAAATA
1 TTTTTAAATA
889467 TT
1 TT
889469 AATTCAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 7 0.23
10 5 0.17
11 9 0.30
12 9 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:889878 original size:16 final size:16
Alignment explanation
Indices: 889838--889879 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
889828 GAACTCAAAA
889838 AAGCCCAAACCTGTAT
1 AAGCCCAAACCTGTAT
889854 -AGTCCCAAACCTGTAT
1 AAG-CCCAAACCTGTAT
*
889870 AAGCTCAAAC
1 AAGCCCAAAC
889880 TCAAATGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (16 bp):
AAGCCCAAACCTGTAT
Found at i:890165 original size:21 final size:22
Alignment explanation
Indices: 890141--890183 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
890131 AAAATAAAAA
890141 AAATTAT-AATTT-TTATAATTT
1 AAATTATAAATTTATTA-AATTT
*
890162 AAATTTTAAATTTATTAAATTT
1 AAATTATAAATTTATTAAATTT
890184 TATTATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATTATAAATTTATTAAATTT
Found at i:896828 original size:20 final size:20
Alignment explanation
Indices: 896798--896869 Score: 76
Period size: 25 Copynumber: 3.4 Consensus size: 20
896788 TTTATACAAA
896798 AAATA-ATTAAAATATTAT-T
1 AAATATATTAAAAT-TTATAT
896817 AAATATATTAAAATTTATAT
1 AAATATATTAAAATTTATAT
896837 AAATATATAATATTAAAATTTATAT
1 --A-A-AT-ATATTAAAATTTATAT
896862 AAATATAT
1 AAATATAT
896870 AATATTTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
19 9 0.20
20 13 0.28
21 2 0.04
22 2 0.04
23 2 0.04
24 2 0.04
25 16 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATATATTAAAATTTATAT
Found at i:896862 original size:27 final size:25
Alignment explanation
Indices: 896821--896884 Score: 110
Period size: 25 Copynumber: 2.5 Consensus size: 25
896811 ATTATTAAAT
896821 ATATTAAAATTTATATAAATATATA
1 ATATTAAAATTTATATAAATATATA
896846 ATATTAAAATTTATATAAATATATA
1 ATATTAAAATTTATATAAATATATA
*
896871 ATATTTTAAATTTA
1 ATA-TTAAAATTTA
896885 ATATTAACAC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 28 0.76
26 9 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATTAAAATTTATATAAATATATA
Found at i:896898 original size:27 final size:25
Alignment explanation
Indices: 896821--896898 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
896811 ATTATTAAAT
* *
896821 ATATTAAAATTTATATAAATATATA
1 ATATTAAAATTTATATAAACACATA
* *
896846 ATATTAAAATTTATATAAATATATA
1 ATATTAAAATTTATATAAACACATA
* *
896871 ATATTTTAAATTTAATATTAACACATA
1 ATA-TTAAAATTT-ATATAAACACATA
896898 A
1 A
896899 AACGTACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
25 28 0.60
26 8 0.17
27 11 0.23
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATTAAAATTTATATAAACACATA
Found at i:897907 original size:40 final size:41
Alignment explanation
Indices: 897831--897907 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
897821 GTTAGTATTT
* *
897831 AGTATTTATATATTTATTTAAATATTTTAATTAATTAAATA
1 AGTATTTATATATTTATTTAAATATTTAAATAAATTAAATA
*
897872 AGTA-TTATATATTTATTT-ATTATATTAAATAAATTA
1 AGTATTTATATATTTATTTAAATAT-TTAAATAAATTA
897908 CTAATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 24 0.75
41 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (41 bp):
AGTATTTATATATTTATTTAAATATTTAAATAAATTAAATA
Found at i:897947 original size:18 final size:17
Alignment explanation
Indices: 897924--897970 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
897914 TAAAATCTTT
897924 AAATTAAAAATGAA-AAA
1 AAATTAAAAA-GAATAAA
897941 GAAATTAATAAAGAATAAA
1 -AAATTAA-AAAGAATAAA
*
897960 AAATGAAAAAG
1 AAATTAAAAAG
897971 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.15
18 16 0.62
19 6 0.23
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (17 bp):
AAATTAAAAAGAATAAA
Found at i:897986 original size:29 final size:29
Alignment explanation
Indices: 897923--897989 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
897913 TTAAAATCTT
*
897923 TAAATTAAAAATGAAAAAGAAATTAATAA
1 TAAATAAAAAATGAAAAAGAAATTAATAA
897952 -AGAATAAAAAATGAAAAAGTTAAA-TAA-AA
1 TA-AATAAAAAATGAAAAAG--AAATTAATAA
897981 TAAATAAAA
1 TAAATAAAA
897990 TAAAACTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
28 1 0.03
29 25 0.76
30 4 0.12
31 3 0.09
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (29 bp):
TAAATAAAAAATGAAAAAGAAATTAATAA
Found at i:899678 original size:2 final size:2
Alignment explanation
Indices: 899671--899698 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
899661 TAATTTAATC
899671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
899699 TTTACAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:899906 original size:3 final size:3
Alignment explanation
Indices: 899898--899942 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
899888 GGTTTTTCTC
899898 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
899943 GATATTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:900222 original size:22 final size:23
Alignment explanation
Indices: 900183--900227 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
900173 ATTCCAAAAT
*
900183 ATAAATTTTTAGTATTTT-AAAG
1 ATAAATTTTTAATATTTTGAAAG
900205 ATAAATTTTTTAAT-TTTTGAAAG
1 ATAAA-TTTTTAATATTTTGAAAG
900228 TTCTAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (23 bp):
ATAAATTTTTAATATTTTGAAAG
Found at i:902377 original size:12 final size:12
Alignment explanation
Indices: 902362--902392 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
902352 AGATTCTAAA
902362 GAAGAAGAAGAC
1 GAAGAAGAAGAC
*
902374 GAAGAAGAAGAG
1 GAAGAAGAAGAC
902386 GAAGAAG
1 GAAGAAG
902393 TTATAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.39, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAGAC
Found at i:903587 original size:22 final size:22
Alignment explanation
Indices: 903562--903618 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
903552 AATGATTATT
903562 AAATATAAATATAATCA-TA-AAA
1 AAAT-TAAATATAAT-ATTATAAA
903584 AAATTAAAATATAATATTATAAA
1 AAATT-AAATATAATATTATAAA
903607 AAATTAAA-ATAA
1 AAATTAAATATAA
903619 ACATCATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.19
22 18 0.56
23 8 0.25
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATTAAATATAATATTATAAA
Found at i:903611 original size:23 final size:22
Alignment explanation
Indices: 903568--903626 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
903558 TATTAAATAT
903568 AAATATAATCATAAAAAAATTA
1 AAATATAATCATAAAAAAATTA
903590 AAATATAAT-ATTATAAAAAATTA
1 AAATATAATCA-TA-AAAAAATTA
*
903613 AAATAAACATCATA
1 AAATATA-ATCATA
903627 TATTAAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.03
22 11 0.34
23 15 0.47
24 4 0.12
25 1 0.03
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATATAATCATAAAAAAATTA
Found at i:904067 original size:77 final size:77
Alignment explanation
Indices: 903968--904123 Score: 276
Period size: 77 Copynumber: 2.0 Consensus size: 77
903958 ACAAGGGCCT
*
903968 ACACGTGAACAAACTCACATGGGGTTAGGCATGAACAGCATAATACACTTGGATTTTGATACCAA
1 ACACGTGAACAAACTCACATGGGGTTAGGCATGAACAACATAATACACTTGGATTTTGATACCAA
904033 GTTAAGCATCCA
66 GTTAAGCATCCA
* *
904045 ACACGTGAACAACCTCACATGGGTTTAGGCATGAACAACATAATACACTTGGATTTTGATACCAA
1 ACACGTGAACAAACTCACATGGGGTTAGGCATGAACAACATAATACACTTGGATTTTGATACCAA
*
904110 GTTAGGCATCCA
66 GTTAAGCATCCA
904122 AC
1 AC
904124 TTAAAACCAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (77 bp):
ACACGTGAACAAACTCACATGGGGTTAGGCATGAACAACATAATACACTTGGATTTTGATACCAA
GTTAAGCATCCA
Found at i:908180 original size:33 final size:33
Alignment explanation
Indices: 908138--908222 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
908128 ATGGATTTAG
908138 AAGGCTTAGAGGTGAGTTCTACAAGGGGTTCAA
1 AAGGCTTAGAGGTGAGTTCTACAAGGGGTTCAA
* *
908171 AAGGTTTAGAGGTGAGGTCTACAAGGGGTTCAA
1 AAGGCTTAGAGGTGAGTTCTACAAGGGGTTCAA
* * *
908204 AAGGGTCAAAGGTGAGTTC
1 AAGGCTTAGAGGTGAGTTC
908223 CCTAAAAAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.31, C:0.11, G:0.35, T:0.24
Consensus pattern (33 bp):
AAGGCTTAGAGGTGAGTTCTACAAGGGGTTCAA
Found at i:909246 original size:26 final size:27
Alignment explanation
Indices: 909199--909249 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
909189 CCTTGCTACC
909199 ATGTTGAAAGAAAAAAAAGAAATTGAA
1 ATGTTGAAAGAAAAAAAAGAAATTGAA
*
909226 ATGTTGAAAG-AAAAGAAGAAATTG
1 ATGTTGAAAGAAAAAAAAGAAATTG
909250 TATTTCTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.20
Consensus pattern (27 bp):
ATGTTGAAAGAAAAAAAAGAAATTGAA
Found at i:920242 original size:22 final size:19
Alignment explanation
Indices: 920214--920268 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
920204 TGTTCTCAAC
920214 AAAGAAAACCAAATAAAGAAAA
1 AAAGAAAA--AAA-AAAGAAAA
*
920236 AAAGAAAAAAAAATGAAAA
1 AAAGAAAAAAAAAAGAAAA
920255 AAATGAAAAAAAAA
1 AAA-GAAAAAAAAA
920269 TTCTTCAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 10 0.32
20 13 0.42
22 8 0.26
ACGTcount: A:0.82, C:0.04, G:0.09, T:0.05
Consensus pattern (19 bp):
AAAGAAAAAAAAAAGAAAA
Found at i:920257 original size:20 final size:20
Alignment explanation
Indices: 920232--920269 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
920222 CCAAATAAAG
920232 AAAAAAAGAAAAAAAAATGA
1 AAAAAAAGAAAAAAAAATGA
*
920252 AAAAAATGAAAAAAAAAT
1 AAAAAAAGAAAAAAAAAT
920270 TCTTCAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAAATGA
Found at i:920265 original size:11 final size:11
Alignment explanation
Indices: 920232--920269 Score: 55
Period size: 9 Copynumber: 3.7 Consensus size: 11
920222 CCAAATAAAG
920232 AAAAAAA-GAA
1 AAAAAAATGAA
920242 AAAAAAATG--
1 AAAAAAATGAA
920251 AAAAAAATGAA
1 AAAAAAATGAA
920262 AAAAAAAT
1 AAAAAAAT
920270 TCTTCAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.36
10 7 0.28
11 9 0.36
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:920850 original size:34 final size:33
Alignment explanation
Indices: 920779--920844 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
920769 CTGATATTTG
*
920779 TGAAAGAATAAGCACAAAGGAATACAAATGAGCT
1 TGAAAGAATAAGAACAAAGGAATACAAA-GAGCT
*
920813 TGAAAGAATAATAACAAA-GAATACAAA-AGCT
1 TGAAAGAATAAGAACAAAGGAATACAAAGAGCT
920844 T
1 T
920845 TTTGAAGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 5 0.17
33 9 0.30
34 16 0.53
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.17
Consensus pattern (33 bp):
TGAAAGAATAAGAACAAAGGAATACAAAGAGCT
Found at i:921221 original size:13 final size:13
Alignment explanation
Indices: 921203--921227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
921193 TATTATGAAC
921203 ATGTATCGATACA
1 ATGTATCGATACA
921216 ATGTATCGATAC
1 ATGTATCGATAC
921228 TAAGTAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:921245 original size:33 final size:32
Alignment explanation
Indices: 921185--921248 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
921175 CTTTTCAAGG
* *
921185 TGTATCGATATTATGAACATGTATCGATACAA
1 TGTATCGATACTAAGAACATGTATCGATACAA
*
921217 TGTATCGATACTAAGTAATATGTATCGATACA
1 TGTATCGATACTAAG-AACATGTATCGATACA
921249 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (32 bp):
TGTATCGATACTAAGAACATGTATCGATACAA
Found at i:922275 original size:16 final size:16
Alignment explanation
Indices: 922247--922279 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
922237 ATTAAAGAAG
922247 GTTAAGTAGAAGCAAA
1 GTTAAGTAGAAGCAAA
922263 GTTAA-TAGCAAGCAAA
1 GTTAAGTAG-AAGCAAA
922279 G
1 G
922280 AAACAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.48, C:0.09, G:0.24, T:0.18
Consensus pattern (16 bp):
GTTAAGTAGAAGCAAA
Found at i:923936 original size:33 final size:33
Alignment explanation
Indices: 923899--923964 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
923889 AATAGTACCT
* *
923899 ATGTATCAATACAAAGAATGCAATATTGATACA
1 ATGTATCAATACAAAGAACGCAATATCGATACA
* *
923932 ATGTATCGATACTAAGAACGCAATATCGATACA
1 ATGTATCAATACAAAGAACGCAATATCGATACA
923965 TCTAGGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (33 bp):
ATGTATCAATACAAAGAACGCAATATCGATACA
Found at i:928563 original size:3 final size:3
Alignment explanation
Indices: 928555--928582 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
928545 CTGAATCTCC
928555 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
928583 TTTTGATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:933931 original size:19 final size:18
Alignment explanation
Indices: 933907--933974 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
933897 TAGTAGCTAA
933907 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
933926 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
933941 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAA-AC
933958 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
933975 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 2 0.05
19 27 0.63
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:933947 original size:13 final size:13
Alignment explanation
Indices: 933929--933953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
933919 ACAATACTTA
933929 TGTATCGATACAT
1 TGTATCGATACAT
933942 TGTATCGATACA
1 TGTATCGATACA
933954 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:933951 original size:32 final size:32
Alignment explanation
Indices: 933910--933972 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
933900 TAGCTAATTA
*
933910 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
933942 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
933973 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:935076 original size:57 final size:56
Alignment explanation
Indices: 934973--935153 Score: 177
Period size: 57 Copynumber: 3.2 Consensus size: 56
934963 GTAATTTTAA
* * * * * *
934973 GCATTTTTGCATCATTTTAGTCATTTGCCATGTTT-TGGACCATTTATGCAATTTCAT
1 GCATTTTAGGATCATTTTAGTCATTTGTCATGTTTAGGGA--TTTTATACAATTTCAT
* *
935030 GCATTTTAGGGTCATTTTAGTAATTTGTCATGTTTAGGGAGTTTTATACAATTTCAT
1 GCATTTTAGGATCATTTTAGTCATTTGTCATGTTTAGGGA-TTTTATACAATTTCAT
* * * * *
935087 GTATTTTAAGATCATTTTATTCATTT-TCTATGTTTTAGAGATTATTATACAATTCCAT
1 GCATTTTAGGATCATTTTAGTCATTTGTC-ATG-TTTAGGGATT-TTATACAATTTCAT
935145 GCATTTTAG
1 GCATTTTAG
935154 CACCATTCCA
Statistics
Matches: 102, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
56 2 0.02
57 70 0.69
58 30 0.29
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (56 bp):
GCATTTTAGGATCATTTTAGTCATTTGTCATGTTTAGGGATTTTATACAATTTCAT
Done.